Human DNA Differences

[bob b]

I just finished listening to Johnny's call-in and believe he made an excellent point which was glossed over by Bob Enyart.

As I understood it, Enyart was saying that the number of differences between ancient apes and humans was too large to have been bridged by favorable mutations in the several million years that evolutionists claim it happened.

Johnny replied that the changes did not have to occur in series, but could occur in the population as a whole and Bob did not take that into account.

This is basically the crux of the topic known as "Haldane's Dilemma", but I don't wish to revisit this right now, because Johnny went on to talk about the number of DNA differences between humans and this is what I want to explore in this thread.

I believe that it is not "cricket" to compare the difference between DNA in an ape to human transition as it is to compare the differences in DNA within the genomes of humans.

I hope I can explain my reasoning for feeling this way.

But first I think we need to make a distinction between two types of DNA: coding DNA, that which codes for the production of proteins, and non-coding DNA (previously called "junk" DNA), that which doesn't code for the production of proteins.

To simplify things, I would first like to concentrate on the coding DNA, even though I recognize that non-coding DNA may have to be considered before final conclusions may be drawn.

If anyone has reliable data on these factors please chime in while I take a break and search the web myself.

 

[Nomad]

I think you need to say what 'cricket' meants...

 

[One Eyed Jack]

Cricket is a British sport with a strong emphasis on fair play -- thus, 'cricket' means 'fair.'

 

[Johnny]

Off hand I know that much of the initial research was done on single nucleotide polymorphisms (SNP), but the latest trend seems to be studies involving copy number variant regions (CNV). The trouble, as you already noted, will be differentiating which parts are involved in exons & euchromatic regions (the transcribed portions) vs. introns and heterochromatic regions.

One good place to start is at the human genome project's homepage, specifically the SNP page.

"For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome."

There's also an international project to document all the SNPs in the human genome. Currently, there are about 12,500,000 SNPs identified (according to http://en.wikipedia.org/wiki/International_HapMap_Project). Again, I'm looking for research regarding how many of these are actually in transcribed regions.

 

[bob b]

Off hand I know that much of the initial research was done on single nucleotide polymorphisms (SNP), but the latest trend seems to be studies involving copy number variant regions (CNV). The trouble, as you already noted, will be differentiating which parts are involved in exons & euchromatic regions (the transcribed portions) vs. introns and heterochromatic regions.

One good place to start is at the human genome project's homepage, specifically the SNP page.

"For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome."

There's also an international project to document all the SNPs in the human genome. Currently, there are about 12,500,000 SNPs identified (according to http://en.wikipedia.org/wiki/International_HapMap_Project). Again, I'm looking for research regarding how many of these are actually in transcribed regions.

Thanks for the information and links Johnny.

It is beginning to look like this is going to be quite a project.

 

[bob b]

I would like to call everybody's attention to the latest article in the "Cell Trends Too" thread which reports the latest cell research which has discovered that cells have encoded in their DNA a sort of "Zip code" which correlates with their position in the body.

This indicates to me that when cells divide that information has somehow been transmitted into the DNA, otherwise how did the zip code information get there?

In addition the information is not obviously from "random mutations".

So I have a question for Johnny.

Do you know whether the human genome project uses germ cells or not for their sequencing of the DNA?

 

[Johnny]

I would like to call everybody's attention to the latest article in the "Cell Trends Too" thread which reports the latest cell research which has discovered that cells have encoded in their DNA a sort of "Zip code" which correlates with their position in the body.

This indicates to me that when cells divide that information has somehow been transmitted into the DNA, otherwise how did the zip code information get there?

In addition the information is not obviously from "random mutations".

I just typed up a long response to this and then accidentally closed the tab. Fun!

No new information was added to the genome -- all the genes are present in all cells, they're just expressed at different levels. The authors discovered that fibroblast gene expression pattern can be divided into three axes: anterior-posterior, proximal-distal, dermal-nondermal. The way this is accomplished is likely through HOX gene expression patterns which specify body axes during somite (early embryonic) development. For example, the HOXA13 gene is expressed in fibroblasts located distally, but more proximal fibroblasts such as in the arms do not express the gene. This represents an epigenetic (nongenetic) tranmission of body-position information; which is the classical model of differentiation.

The research didn't appear to produce any suprising results. Indeed the same thing has been found all over the body with different tissues. Nonetheless, it is significant for a variety of reasons which I won't go into but the authors do in the paper if you're interested.

Suffice it to say that all the cells still contain the exact same information, so it's not of concern whether or not the human genome project is sequencing fibroblasts, neurons, melanocytes, etc. But for reference I found that they are using white blood cells from women and sperm cells from men because of the high nuclear/protein ratio.

 

[bob b]

I just typed up a long response to this and then accidentally closed the tab. Fun!

No new information was added to the genome -- all the genes are present in all cells, they're just expressed at different levels. The authors discovered that fibroblast gene expression pattern can be divided into three axes: anterior-posterior, proximal-distal, dermal-nondermal. The way this is accomplished is likely through HOX gene expression patterns which specify body axes during somite (early embryonic) development. For example, the HOXA13 gene is expressed in fibroblasts located distally, but more proximal fibroblasts such as in the arms do not express the gene. This represents an epigenetic (nongenetic) tranmission of body-position information; which is the classical model of differentiation.

The research didn't appear to produce any suprising results. Indeed the same thing has been found all over the body with different tissues. Nonetheless, it is significant for a variety of reasons which I won't go into but the authors do in the paper if you're interested.

Suffice it to say that all the cells still contain the exact same information, so it's not of concern whether or not the human genome project is sequencing fibroblasts, neurons, melanocytes, etc. But for reference I found that they are using white blood cells from women and sperm cells from men because of the high nuclear/protein ratio.

I would be very interested in reading the paper, but unfortunately my local library only subscribes to Nature and Science. They spend their money mostly on buying new DVDs and CDs, which is where the most public demand is. This is why I can stock my personal library with many recent science books for a buck a crack, because they are rarely checked out and thus are quickly sold at the surplus sale to make room for the more popular stuff (DVDs, CDs and children's books). It is amazing that they bother to buy any science books in the first place.

Sometimes I do get stuff on interlibrary loan, but it is much more of a pain to go that route.

 

[Johnny]

It was published in PLoS Genetics, which is open access. Here.

 

[bob b]

It was published in PLoS Genetics, which is open access. Here.

Thanks.