Category: Nerdity

Nerdy science stuff not directly affiliated with any particular category

Why you really do or don’t want me as a student…

Of the classes I took this last semester, there’s only one I haven’t blogged about at least once.

Masochist that I am, I went and took “Applied Calculus”, even though I’d gotten approval to count my previous semester of calculus (about 8 years ago) as fulfilling the mathematics requirement for graduation. The “applied” in the title of the class caught my eye, and after speaking to the instructor before the semester to find out what the class was like I decided that if there was time and money left I’d take the class. So I did.

Although I’d rank it as only the second most useful “Mathematics” course I’ve taken so far, Dr. Wolper was one of the best mathematics instructors I’ve had up to this point, so I’ve got no regrets for having spent the time and money to take it. I suspect I’ll remember a lot more of it than I did of the previous calculus class.

Anyway, getting to the point of this post:

There are times when I am unable to restrain myself and answer homework or exam questions in a terse, boring manner, regardless of the subject. If you’re an instructor and are wondering if you want me in your class, here is something to judge by.

Calculus (for those who don’t know) is more or less the math you use to deal with when, how, and how fast things change. In practical terms, when dealing with real-world applications this often means dealing with a graph of some data. A number of homework (and exam) problems this semester dealt with questions along the lines of “what would a graph of such-and-such a situation look like and how would you interpret it?”. Here’s one from early in the semester:

This was my answer:

You may judge for yourself whether this is a good answer or not…

I can has graduation?

The last undergraduate final is over.

Everything it taken care of save for one overdue library book, which I intend to take care of tomorrow.

All the other fees are paid. All the paperwork is done. I’m pretty sure I got well above the F– that was the minimum I needed on the Philosophy final to achieve the minimum passing grade. In fact, my only current stress about my grades is whether or not I managed to end out my last undergraduate semester with a 4.0 or not.

I FEEL BETTER THAN JAMES BROWN! WHEEEEEEEEEEEEEEEE!!!!!!!!!!!!!!!!!!!!!!!!!!

Let the wild, uncontrollable drunken orgiastic celebration begin!

After my nap…

I’m having too much fun with this.

I finally managed to get Hugin to work, as you can see from the picture of the Dead Fish Museum above.

Okay, it’s the visitor’s center at the Fossil Butte National Monument, but it really is a museum of dead fish. And other fossils. If you click the image to get to the Panoramio page, you can even see where it is on the map: in fact if you zoom in, the building itself is visible in the aerial photo imagery.

Between digiKam’s ability to handle geocorrelation with tracks from my GPS, Panoramio’s support for geolocation and mapping (and connection to Google Earth…), playing with High Dynamic Range digital photography, and now panoramas, I’m beginning to develop an increased urge to travel around and take pictures again…

Nerd Photography in the Big Room

Readers may have noticed by now that I have a cheap but serviceable digital camera that I’ve been using to take pictures which occasionally show up here on the blog. (Hey, there’s another thing that the External Deliverer, in Its benevolence, might bring me: a nicer digital camera.)

I’ve been playing with geolocation for a while now. Just recently, I started also doing some crude playing with High Dynamic Range digital photography. It’s obviously going to take me some work to get it figured out and get better results, but what I’m getting so far doesn’t look too bad, at least in my own opinion. Kind of surreal, like Mars Rover pictures…

I’ve discovered that my Handy-Dandy Linux box has access to a couple of tools that make these easy.

I noticed a few days ago that digiKam is actually able to read .gpx format files downloaded from my GPS and then correlate the track from the GPS with the timestamps on the photos automatically, so in what little spare time I have I’ve been going back through my archives of GPS tracks and timestamped photos and trying to find as many to correlate as I can. I managed to get geolocation tagged into pictures from as long ago as three years or so. I also tagged this more recent one. I saw this place half a decade ago and had been wondering if it was still there. Last week we finally had a chance to visit and sure enough, it was there. If you were wondering where one could go to learn to do the Squirrel Dance, here it is.

Landscape and Sign:Don't Trespass on the 'I'

Today after classes I trudged up to the top of the hill at one corner of the campus with my trusty GPS in hand and took a few pictures, as you can tell. Since Google Earth seems to get most of it’s photos from Panoramio, I’ve started uploading them there. I may also get around to uploading them to flickr one of these days, too. I kind of need some pleasant distraction – I’m starting to hit the “Am I there yet???” phase of the semester. Just another week-and-a-half of classes, then finals, then I’m finally done. At least with the undergraduate stuff.

If you’re bored, there are a couple of additional pictures on the Panoramio site, here. You can also get the ICBM address there, and a .kml file for Google Earth so my pictures will pop up if you happen to run past an area where one of them is while you’re browsing the globe.

