Protein Folding and Evolution

Proteins consist of hundreds of amino acids attached to each other like train cars, and when they fold up they consistently find the same three dimensional shape. Like a necklace that magically falls into the same shape every time it is dropped onto a table, the consistency of protein folding once seemed like a paradox. For there is an astronomical number of shapes the protein could possibly take on. How does it find the same one so consistently, and so quickly? The answer has interesting implications for evolution.

When a protein folds to a given shape, it is fighting nature’s tendency toward disorder. The protein faces a universe of possible shapes, how does it always fold up to the same one? The answer is that this entropy barrier is overcome by the many chemical interactions tugging the protein toward its final destination.

A protein structure is subject to a wide variety of chemical forces and influences. Some of its amino acids have an oily side which means they want to huddle together, shielded from the aqueous environment. Other amino acids fit well with water and so have no such repulsion from the environment. Some amino acids are charged, so they mutually attract or repulse each other. And some amino acids have sulfur atoms which can bond together.

These various influences help to guide the unfolded protein to its final shape. They overcome the entropy barrier, but just barely. The result is a folded protein that is marginally stable, which means they wiggle and shake a bit—a good thing for many protein functions. The marginal stability of proteins also helps when it comes time to take them apart. Proteins are temporary wonders. They are created for a need, and just as quickly torn down.

Kicking the paradox down the road

So the paradox is resolved. Proteins overcome their enormous entropy barrier with their various chemical interactions, as determined by their particular amino acids. In fact, just as the words on this page determine the message, so too the amino acid sequence determines the particular characteristics of a protein.

The vast majority of amino acid sequences one could dream up don’t work. Most won’t successfully fold up, and most of those that do result in a structure that is too stable. And most don’t result in any meaningful protein function. As discussed here, useful amino acid sequences are rare.

So while the protein folding paradox is resolved, there is a nagging feeling. Yes, the protein overcomes its entropy barrier—it all works just fine. But it works just fine only because a very special amino acid sequence was specified. That amino acid sequence is just as astronomically rare as the three dimensional structure that the unfolded protein was able to find. So from where did this amino acid sequence come?

The string of amino acids that make up a protein comes from the cell’s translating machine called the ribosome. The ribosome takes as input a string of nucleotides and produces as output a string of amino acids. The translation is done according to the genetic code.

And from where did the string of nucleotides come? It came from the DNA. A massive protein copying machine slides along an opened section of DNA and copies a gene.

And from where did the DNA gene come? According to evolution it evolved, but it is here that we find another entropy barrier. Just as the folding protein is confronted with an astronomical number of structures, so too the DNA gene is confronted with its own nightmare of choices. But that is where the similarities end.

A different kind of entropy barrier

A typical gene has something like a thousand nucleotides. Given that there are four different types of nucleotides, this means there are 4^1000 different sequences that could make up the gene. This is equal to a 1 followed by about 600 zeros—a big number. That’s more than the number of nano seconds since the Big Bang—by about 10^574 (a 1 followed by 574 zeros).

Finding the right gene sequence to get a particular job done in the cell would make finding a needle in a haystack seem easy. The problem is so difficult that we haven’t yet figured out the answer, but it would be a 1 in 10^100++ long shot. Do not try this at home.

It is a huge entropy barrier, but it has some important differences compared to the protein folding entropy barrier we saw above. First, this gene entropy barrier is due to the large number of possible DNA nucleotide sequences whereas the protein folding entropy barrier was due to the large number of possible protein shapes.

And the protein folding entropy barrier was overcome by those fortuitously coordinated chemical interactions, which as we saw traced back to the amino acid sequence, which in turn traced back to the gene sequence.

But the gene entropy barrier has no such convenient explanation. Genes don’t come together via prearranged, specified information to overcome all odds.

In fact evolution’s proposal is that genes first arise via some sort of random change mechanisms, such as mutations. Nucleotides somehow come together, somehow provide some function, somehow are able to replicate, somehow vary, and somehow find new gene sequences against the astronomical entropy barrier.

Implications for evolution

The fact that evolutionists do not have all the answers or details does not mean it did not happen, or is impossible. But it is a significant problem. Evolution is hardly the sort of idea one would call a fact. Unless one were an evolutionist, that is.

Evolutionists say evolution is a fact, and that all the evidence lines up behind the theory. There are no serious problems or issues. Only minor details to be worked out. Consequently for them this gene entropy barrier is no big deal. In fact, amazingly they argue it is not a problem at all.

This is another unfortunate example of how evolution corrupts science. In the hands of evolutionists, science is manipulated in strange ways to support their theory. In the case of this gene entropy barrier, evolutionists such as Ard Louis argue that the fact that since biology operates successfully everyday inspite of tremendous entropy barriers such as in the protein folding case, that therefore entropy barriers are really no problem for evolution either.

But as one can see from the protein folding and gene example discussed above, this argument makes no sense. As we saw, proteins overcome their entropy barrier via the many fortuitous chemical interactions that arise as a consequence of the very special amino acid sequence specified by the DNA gene.

The protein successfully folded because it was setup to fold. The scientist cannot then conclude that since this worked out so nicely that the origin of the gene itself (responsible for the special amino acid sequence) has no serious entropy challenge. They are two very different problems. The fact that the protein folds does not mean the gene evolves.

This argument that biology’s everyday overcoming of entropy shows that evolution can do the same thing (somehow), is simply a corruption of science. It is an unfortunate, yet common example of what evolution has done to our thinking. Religion drives science, and it matters.