Thursday, February 6, 2014

The Geologic Column

I have worked with all different kinds of columns. I made a smaller one in microbiology lab in college, and helped with much larger 20 L columns in a lab I worked at after college. I have also worked with gas chromatography (GC) and liquid chromatography (LC) as well as gel electrophoresis which all work according to the same principle. What's a column you ask? Do I mean this:

Or this:

No, I mean something more like this:

Or this, a LC column:

Or this, a GC column:

What are these columns of which I speak? The short version is they are all techniques used to separate molecules of different sizes. (Not the first two. Don't be a smartass.) The long version is this is how creationists understand the geologic column and along with it, the fossil record.

The basic principle behind columns like these is very simple. Ready? I'm going to say it really fast so pay attention. Maybe bold font will help.


Got it? Good. But you might be thinking this doesn't make a whole lot of sense. After all, a thing will either go through a hole if it's small enough or it won't if it's too big. True, that's why scientists use a column instead of a sieve. With a sieve, you put the stuff in, shake it up, and the stuff that's too big will stay on top and the smaller stuff will shoot right through. A column acts on the same principle except it will separate things based on distance traveled through the column, like so:

You'll see that the green molecules in this diagram travel through the spaces between the white balls faster than the red molecules do. This is a bad example diagram to use because the green ones are actually larger than the red ones, however that brings up another point. If you just put a bunch of pebbles and water in your homemade column and put a bunch of dirt on the top as your sample, the smaller particles of dirt would likely come out the bottom first and the larger particles later. But we can actually monkey around with the stuff in the column and get it to separate molecules based on things other than size, like shape, reactivity or electric charge. All you have to do is choose the right stuff to put in your column.

So in the above diagram, you'll see that the red molecules are all attracted to the white balls and the green ones are just shooting right through even though the green ones are larger. Some columns work by electrostatic attraction, and that's probably what this diagram is showing. The balls in the slurry might be positively charged and so they will attract negatively charged molecules and "stick" to them, but repel positively charged molecules. This basically means that positively charged molecules will shoot through the column and negatively charged ones will go more slowly, or perhaps won't even make it through at all, because they keep getting "stuck" to the white balls in the slurry, sort of like a magnet. Some beads even have little notches in them designed to grab a specific type or size of molecule and hold it, sort of like an enzyme and its substrate, allowing everything else to shoot through. Then once all the junk goes through, a different liquid is added that causes the beads to release the molecules and out comes your purified product. These types of columns are important steps in purification methods, including purification of protein products like insulin and vaccines. I have used columns like this as big as twenty liters when working at a R&D lab for vaccines, and it's really neat watching the slightly yellow colored layer of random proteins and other junk slowly move down the column.

Gel electrophoresis, the detection step for your basic genetic test, uses sort of a combination of electric charge and size. Instead of the force of gravity pulling the sample through the column, gel electrophoresis uses an electric current, which pulls negatively charged DNA samples through an agarose gel (agarose is a type of sugar harvested from seaweed). The larger DNA molecules will travel more slowly and the smaller ones more quickly. Combined with a standard, you can get a pretty good idea of the size of DNA fragments using this tried and true method. My first lab job in college was in a soybean genetics lab, and we did this with soybean DNA all day every day. We would actually measure out the agarose and water into a flask and microwave it to dissolve it faster, then pour it into plastic gel molds and put it in the refrigerator until it cooled and hardened, just like jello. The runs themselves lasted five hours and the gels were the size of sheets of paper because the size difference we were looking for was so small we had to have a very sensitive test.

Liquid and gas chromatography work the same basic way, except that the columns are hollow and the interactions between the sample and the column occur because of the type of molecule attached to the inside surface of the column. The force pushing the sample through is neither gravity nor electricity, but the high pressure flow of liquid (for LCs, called the aqueous phase) or gas (for GCs, called the carrier gas) through the column. LC and GC machines are almost universal features of industrial analytical labs and are used to test the purity of products by measuring the size of the "peak" that comes out at the time in the run that the molecule you're looking for is supposed to come out. LC and GC are much more sensitive methods and are more often used for small organic molecules, not for proteins and DNA. LCs and GCs are extremely important in the manufacture of drugs, for instance, since they are used to measure the purity of the active ingredient which determines the dosage given to the patient. Unfortunately, since these types of tests have to be run by precision machines they are quite a bit more boring than regular columns and gel electrophoresis.

I have used all kinds of other columns like sucrose gradients for purifying RNA (that's a sticky one!), polyacrylamide gels for separating and identifying proteins and sometimes a sample can just be put in a test tube, centrifuged and it will sort itself out with the dense or large particles going to the bottom and the less dense or smaller particles rising to the top. In one lab I just stuck a syringe into the sack type container after centrifuging it and drew out the layer with the virus I wanted just like a nurse draws blood.

So what does all this have to do with the geologic column and the fossil record? Well, what about all those rock layers? Evolutionists say that the layers are there because they represent different epochs in earth's history. Over a period of time a certain type of sediment was laid down, and then during a different time another type of sediment was laid down, and over hundreds of millions or billions of years everything got compacted down into rock, preserving these layers and the fossils buried inside them. But creationists view the geologic column, and the fossils within it, just like a chemist views any of the columns I've talked about above. There was a global flood and lots of sediment with all types of particles large and small, as well as all shapes, sizes and densities of dead plants and animals all mixed up together in a giant, planet-wide slurry which eventually settled down and sorted itself out into layers based on their different properties. In fact, some of the most popular examples used to demonstrate evolution in the fossil record involve small animals "evolving" into later larger versions, like the horse tree. A creationist looks at that and says, "Looks like a global flood makes a half decent column!"

Now that's whack.