pangloss

Hmmm... I wonder if you ever had plans to address my comments and posts directed at you.

Guess not.

lpetrich

Looks like my earlier comments were in error; I had been guessing as to what was being compared.

pangloss

Sadly, it isn't what the titles of the news articles make it out to be:

"But he also found that the DNA of both species was littered with indels. His comparisons revealed that they add around another 4.0 per cent to the genetic differences."

Indels - insertions and deletions - can be many hundreds of base pairs in length.

Such insertions and deleteions are most likely one-time events, so phylogeneticists, for example, consider them as a single unit of change.
Britten just included the base pairs of indels in his count.

It really does not have the impact that the news articles' titles imply.

GeoTheo

Vander,
I am taking molecular genetics and so have recently gained some understanding of the issue.
Basically these portions of Chimp and Human DNA are compared through a process called "hybridization" a portion of double stranded chimp and human DNA are denatured or melted.
Then chimp single strands and human single strands are reannealed together. They complementary molecules join together and molecules that don't complement one another create a little buckle in the DNA.
The fact that hrbridization can occur at all between two different species DNA very strongly points to common ancestry. This can be done with frogs, mice, bacteria, you name it. In fact we pretty much have all the genes mice have.
We share a gene with frogs that is different by only one codon. This gene codes for a hormone that is composed of only 9 amino acids. In frogs the hormone makes them expell eggs. In human women this hormone induces labor. Doctors give this hormone to expecting women. You can give the human hormone to frogs and it will still work even though one amino acid is different.
Here is the interesting part: The human genome is huge. Most of it does not code for anything. I would not call it junk DNA because it may serve some purpose, but the fact is, it is composed of long repettitive non coding sequences. Mutations in these portions do not affect phenotype. But if there is a mutation in a coding portion it causes a loss or gain of function and can screw things up.
Think about this. So what happens is the genes we share with frogs and mice and bacteria that actually code for things are preserved by natural selection.
But, the non coding portions continue to change over time. There are also things called "pseudo genes" that once were a functional gene but were rendered inoperable by a mutation. Guess what happens to these? They collect mutations over time because they serve no purpose and therefore aren't preserved through natural selection.
Humans only have an estimated 34,000 functional genes. These are all the same genes found in other animals pretty much but we use them differently. They have been preserved over eons because they are usefull. We are made with interchangeable parts basically. We actually have the same genes as other animals. We have perhaps 95% of what a chimp has. We also have a lot of DNA that just takes up space. We even share that. As humans and chimps continue to diverge the "introns" or non coding DNA will continue to collect mutations but most of the coding portion will remain the same because we use it. The only way it is preserved is through natural selection. That is an incontrovertable fact. We have the genes we have today because of natural selection.
Even if you say they were created the only reason they are around is natural selection. But we can measure rates of mutation and it occurs at a 1 percent change in total genome every 10 million years. That makes a young earth and special creation of individual species very unlikely.
You have to account for the creation of the 98 % percent of our DNA that is non-coding.

Doubting Didymus

Geo, I'm so jealous! I can't wait to get to molecular genetics.

But was this test in question performed by hybridization? It looks more like a short sequencing compared by a computer program.

Speaking of hybridiztion methods, did it crack you up when you first heard about it?

"You're telling me we are going to glue these DNA molecules together and then set them on fire?" I laughed and laughed.

GeoTheo

It's kind of a hellish class actually. The professor basically throws all this info at us we can't quite absorb. Everybody looks dazed. She tests us with exam questions no one can quite figure out. For example we had to memorize a calculus equation of the kinetics of hybridization and calc is not a pre-requisite and most have not taken it. The kenetics thing actually involved a whole lecture. I think O.Chem and Gen. Chem would also be valuable pre-requisites. I got a B on the first exam even though I got a 63%. The curve was
steep I went home thinking I had bombed it (actually by most standards I had)
I wasn't aware of the setting on fire thingy. Perhaps that is in the lab portion.
One thing I like about the class though is that I can now read about the human genome project and know what they are talking about.
I think it is a really cool class though and now I know why I need to take physics and calculus and chemistry even though I never liked those subjects before. Good luck taking it. It is truly mind expanding.

Doubting Didymus

The setting on fire thing was a joke. I don't know exactly how they melt it.

I don't mind chemistry, but I hope to goodness I don't need much calculus! My math skills reach their limits at basic trigonometry!

GeoTheo

Well actually they don't really melt it in the sense you would melt metal. They just break the hydrogen bonds that hold the bases together.
I think they also add a sulfur compound to that does somthing with the ions (I got a 63 remenber?)
Then the single strands are kind of just hanging around limp. Then they heat them to just lower than the temperature they used to melt them.
The bases A and T and C and G attract each other.
So then the strands zip up like a zipper if they match each other. For example if one strand was composed of AGC TGA GAA it would join up with a strand like ACG ACT CTT. Because they complement each other. But they would be a lot longer. I wrote them in triplets just because that is how they are read. So if the chimp DNA joins up with Human DNA it is only because they match. Then by counting the base pairs that don't match yopu can get an idea of how they vary. I have kind of a loose grasp of how it works. This match up is called a zooblot. They do it with all kinds of different species, even eukaryotes with prokaryotes.
The double helix is very elegant IMO but also the aspect of mutation and natural selection is very obvious also. So in a sense I can see why IDsts would say DNA shows intelligent design, but it really looks as though it was designed to evolve through mutations. I can see clear evidence of common ancestry of all living things but I have to admit that it seems hard to fathom how DNA itself started. I am not postulating a God of the gaps theory here, however. I'm just saying DNA is really cool.

Doubting Didymus

Very interesting indeed! I have never actually known the details of how they do that.

As for DNA getting started, surely you would agree that it could have come from RNA world (remember that RNA can naturally generate 'microspheres' that resemble the earliest known fossils, but beyond that I agree that is gets rather complicated.

Jesse

Can we still be confident that humans are more closely related to chimps than the other great apes, or might this new study call that into question? Does anyone know how much of our DNA we share with Gorillas and Orangutans?