Thursday, February 19, 2009

Chimpanzee DNA is very much like human DNA

Chimpanzees are considered to be the organisms most closely related to humans. Many people don’t know that there are actually two species of chimpanzees. “The better known chimpanzee is Pan troglodytes, the Common Chimpanzee, living primarily in West, and Central Africa. Its cousin, the Bonobo or "Pygmy Chimpanzee" as it is known archaically, Pan paniscus, is found in the forests of the Democratic Republic of the Congo. The Congo River forms the boundary between the two species[1].” Each are equally closely related to humans.

How close is that?

Based on a great deal of data, scientists believe that the common ancestor of humans and chimpanzees lived from five to eight million years ago[2].

The most interesting evidence that chimps and humans are related to each other is found in the DNA of the species.

There are different ways of quantifying DNA. As most of us are aware, DNA is shaped in something called a double-helix with the two parts of the “double-helix” connected by a very long sequence of hydrogen bonds called “nucleotides” (also called “base pairs” or even “base units”). The picture below is an artist’s sketch of the structure of DNA[3].

Both human and chimp DNA contain about 3 billion nucleotides (hydrogen bonds in this picture).

So, one simple way to compare the DNA of the different organisms is to compare the sequence of nucleotides.

But much of the DNA is non-functioning (it doesn’t do anything). That DNA is called “Junk” DNA. So should only the DNA that performs a function be compared? Does the non-functioning DNA really give us any hints about how different (or similar) chimps and humans are to each other?

As an extra complication, even within humans, there are differences in DNA. If everyone had identical DNA, then everyone would be identical. As one might expect, only identical twins have identical DNA (and even they most often have very minor differences generally involving only a handful of nucleotides). Among all humans, the Human Genome Project found that there is a bit less than a 1% variation in DNA[4] (again, depending on how you quantify the differences). Although chimpanzee DNA has been less well studied than human DNA, it is surely reasonable to expect that a similar amount of variation in DNA is present between different chimpanzees. Therefore you would expect some chimps would have DNA closer to that of some humans than other chimps would have DNA similarities to other humans.

All of these factors make it difficult or even impossible to assign “a single number” that quantifies the differences between chimp and human DNA.

So how different are the DNA sequences of the two species?

One summary puts it this way:

“Humans and chimps each have some 3 billion base units of DNA in their genomes, differing by only 1.2 percent when compared in this way. Other methods of comparison estimate a genetic difference of at most 4 percent.[5]
It is important to note the differences. If you simply count nucleotide differences, then there is only a 1.2% difference. That is actually on the same order of magnitude as the sum total of the DNA differences just among humans (which approaches 1%)!

But there can be no doubt that chimps are different from humans! No one would mistake a human for a chimpanzee. Clearly, and logically, we should compare the DNA in other ways. Probably a better way to compare the genomes is by comparing the functioning DNA. When we do that, we find a larger, though not a large, difference – one that approaches 4%.

So, depending on how we quantify DNA, they are either about 98.8% the same or about 96% the same.

We can learn a few things by comparing these numbers.

First, the largest differences come if you ignore “Junk” DNA. Creationists insist that there is no such thing as “Junk” DNA. (Basically “Junk” DNA implies an incompetent “designer”.)

That creates a paradox for creationists.

If there is no “Junk” DNA, then all DNA should be compared. In that case chimp and human DNA are uncomfortably close to each other.

On the other hand, if you ignore “Junk” DNA, then you are implicitly acknowledging that such “Junk” DNA exists and, therefore, if it is indeed “intelligently designed” then that “designer” has a high error rate in His “designs”.

As would be expected, creationists ignore “Junk” DNA when they give numbers for DNA differences but they then, inconsistently, continue to insist that “Junk” DNA does not exist. (They hope that no one notices.)

Evolution, as always, has an answer to this puzzle.

‘Junk” DNA does not have any function. Because of that it is invisible to natural selection. Since it has no function, natural selection works to neither remove it nor to propagate it throughout the genome of the population.

Because “Junk” DNA is invisible to natural selection, it moves through the population’s genome through a process called “genetic drift” which operates much more slowly than the process of natural selection. Therefore evolution would predict that there would be smaller differences in “Junk” DNA than there are in functioning DNA when comparing chimpanzee genomes to human genomes.

