Year: 2012

Microbe from the Creek

Microbe collected from the TFS Creek on 9/10/2012. Possibly a species of desmid.

The TFS campus has an excellent ecological gradient. It starts at the hydrologic base-level, with the small, usually permanent, creek in the valley. Then the landscape ranges up, past a narrow but dense riparian zone to the anthropomorphic campus, then up a shrub-covered hillslope that transitions abruptly into the advancing, mature, forest of the hill-top nature reserve. My environmental science class is taking advantage of our geographic proximity by doing a year-long ecological survey project.

We’ve just started, this fall, on the stream and riparian zone. I asked each of them to identify and do some research on a single organism. They all chose some type of macro-organism: spiders, crayfish, flowering herbs (note: just because it’s called an herb does not mean it’s edible), mushrooms, and more. There’s quite a bit of biodiversity down there, although, with the creek just now coming back from our particularly dry summer, the fish are few and far between.

Close-up view of the micro-organism under 1000x magnification (oil immersion lens).

Since no-one chose to look for micro-organisms — even though I did suggest they were an important part of the ecology — I decided do so myself.

I found a loosely held together patch of algae, which I collected with the hope that it would harbor its own little microscopic ecological system. And it did. There were amoebas zipping around, the filamentous algae itself, and these little organisms that I can’t quite identify yet. T

hey may be desimids, but I’m not sure. They look slightly green, but I can’t see any clear chloroplasts (like these). I’ll try staining them tomorrow to see if I can identify any organelles.

A terrible picture "showing" the patch of fillamentous algae I collected from the creek.

The Digestive System

In his critique of research on the beneficial-bacteria storing role of the appendix, PZ Myers includes an excellent overview of the digestive system.

When you eat something, it first goes into the stomach, where it’s treated to an acid bath, some enzymes, and a lot of muscular churning to break it up. Then it’s squirted into the small intestine, where the acids are first neutralized and more enzymes are tossed onto the watery, mushy soup that the food has been rendered down into, called chyme. The primary job of the small intestine is to suck all the nutrients out of the chyme and pass them on to the circulatory system.

Once as much of the good stuff has been leeched out of the chyme as your system can do, the soup is passed on to the large intestine …. This stuff is still very watery — if you’ve ever experienced diarrhea, that’s what it is at this point. The primary job of the large intestine is to resorb water from the waste, condensing it down into the thick, pasty glop we all know and love as excrement. The large intestine is basically the sewage treatment plant here.

— Meyers, 2009: Evolution of the appendix? in ScienceBlogs.

“Junk” DNA: Not so much

It has always strained credibility that the 98% of our DNA not used to code proteins would be useless. But this non-coding DNA picked up the name “junk DNA” because no-one quite knew what it did. In fact, one study (Nóbrega, 2004) found that deleting large chunks of DNA had no discernible effect on mice; the mice born without these pieces of non-coding DNA were viable.

However, a slew of papers from the Encode project indicate that the part of our genome formerly known as junk DNA, regulates the 2% that does the protein coding:

The researchers … have identified more than 10,000 new “genes” that code for components that control how the more familiar protein-coding genes work. Up to 18% of our DNA sequence is involved in regulating the less than 2% of the DNA that codes for proteins. In total, Encode scientists say, about 80% of the DNA sequence can be assigned some sort of biochemical function.

— Jha (2012): Breakthrough study overturns theory of ‘junk DNA’ in genome in The Guardian.

This is more good news for useless bits of biology (see the appendix).

Sections of non-junk DNA transcribe messenger RNA which code proteins. Image from Talking Glossary of Genetics via Wikipedia.

The Appendix: A Useless bit of Biology? Perhaps Not

The appendix has long been supposed to be a vestigial, useless organ. But a 2007 study suggests that it might have had — and may still have in many developing countries — an important role in digestion. It may provide a refuge for helpful, commensal bacteria to repopulate our guts after we purge when we get sick (Bollinger et al., 2007):

The organs of the lower digestive system. The appendix is located in the lower left, near where the small and large intestines meet. Image from Wikipedia.

… the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen.

— Bollinger et al., 2007: Biofilms in the large bowel suggest an apparent function of the human vermiform appendix in the Journal of Theoretical Biology.

Why do they think that? What’s the evidence?

The shape of the appendix is perfectly suited as a sanctuary for bacteria: Its narrow opening prevents an influx of the intestinal contents, and it’s situated inaccessibly outside the main flow of the fecal stream.

–Glausiusz (2008): And Here’s Why You Have an Appendix in Discover Magazine.

And thinking about supposedly useless bits of biology, there’s a bunch of interesting papers coming out about so-called “junk” DNA.

Using Real Data, and Least Squares Regression, in pre-Calculus

The equation of our straight line model (red line) matches the data (blue diamonds) pretty well.

One of the first things that my pre-Calculus students need to learn is how to do a least squares regression to match any type of function to real datasets. So I’m teaching them the most general method possible using MS Excel’s iterative Solver, which is pretty easy to work with once you get the hang of it.

Log, reciprocal and square root functions can all be matched using least squares regression.

I’m teaching the pre-Calculus using a graphical approach, and I want to emphasize that the main reason we study the different classes of functions — straight lines, polynomials, exponential curves etc.— is because of how useful they are at modeling real data in all sorts of scientific and non-scientific applications.

So I’m starting each topic with some real data: either data they collect (e.g. bring water to a boil) or data they can download (e.g. atmospheric CO2 from Mauna Loa). However, while it’s easy enough to pick two points, or draw a straight line by eye, and then determine its linear equation, it’s much trickier if not impossible when dealing with polynomials or transcendental functions like exponents or square-roots. They need a technique they can use to match any type of function, and least squares regression is the most commonly used method of doing this. While calculators and spreadsheet programs, like Excel, use least squares regression to draw trendlines on their graphs, they can’t do all the different types of functions we need to deal with.

The one issue that has come up is that not everyone has Excel and Solver. Neither OpenOffice nor Apple’s spreadsheet software (Numbers) has a good equivalent. However, if you have a good initial guess, based on a few datapoints, you can fit curves reasonably well by changing their coefficients in the spreadsheet by hand to minimize the error.

I’m working on a post on how to do the linear regression with Excel and Solver. It should be up shortly.

Notes

If Solver is not available in the Tools menu you may have to activate it because it’s an Add In. Wikihow explains activation.

Some versions of Excel for the Mac don’t have Solver built in, but you can download it from Frontline.

Water Scarcity in Yemen

Groundwater tends to be a common property resource. In places like Yemen, where ownership rights are not clearly defined it tends to be overexploited. So much so, that they’re looking at running out within the next 10 years. Peter Salisbury has an article in Foreign Policy.

Most potable water in Yemen is produced from a series of deep underground aquifers using electric and diesel-powered pumps. Some of these pumps are run by the government, but many more are run by private companies, most of them unlicensed and unregulated. Because of this, it is nigh on impossible to control the volume of water produced. By some (conservative) estimates, about 250 million cubic meters of water are produced from the Sanaa basin every year, 80 percent of which is non-renewable. In recent years, the businessmen who produce the water have had to drill ever-deeper wells and use increasingly powerful pumps to get the region’s dwindling water reserves out of the ground.

–Salisbury (2012): Yemen’s water woes in Foreign Policy.