The problem is that simply lining two genomes up and looking for overlap might not be the best way to compare them. After all, it seems that genomes have been designed to change. Genes and their regulatory agents can move around, be copied to different parts of the genome, etc. As a result, when you compare genomes between species, you might need to be a bit more careful in how you do it.
One popular means by which geneticists compare genomes today is by looking at chunks of DNA in one organism and comparing them to the genome of the second organism. One common way to do this is to use the computer program called BLAST (Basic Local Alignment Search Tool). This program takes a chunk of DNA from one organism and splits it into a series of short sequences called “words.” It then looks through the genome of the second organism, trying to find regions where there is a lot of similarity with the words generated from the first organism. If the similarity is above a specified threshold level, BLAST scores it as an overlap, keeping track of precisely how similar the two sections of DNA are within that overlap.
In other words, rather than looking for long stretches of DNA that overlap between two organisms, BLAST looks for smaller regions of overlap. This makes sense, of course, since a given gene or a given regulatory piece of DNA takes up only a small part of the total genome. By comparing small parts of two genomes rather than the genomes in their entirety, you are better able to find the functional units within the DNA that are similar.
So…when scientists use a comparison method such as BLAST, how similar are human and chimp DNA? Surprisingly, the jury is still out on the definitive answer to that question!
Earlier this year, Dr. Todd Wood presented the results of a study in which he used BLASTN to compare the human and chimpanzee genomes. BLASTN is a program that uses the BLAST method to look at the actual nucleotide base sequences in each of the two genomes being compared. Since DNA stores its information as a sequence of nucleotide bases, this is the most fundamental way you can compare two sets of DNA. His analysis showed that the human and chimpanzee genomes were more than 97% similar. More importantly, his analysis concluded:
The probability of the chimpanzee genome being less than 95% identical to the human genome is therefore <2.2 x 10-16
So according to Dr. Wood, the human and chimp genomes are probably more than 97% similar, but they are almost certainly more than 95% similar. Interestingly enough, some intelligent design advocates were rather unhappy with Dr. Wood’s conclusions. The folks at Uncommon Descent actually called him an “evolutionary biologist,” despite the fact that he is a well-known young-earth creationist!
Dr. Wood’s analysis is not the end of the story, however. Another young-earth creationist, Dr. Jeffrey P. Tomkins, has done his own BLASTN analysis of the human and chimpanzee genomes. Dr. Tomkins has a PhD in genetics from Clemson University, and he was the director of the Clemson University Genomics Institute from 2002 to 2006. He also started the Clemson University Environmental Genomics Laboratory in 2006 and was its director for two years. When it comes to genetics, then, Dr. Tomkins knows a thing or two.
Dr. Tomkins’s analysis seems more detailed than that of Dr. Woods, and his results are strikingly different. As he says:
…an unbiased conservative estimate of genome-wide human-chimp DNA similarity is not more than 86–89% identical.
So who is correct? I really have no idea. Both Dr. Tomkins and Dr. Wood are experts in genetics. In fact, Dr. Wood was Director of Bioinformatics at the Clemson University Genomics Institute before Dr. Tomkins became the overall director there. Thus, they have similar credentials and similar research experience. They both used the same basic program for their analysis, but the program has many input parameters that can affect the results. Indeed, in Dr. Tomkins’s analysis, he shows how two of those parameters (the length of the words searched and the threshold level) change the reported similarity between the two genomes.
The take-home message I get from these two analyses is that comparing the genomes of two different species is really difficult. As a result, I don’t think we yet have an answer to the question of how similar the human and chimpanzee genomes are to one another. Hopefully, as more work is done, we will zero in on a reliable conclusion.