’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…

This blog does not exist

I say that because in order to exist I must have used my computer to type it in, but George Berkeley “proved” that material things don’t exist. No pictures either this post, because after all my camera doesn’t exist, either.

Okay, the fact that I’ve got a whole cluster of time-sucking school stuff last week and this week to deal with is also a factor in keeping the posts here sparse at the moment. Berkeley just happens to be one of them.

Berkeley was what I would call a “philosophical” Empiricist (whereas I would describe myself as a “practical” empiricist – hence the “Applied” in this blog’s “Applied Empirical Naturalism” subtitle. Put simply, empiricism means that knowledge comes from observation via the senses. I’m a practical kind of guy, and I don’t think this in any way invalidates the use of the intellect to infer additional (testable) knowledge from one’s observations beyond what is directly observed. Berkeley, on the other hand, is a solipsist: he claims that nothing exists unless it is perceived – or is a perceiver.

His argument is a little hard to follow. As best I can tell, he’s starting with a Descartes-like observation that the only thing we ever actually experience are sensory perceptions. In other words, we can experience and know about the sensation of “heat”, but this sensation is just an idea in our minds. Even if there were something “behind” the sensation of heat that was causing it, we could not know anything about it directly, since we only ever experience the sensation.

In a way that is still not entirely clear to me, Berkeley then seems to take the leap from Descartes-style “the only thing I can be certain of existing from my direct observations are ideas, and my mind which contains them” to “since there is no direct empirical basis for claiming the existence of anything else, matter cannot be said to exist”.

Berkeley then goes on to claim that since only minds and ideas exist, and since there are some ideas that seem to be imposed on him (like if he sticks the idea of a red-hot-poker up the idea of his left nostril, he will have the idea of excruciating pain whether he wants to or not), that therefore there must be some other mind from which these ideas come. From this, he makes the leap to claiming that there must be an “infinite” mind which contains all these other ideas, by which he means God™.

This also gives him a convenient explanation for things existing when nobody’s looking at them. See, God is always looking at everything, so nothing that exists is ever not being perceived.

Personally, I’m finding myself wondering if his argument also leaves open the possibility of an animistic reality instead. He claims that everything we experience (including “sensible things”, i.e. things we see, feel, smell, etc.) is just an idea, and an idea existing without a mind is absurd. Instead of postulating the existence of an “infinite” mind, though, wouldn’t the notion that anything that exists actually does, itself, have a mind (or “spirit” if you prefer) also satisfactorily explain how things can continue to exist even when nobody is observing them? Berkeley makes the claim that inanimate objects don’t have minds…but he gives no justification for this claim. I mean, he admits that he can’t directly observe other people’s minds (or the “infinite” mind either) and therefore can’t prove that anyone but him exists, but he never claims that other people don’t exist. So why couldn’t the continued existence of the fork that I ate dinner with be due to the fork’s own mind?

That “thump” you may have imagined hearing was probably Berkeley turning over in his grave. Berkeley was, after all, a Bishop, going through this whole philosophical exercise out of hatred of “skeptics” and “atheists”, and it amuses me to imagine how appalled he’d be to have his arguments used to support something that he probably felt only “heathens” and “savages” would consider…

Yeah, I know, not much of a post, but I’m a bit overloaded at the moment. Nonetheless, more to follow this week over the next few days, at least.

“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

More Search Amusements. (p.s. I Ain’t Dead Yet.)

A bit longer of a delay between posts than I’d like, but here you go:

+ =?????

I am often amused (and regularly baffled) by the kinds of search queries that lead people to this blog.

I wrote a sloppy little script to parse the server’s access logs and figure out who’s searching for what, where. Since I added the ability to recognize Google Image Searches, it’s gotten even stranger.

I do get a lot of perfectly understandable hits – people looking for information about “heat-fixing slides”, expired jello, and looking for pictures of lactic-acid bacteria or whatnot. Some of them are pretty interesting questions…but first, some oddities.

At the top of my current wierd-o-meter: “carbonated leprechaun”…what??? What’s funnier is that this was a Google Image search – someone doesn’t just want information ABOUT carbonation of leprechauns, they want pictures. Now I can’t stop imagining a mash-up of “Darkman” and Leprechaun. Thanks a lot, whoever you are…”I needs me gold! ARGH! SUNLIGHT! [bubblebubblebubble…]”

Another recent one was just a search for the phrase “new england sucks”. As another Image search. Somebody not only doesn’t like New England, but they want pictures of “new england sucks”?…

Less risible but still kind of funny are searches influenced by unfamiliarity with the English language. I have no idea what the search for pictures related to “useful of DNA” was hoping to find. (Uses of DNA? How to “use” [work with] DNA? Diagrams of genetic processes?). I also see a number of searches just based on the name of the blog – people looking for information about furnishing “big rooms”. I have no idea what the search for “name of thing in room” was expected to turn up. This one’s another language issue, but even taking that into account I’m still baffled about this one. I wouldn’t expect google.de to return any useful information for “Sache im Zimmer” (the original search was actually from a Spanish-speaking area, but No Entiendo Espanol, so I’ll use a German analogy instead.)