It goes without saying that is exactly what we see.

So what we see is that chimp and human DNA provides strong evidence supporting evolution.

But there is more.

Scientists have learned a great deal since they were learned how to sequence DNA. One of the things that they have learned about is the so-called GULO gene.

There is a gene named “L-Gulono-γ-lactone oxidase”. That long name is generally shortened to “GULO” or even “GLO”. That gene synthesizes vitamin C. If you don’t get any vitamin C at all, you will get a disease called “scurvy”.

However, there is another way to get Vitamin C other than through the GULO gene. That is by including fresh fruit in your diet. Fresh fruit has vitamin C. So if you have vitamin C in your diet because you can eat fresh fruit, then you don’t need a working GULO gene. In that case, the GULO gene becomes a sort of “Junk” DNA gene that isn’t needed for survival. Therefore, from the perspective of natural selection, it makes no difference whether or not the gene stops working. In either case, organisms with a non-functioning GULO gene have no selective advantage or disadvantage over others in the same population.

As it happens, the GULO gene doesn’t work in humans. In fact the reason that a couple of centuries ago, English sailors got the nickname “limies” is because they took limes along with them on long voyages in order to avoid getting scurvy on those voyages.

No big deal, right?

Actually, it turns out that most mammals have a working GULO gene. But contrary to what we see in all of those other mammals, it seems that all primates have the same “broken” GULO gene. Not only is it “broken”, DNA studies have shown that it is broken in exactly the same place in all of these primates.

To understand the significance of these DNA sequences which are broken in “identical” ways, look at DNA as a word made up of letters associated with each of the different possible nucleotides that can be present in DNA (in any particular order). Those nucleotides are called adenine (A), guanine (G), cytosine (C) and uricil (U),

There is only one way to spell a word correctly[6]. However there are many ways to misspell a word.

Because of that if two people identically misspell the same word, the most likely explanation for that identical “mistake” is that one was copied from the other. In other words the mistakes had a common source.

In order to detect such plagiarism, occasionally people will intentionally misspell some words. This happens so often that there is even an expression for such intentional misspellings. They are called “Easter Eggs”.

Here’s how one Internet resource described his ingenious use of “Easter Eggs”:

“I'm the author of one of the dictionaries that Google ‘adopted’, and I deliberately inserted some ‘misspelled’ (aka ‘easter-egg’) words into the dictionary, so I can immediately recognize a spell-checker based on my dictionary - and it turns out that Google's Gmail spell-checker is indeed based on my dictionary.[7]

Moreover, phone book companies do it. Even the New Oxford American Dictionary inserted an intentionally misspelled word in their dictionary in order detect when someone is copying their words (it took the New Yorker magazine to discover that word)[8].

Similarly, Swiss banks often introduce “misspelled or spelling errors…in their…documents as part of the banks own internal authenticity code”[9].

The point of all of this: identical misspellings are very strong evidence of one document being copied from another. Different misspellings don’t have the same implication.

As it happens, Guinea Pigs also have a “broken” GULO gene. But the gene is “broken” differently from how it is “broken” in primates. A creationist source, arguing against the GULO gene being evidence supporting evolution says this:

“…independently-derived guinea pig and human GULO pseudogenes have an astounding 36% identical `disablement'”[10].

Yes. Creationists are indeed clueless. If it is not identical, then it doesn’t count. In fact a mere 36% match isn't even close to being identical.

These primates have the GULO gene “broken” (or misspelled) identically:

Both species of chimpanzees and humans.

There are no other species of organisms on Earth that have the same “misspelling”.

The only rational conclusion: these species have GULO genes copied from the same source. In other words, they share a common ancestor.

The bottom line: evolution has been confirmed.

[1], referenced on August 16, 2008
[2] McBrearty, S.; N. G. Jablonski (2005-09-01). "First fossil chimpanzee". Nature 437: 105–108
[6] There are, as many of us know, a very few words in the English language that can be correctly spelled in more than one way. Since this is simply an analogy and since that number is small, we will ignore those words here.

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