Wednesday, February 26, 2014

The Making of a Paradigm Shift: An Exception Which Proves the Rule

I mistakenly referred to the ice fish video as the fourth video in my last post. I have edited it to the third video.

The ice fish is a very interesting example of evolutionary adaptation, and probably the very best evidence for evolution that I have ever seen. But it is an exception to the rule that random mutation plus natural selection never produce novel functions for a very important reason having to do with probability and protein structure.

The first time I watched this video, I thought the fish they were talking about might be the coelacanth, a famous failed prediction of evolutionary theory. Of course I should have known better, as these videos are intended to promote positive evidence of evolution, not to inform anyone of its deficiencies. Briefly, the coelacanth is a species of fish that evolutionists thought had gone extinct many millions of years ago because it disappeared from the fossil record at that time, according to their dating methods. Then, what do you know it, somebody who knew what they were about realized that fishermen off the coast of Madagascar had been catching live coelacanths. Epic fail.

But the fish caught in the video is the so-called ice fish. There are lots of "ooohs" and "aaahhs" in the video, but most of it in the end boils down to destructive random mutations. To its credit, the video explains this quite well. Random mutation broke the hemoglobin gene, and because the fish was able to absorb oxygen through its skin, it could survive without hemoglobin. I have discussed this type of mutation before, and it's really not evidence that evolution can create anything new, just more evidence that it can break things which already existed. Whoop-dee-doo.

The really interesting part of this video, and probably the entire series, is the creation of the anti-freeze protein. Here, finally, we have a serious claim that a brand new function has been created where none existed before that requires a brand new molecular mechanism. This is a positive, gain-of-function mutation. This is what evolution needs in order to explain the existence of so many biological mechanisms. Does it? Would I or any critic of Darwinian evolution change our minds based on this evidence?

The first question to ask about the anti-freeze protein has nothing to do with the protein itself, but rather its function. How does anti-freeze in general, from your car to sea water to the blood of the ice fish, actually work?

Water has a unique freezing mechanism in the world of molecules and chemistry. Water is the only naturally occurring molecule, and one of a very rare number of known molecules, that decreases in density when it freezes. Normally when a substance gets cold, it's molecules move slower and slower, which results in them slowly moving closer and closer together. This increases the density as a substance freezes from a liquid to a solid. But ice has a special crystal structure in its solid phase that gives it a lower density as a solid than as a liquid. For pure distilled water, the process of crystallization starts at 4° Celsius and continues until completion at 0°. For impure water, however, the temperature at which the crystallization occurs is lower because any impurity in the water disrupts the crystallization process.

Sea water is dangerous because it can get below the freezing point of the human body. This is why you can freeze to death in water that is not frozen. In sea water, the impurity which interrupts the crystallization process is primarily sodium chloride (table salt), but any solute will have the same effect. The solute used in your car's antifreeze is likely ethylene glycol. This effect is called "freezing point depression" and most basic chemistry courses teach it. For this discussion, the important thing to note about freezing point depression is that it does not depend on the properties of the solute at all, only on its concentration and the crystal structure it interrupts. In the jargon of intelligent design theory, the anti-freeze function has a very low specificity.

"Low specificity" means almost any small molecule dissolved or partially dissolved in water will lower its freezing point. The mechanism is basically the same, and it is very simple. The water molecules want to form a nice, tidy crystalline structure, and anything that's in the water but is not water will get in the way. It's sort of like hair clogging your bathroom drain. If you want, you can substitute a hairball for a drain plug and it will work. But evolutionists don't claim the Darwinian mechanism can make drain plugs. They claim it can make the entire bathtub, in fact, the entire house. Is that really plausible based on the example of anti-freeze proteins? Do all biological functions have low specificity?

No. In fact virtually all biological functions have a ridiculously high specificity, so high that only precise sequences of amino acids, folded into a precise three dimensional shape called secondary and tertiary structure, can perform them at all. Dissolved table salt won't catalyze the reactions in the citric acid cycle or pump hydrogen or calcium ions across the plasma membrane against ionic gradients. Ethylene glycol doesn't change conformation when hit by specific wavelengths of light and send the signal down your optic nerve like the proteins in your eye. These functions are not simple and cannot be performed by just any small molecule sloshing around in a solution. Most of the proteins that perform these highly specified functions will break when hit with a random mutation, and when they don't, their functions are compromised in some way, either cumulatively or functionally. That's why random mutations break biological functions so easily.

The second question to ask about the anti-freeze proteins is how likely they are to come about by random mutation. What is their probability? Here the video leaves out a key piece of information: these anti-freeze proteins are only twenty to thirty amino acids in length. Normal, functional proteins are at least ten times that in length. Some are a thousand times that long. This matters because it greatly affects the probabilities involved. Whereas a normal protein like hemoglobin requires a precise sequence several hundred amino acids long, an anti-freeze protein could have just about any primary sequence and only requires an existing, working gene and a single mutation which creates a stop codon somewhere close to the promoter and the beginning of the gene. The one has a very low probability; the other has a very high probability. The combination of high probability and low specificity does not trigger a design inference. In other words, this is something that, despite the fact it does constitute a new function, intelligent design theorists would readily accept can come about through random mutation. It does not break the probability barriers erected by intelligent design theory.

And why would it, after all? It's just a wet noodle, not anything in the way of a "real" protein. The only highly specified working part is the promoter, which didn't evolve at all and was part of the original sequence, and the gene it was designed to promote gets lopped off by a mutation leaving just the promoter connected to a short sequence of "meaningless gibberish". The video does actually show this but doesn't explain it. These anti-freeze proteins really could be just about any primary sequence, because, in another point completely left out of the video, they have no secondary or tertiary structure at all. While biological proteins are precisely engineered, three-dimensional, fully-automated machines with complex interlocking moving parts, the anti-freeze proteins are wet noodles flopping around helplessly in solution whose confirmation is completely at the mercy of Brownian motion. Whereas real proteins usually have multiple independent interactions with other complex proteins, identifying their target precisely in a cellular environment chock full of potential targets, anti-freeze proteins perform a function that can literally be performed by any small molecule with some polarity, or even just by elemental ions that have no chemical bonds at all. At a polite dinner party, we might be forced to call these things proteins. At the nerd bar with the beer flowing we could be less polite and call them what they really are: oligopeptides sucking at the tit of some destroyed gene's leftover promoter. What a bunch of losers. They dontsh effin haff aany tersheriairy struc....suuurre. Oh hey occiffer!

Now that's whack.