Or from Sweden: “Aerobic Oxygen fraud”. Somebody’s figured out that we don’t actually need to breathe and that it’s all a ploy by the Oxygen Lobby to enslave us, I guess.

Maybe just because “chemicals” get mentioned here from time to time, I get the occasional hit from someone looking for illegal drug information (either technical or just news of drug busts or whatever). Note to “HILLBILLY METH” searcher: Hillbillies do moonshine. Meth comes from Rednecks. Jeez, doesn’t everyone have to do a semester of Rural Population Stereotype Taxonomy in college anymore?

There are some more relevant and interesting questions that show up here, too.

Oreo CookieI guess someone in southern California used an interesting analogy in their microbiology class, because I recently got a couple of searches from there looking for why the cell membrane is not like an Oreo® cookie. The answer: There’s no “creme” filling. No seriously – the membrane is two layers of the same kind of molecule stuck together. The phrase you’re looking for is “Phospholipid bilayer”. In a way, the molecules are a lot like detergents – they’ve got one end that “likes” water, and a long tail at the other end that doesn’t (much as oil doesn’t). Since the cell is surrounded by and full of water, you end up with one layer with all its hydrophilic ends touching the water outside the cell, and the other layer with its hydrophilic ends on the inside of the membrane touching the water inside the cell, and the hydrophobic ends of both layers all tangled up together in the middle – without anything between them. See? Not like an oreo cookie at all. Aside from this, cell membranes are also squishier and not chocolate flavored most of the time.

I’ll deal with “does beer and ice cream make gas” in another post later…

It’s over!

No you can't have $10,000. Not yours.

I am proud to announce that I am 5th Loser in this 2007 College Blogging Scholarship competition!

Lacking the emotional appeal and/or existing promotional network of the top scorers, I was pretty much up the creek without a plunger. Given the popularity contest format of the competition, I’m actually pretty pleased with how I did. My regular readers (judging by the hits to the RSS feed) have approximately tripled or quadrupled, and I did get a small but useful amount of feedback to help improve things. Oh, and hey, I seem to have readers in Berlin and somewhere in Chile, among other places, so now I can say I’m “world famous™”. Though the proportion of voters who actually did check out all of the blogs was pitifully low, it does still look like it was around 1-2% of the voters, which is actually higher than I would have predicted.

I get the impression that some of us running less well known blogs were a little disappointed about the format of the competition, but there’s really no reason to be. All it means is that rather than being a contest for “highest quality” blog, it was a contest for “most effective” blog. Certainly, being able to get your “vote for me” message out to a larger range of people is a valid measure of effectiveness, so the results seem reasonable to me. And I wasn’t the bottom scorer. Judging by the way my score moved, at least some portion of the people who were examining all of the blogs actually did like what they saw here as I was getting a couple of votes a day on average, so I’m doing something right at least.

The only complaint I really have about the “popularity contest” format is this: I think one of the major benefits to humanity of “blogging” is the fact that unlike mainstream media, a blogger can afford to present unusual, less broadly popular content which otherwise would never be made available. Not having to worry about the internet equivalent of “Nielsen Ratings”, we can afford to put up obscure or strange things that only a fraction of the world might be interested in, which is why if you poke around the internet, you can find something that isn’t the latest celebrity crap or badly-reported political scandal. I actually don’t know how much of a role it played in this particular competition, but this sort of approach in general strikes me as something that would be strongly biased towards “mainstream” content. I think a little more love for all of us off-center folks would be in order.

I also hope they’re offering runner-up prizes again this year. Even if *I* don’t win, at least one of “my people” (nerds, that is – hey, you don’t go for a PhD in Neuroscience without being at least a little bit of a nerd…) would get something again this year if they do.

This does mean, though, that I won’t have $10,000 to buy a microscope with. Woe is me. On the other hand, that means I’ve got no excuse not to try begging in front of scientific conferences. I figure that ought to be worth some entertainment, once I get some time to try it. Perhaps by this time next year, I’ll have a bit more fame and popularity and have a better shot at the prize.

Hey, scienceblogs.com, if you want to promote my blog next year when I’m (hopefully) in graduate school, I may have a shot at the prize next time around… (UPDATE: It may not be obvious, but this should be read as good-natured jealously, not some kind of complaint or accusation…)

And now that all that’s over, we’ll be returning once again to my usual nerdity. Stay tuned (some more).

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…