The inability of scientists to create a complete Tree of Life (TOL) has been a talking point of ID proponents for some time. Indeed, a complete TOL based on DNA sequence alignments has yet to be completed. Instead of a single tree, usually ‘bushes’ of different clades are about as close as we have gotten. I don’t believe this is because it is impossible to make a complete tree that encompasses all known living organisms, it is simply another example of where the science is a work in progress. Molecular biology is in its infancy and the era of bioinformatics has just started. Nonetheless, IDers take our incomplete understanding as evidence against evolution (For the Discovery Institute’s take, see here and here).
These phylogenetic trees are made by taking DNA sequences from different organisms and aligning them with each other. Organisms that are closer evolutionarily will have more DNA in common and therefore the sequences will mostly match and be easily aligned. Organisms that are distantly related will have less similarities in their sequences. This is not an easy task and is fraught with error due to mutations that lead to an insertion of a piece of DNA, deletion of pieces of DNA, substitutions of DNA, etc.
In the June 20, 2008 issue of Science, Ari Löytynoja and Nick Goldman report a new and better way to align DNA sequences thereby creating better phylogenetic trees. Aligning DNA sequences is a mathematically complex process with several different algorithms designed to take into account small changes in the sequence. Don’t be scared, I am not going to bore you with the mathematical details (mostly because I don’t understand it).
According to the authors, the biggest problem with the current algorithms is that:
Traditional multiple sequence alignment methods disregard the phylogenetic implications of gap patterns that they create and infer systematically biased alignments with excess deletions and substitutions, too few insertions, and implausible insertion deletion–event histories”
Surprisingly, they found that simply adding more and more sequences from similar organisms did not increase the accuracy due to every additional sequence adding evolutionary time to the analysis and therefore more DNA deletions, insertions, or substitutions. This is where the authors say that their new method really shines due to its ability to utilize the phylogenetic relationship of sequences.
What does this all mean for the theory of evolution? Hopefully this will lead to better phylogenetic trees and bring us one step closer to that all important TOL. On the more technical side, the authors think that their new method will allow for a better understanding of the frequency of DNA insertions, deletions, and substitutions.