subscribe to the RSS Feed

Saturday, August 30, 2014

More on Comparing the Human and Chimpanzee Genome

Posted by jlwile on January 3, 2012

A schematic representation of DNA, concentrating on the nucleotide bases that encode biological information. (Click for credit)

How similar is the human genome to the chimpanzee genome? Since both genomes have been fully sequenced, you would think that would be an easy question to answer. Unfortunately, it is not. After all, how do you compare the genomes of two different species? You might think that the most straightforward way would be to simply line the two genomes up and see how much they overlap. If that’s the way you are comparing the genomes, then the answer is relatively easy. Based on the analysis done by the Chimpanzee Sequencing and Analysis Consortium, about 75% of the two genomes overlap well. There is an error rate of about 3% within that overlap, however, so the two genomes are 72% similar based on this kind of analysis.


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.

Comments

17 Responses to “More on Comparing the Human and Chimpanzee Genome”
  1. Winston Ewert says:

    Is it inaccurate to call Dr. Wood an Evolutionary Biologist? He is a biologist who studies evolution, thus an evolutionary biologist. I think you are reading an implication into that which the author did not intend.

  2. josiah says:

    There’s another message there. Whatever credentials someone has, you can’t just believe everything they say or write. You also have to be very careful checking what they actually do say, since simple statements like “The Human and Chimp Genomes are XY% similar” mask a huge amount of complexity.

  3. jlwile says:

    Winston, Dr. Wood himself took umbrage at the term, so I don’t think I am reading anything into it. Also, why don’t the folks at Uncommon Descent refer to Dr. Jonathan Wells or Dr. Michael Behe or Dr. Douglas Axe as “evolutionary biologists”?

  4. jlwile says:

    Excellent point, Josiah!

  5. Winston Ewert says:

    Uncommon Descent does at times refer to ID proponents as evolutionary biologists: http://www.uncommondescent.com/evolution/retroviruses-and-common-descent-and-why-i-dont-buy-it/. The usage is rare, but it does exist. Yes, Dr. Wood took umbrage, but that doesn’t establish the author of the post was trying to imply that Dr. Wood was a card carrying Darwinist. The post links to a previous post about Dr. Wood and refers to him as a “born again” evolutionary biologist. This suggests they are aware of who he is.

    I have to agree, the post takes a overly dismissive view of Dr. Wood’s paper and appears overall confused about various issues as Dr. Wood pointed out. Calling Dr. Wood an evolutionary biologist, while true for some definitions of evolutionary biologist, isn’t particular helpful terminology.

  6. jlwile says:

    Winston, the link you provided demonstrates what I was talking about. Uncommon Descent uses the term “evolutionary biologist” to refer to Dr. Richard Sternberg and Dr. Michael Lynch, both of whom are evolutionists. I never see them refer to creationists or intelligent design advocates as “evolutionary biologists.” I think it is clear the author thought Dr. Wood was an evolutionist. The fact that previous posts refer to Dr. Wood as “born again” merely shows that they recognize he is a Christian. Since there are many Christian evolutionists, that means very little.

  7. Winston Ewert says:

    Dr. Richard Sternberg:

    Is a fellow of ISCID: http://www.iscid.org/fellows.php
    Signed the scientific dissent from Darwinism: http://www.dissentfromdarwin.org
    Spoke at RAPID: http://www.iscid.org/rapid/schedule.html

    He might well reject being called an ID proponent, but he’s not an “evolutionist.”

    You may well be right in your assessment. I don’t think that intent is clear. Mostly, I find it hard to believe that anybody could figure out anything about Dr. Wood (such as that he was a Christian or his previous criticism of Doug Axe) without figuring out that he was a Young Earth Creationist.

  8. jlwile says:

    Dr. Sternberg is most certainly an evolutionist. In fact, even Uncommon Descent says that:

    Richard Sternberg, an associate of ID and an ID theorist in the broad sense, is also an evolutionist

    More importantly, you can read his own discussion of his views on evolution. Note that in this discussion, he calls himself an evolutionary biologist. Also note that he is a part of the Biologic Institute not because he agrees with the Intelligent Design movement, but because he thinks he has more academic freedom there.

    If nothing else, Uncommon Descent has admitted that they think Dr. Sternberg is an evolutionist. That’s why they call him an evolutionary biologist. Once again, they seem to use that term only with people who they think are evolutionists. The most logical inference, then, is that they thought Dr. Wood is an evolutionist. If you are wondering how they could possibly think that, my response is simple: if you don’t bother to check your facts, you will make all sorts of absurd mistakes.

  9. W. Brown says:

    I find your method of not just recklessly attacking people who have different viewpoints on the origins question, but carefully picking apart even arguments that seem to support your side of the argument, to be absolutely sure that the facts are on your side. The world needs more people like you. This is a refreshing break from the dogmatic blogs offered by creationists and evolutionists alike.

  10. W. Brown says:

    Oh, I’m sorry, there seems to be an error with the grammatical syntax that’s quite confusing. What I meant to say was, I find your method to be refreshing! That word seems to have gotten lost.

  11. jlwile says:

    Thanks so much, W. Brown. I have always considered dogmatic thinking to be an enemy of both theology and science. I am glad that you find my method refreshing. There are many who don’t!

  12. W. Brown says:

    Agreed about it being an enemy of science and theology. Also, this article in particular emphasises the need for many scientists to tackle the same given problem, rather than working from and relying on results from only a few experiments. Anyone reading just one side of this discrepancy would have sufficient information to argue for their side’s correctness, but it is only after reading both sides that one sees that somewhere, somehow, the same type experiment by a different scientist got a rather different result. This example can be extrapolated to other experiments as well, bringing us to the realisation that before solid positions can be taken, both sides must be read thoroughly and without preconceptions about the answer. Sadly, not everyone seems to notice…

  13. Winston Ewert says:

    I have to agree, Uncommon Descent does seem to restrict use of the term “evolutionary biogist” to those not fully alligned with ID or creationism, while it does apply to some such as Sternberg who are not fully ID although also not Darwinists at least in the fullest sense. I had the impression that Sternberg had more fully aligned himself with ID, evidently I was mistaken on that point.

    Did they think Dr. Wood was an evolutionist? You make a very good point that they seem to restrict usage of that term. I have to agree that your explanation is the most reasonable given those facts. I don’t think its neccessairly incorrect to call him an evolutionary biologist, depending on how you define that term, but that’s not what they seem to be doing here.

  14. W. Brown says:

    “Interestingly enough, some intelligent design advocates were rather unhappy with Dr. Wood’s conclusions.”
    That in itself is interesting, as being happy with the conclusions doesn’t make a whit of difference to the correctness of the statement. Are they unhappy with his research? Or just the conclusion…

  15. jlwile says:

    It’s definitely the conclusion they don’t like. As you say, of course, that doesn’t make a whit of difference as to its correctness.

  16. Rio says:

    When we look at a car or an airplane, it is only logical to suggest that it was designed with the features that it has. The human body is much more intricate and complex than the most complex machines we can design. Why is it considered illogical to consider that the human body has a designer? This is a great question to consider to evolutionist.

  17. jlwile says:

    Excellent point, Rio!

home | top