Friday, September 5, 2008

Exaptation


The number of possible combinations of amino acids in proteins is directly related to the number of combinations of sections of DNA called "nucleotides." The central rungs of the "ladder" in DNA as seen in the picture on left and the August 19 post are composed of a sub-unit called a nitrogenous base. Every set of three of these rungs is coded for one of the 20 amino acids used in proteins. So you need the right order of 4 possible nucleotides to get the right order of amino acids in the protein. The four nucleotides contain cytosine, thymine, guanine and adenine, designated c, t, g or a. It seems a little easier to talk about 20 amino acids than the codes of 3 nucleotides from combinations of 4. In the last post I said it is estimated that about 1 in 10^65 proteins are specifically functional. This was estimated for proteins of about 100 amino acids in length. Therefore, 300 nucleotides would have to be in correct order for the proteins to have 100 amino acids in correct order. It gets a little complicated because some sets of nucleotides can code for the same amino acid. But this gives us at least an idea of the numbers we are talking about.

I put all this in to comment on the theory of the "RNA world" that many are touting as the answer to origin of life. It wasn't protein, they say, that had to form by chance, but RNA. Well, RNA still has to overcome the numbers just like protein. The RNA nucleotides have to be in the right place to do the work it is supposed to and to "evolve" to the right molecules that we find in the bacteria and archaea. (RNA has one different nitrogenous base from DNA--uracil for thymine).

Another concept that some scientists insist is the answer to all our questions about evolution is "exaptation." So what if the flagellum of the bacteria is a complicated machine made of 25 types of proteins? All we have to do is realize that these proteins had other jobs on their way to evolving a flagellum. The Cyanobacteria DNA polymerase protein has over 900 amino acids. That is a total of 10^1200 possible combinations of 20 amino acids for the molecule. How long before it falls into the configuration that copies Cyanobacteria DNA? What about the other 3,100 or so proteins of Cyanobacteria (as reported by Kaneko et al.)? And what about the hundreds of amino acids that are not found in protein?

With information theory, Hubert Yockey gives us the number of 1 in 10^65 amino acid combinations (of the 20 biological amino acids) is functional for a specific job. That's a 1 with 65 zeroes after it. With the kinds of numbers of intermediates, exaptation means little. Who can think of all the other functions these proteins would need to take on the way to becoming what they are? What would carry on the work of replication while we waited? And many of the "one in 10^65" combinations for DNA polymerase would not even have folds which proteins need for function. These unfolded proteins as well as folded on their way to the right use would be hanging around looking for a place to work like the jobless at an employment agency.

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