Evolution and common genetics

Well, there have been several partially successful attempts to hijack this thread. I am now going to return to the original subject. Perhaps we can hear some of those alternate explanations for the real data being presented or perhaps we will continue to see a demonstration of the inability of YE to deal with actual data instead of strawmen and misrepresentations.

In my last on topic post [ http://www.baptistboard.com/ubb/ultimatebb.php/topic/3/3200/2.html#000019 ] I gave some information about one way in which the genome shows evidence of evolution having actually occurred, how that example gives an example of a mechanism of ways in which the genome evolves and how that example is a problem for a YE paradigm.

I want to spend a few moments further on background for that example and then give another case of the same process.

First off, there was a mention of retroposons. These are segments of DNA which have the ability to copy themselves around the genome. They are sort of like little viruses.

The example discussed a particular retroposons called an Alu. An Alu is a sequence which is copied around primate genomes extensively. The one estimate I remember is that just this one sequence has over 500,000 copies in the human genome. (Just when did that happen in a young earth?) Alu sequences can provide genetic diversity because when they insert themselves, they change the DNA sequence in that location. Hold that thought for a moment.

Genes are generally broken into pieces called exons which must be spliced together to make the actual gene. As it turns out, a given exon can be spliced into more than one gene. Some genes even use just part of a particular exon. So by using a process of alternative splicing or of exon shuffling, new genes can be created simply by alternating which exons are joined together and this can be done without affecting other genes.

Back to the Alu. As it turns out, it is not hard to mutate part of the Alu sequence into the three letter code that signals the end of an exon. So when an Alu sequence is copied into an area of DNA and mutates, it can provide a new exon. This exon can then be alternatively spliced with other exons potentially resulting in a new gene. That is just what happened in the example above.

Here is a different paper that talks about alternative splicing. In this specific case, alternative splicing leads to a variety of genes. In this case, 23 exons form 14 different isoforms. Included here is a variation in the splicing where new sequences are produced by alternatively including or excluding section of DNA from within a given exon as mentioned above. It also provides another method of generating novelty by including expressions of Alu, LINE and MER repeats very similar to the expressed Alu sequence in the previous post.

Lipovich L, Lynch ED, Lee MK, King MC., A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31, Genome Biol. 2001;2(4)

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11305939&query_hl=1

 

I also want to return to some of the actual genetic methods that can be used to trace ancestry to highlight the lack of a YE response to the specific types of data that are available.

The subject I wish to explore here is chimeric retrogenes. They happen to be functional but they arise in a specific way that allows them to be used to trace evolutionary family trees.

The basics are that mRNA is turned into cDNA through reverse transcription. This sequence is then permantently integrated into the genome by endogenous integration proteins.

The evolution of the primates and apes can then be traced by when specific sequences were integrated into the genomes of the various common ancestors.

When looking at this 12 specific chimeric retrogenes, you get the following chart.
http://nar.oupjournals.org/cgi/content/full/31/15/4385/GKG496F3

The distribution of the various genes in the various primates and apes, including humans, matches that which would be predicted through other techniques. That this technique matches that as done by other genetic, molecular and fossil methods is a very powerful combination of factors that strongly indicate the descent of humans from a common ancestor with the other apes.

"The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination," Anton Buzdin*, Elena Gogvadze, Elena Kovalskaya, Pavel Volchkov, Svetlana Ustyugova, Anna Illarionova, Alexey Fushan, Tatiana Vinogradova and Eugene Sverdlov, Nucleic Acids Research, 2003, Vol. 31, No. 15 4385-4390.
http://nar.oupjournals.org/cgi/content/full/31/15/4385

The problem that arises for YE is that it does not matter what kind of genetic data that you examine, they all contain patterns that are only explainable by common descent. This is just one example of one kind of data. The amazing thing is how all of the different techniques continue to give the same answers. There is no better explanation than common descent. Just pay attention to the lack of an alternate theory and how one would test it to differentiate it from common descent.

And in the same vein, the details of the genomes give very strong evidence of having been made by the evolutionary mechanisms that are being proposed. No explanation will be proposed that can be tested to explain the details of the genes that show that they are the product of evolution.

 

OK let's get back to genetics, as in human and chimp. 98% similarity? One interesting thing about these numbers, they are not based upon the entire genome. There are many regions (some very significant) where a large portion of one of the human chromosomes is not found in the chimp genome. But, rather than counting such areas as differences, they are ignored. Clearly, doing so makes the percent similarity more than it really is. Including such regions may reduce the percent similarity to closer to 90%.

Another thing is that while similar segments of DNA can be found in chimp and human chromosomes, the DNA found on a specific human chromosome is often scattered among several of the chimp genomes. Not very consistent with common descent, I wouldn't think.

Note: the information in this post was provided by a geneticist.

 

Could you provide references so we can know specifically what you are talking about?

And could we get those elusive alternate explanations to the observations that have been presented?

 

Actually, this is consistent with chromosome remodelling, which JWI has so kindly given us evidence for.

 

Yup, the evolutionist grab-bag has an answer for everything. Thus, there is NO evidence they cannot accomodate one way or another and thus NO evidence they will accept as being evidence of a special, recent creation.

Evolution from bacteria to bear, the way all the excuses run, is absolutely unfalsifiable, and therefore not science at all, but a belief system.

 

You know, Helen, if it looks like a duck and quacks like a duck, it really might be a duck!

I'll go ahead and provide a paragraph from a very interesting book I'm reading.

Human Gene Evolution, David N. Cooper. Academic Press, Inc.; San Diego, CA. 1999, p. 72.

 

[sarcasm]What was that, Petrel?

That looks like a quote from some sort of authority that backs up your assertion while showing that another's assertion was groundless. There even seems to be some sort of text there at the end that would allow one to verify what you say by looking it up for themselves and reading it.[/sarcasm]

"Yup, the evolutionist grab-bag has an answer for everything. "

Pretty much. It is good when your theory describes reality well. It is good when the most surprising findings merely teach you something you did not know about your theory without requiring you to ditch it.

"Evolution from bacteria to bear, the way all the excuses run, is absolutely unfalsifiable, and therefore not science at all, but a belief system."

Absolutely false.

Just this thread provides a small sampling of the actual data on which it is based. So no faith required. It is very good science.

And plenty of ways to falsify evolution have been proposed. No one has yet provided such evidence.

But it would be nice if YEers would stick their neck out with testible, falsifiable ideas which attempt to provide alternate explanations to the rich set of observations on which evolution is based.

 

Another morning, time for another genetic example for which YE has no theory to propose.

This time I will stick with the first subject, using genetics to trace relationships between the species. I also wish to cut the common designer assertion off by sticking with non-coding DNA. Surely an intelligent designer would not feel the need to fill the genomes of perfect creations with "junk." And although some often point out that some use has been found for some junk, much of the junk really is just that. And you will see that this study includes some of those things which are just junk.

I want to look at pseudogenes and other bits of DNA can be used to trace the evolutionary history of apes. For this paper, they used "53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan." These segments included "Y-linked noncoding regions, pseudogenes, autosomal intergenic regions, X-linked noncoding regions, synonymous sites, introns, and nonsynonymous sites."

When all the various sequences are considered as togther, they "supports the Homo-Pan clade with a 100% bootstrap value." This is pretty clear evidence of the shared common ancestor for humans and chimpanzees.

So, at least for this one analysis, the common ancestor of the chimps and humans is almost certain.

"Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees," Chen FC, Li WH, American Journal Human Genetics, 2001 Feb;68(2):444-56.

 

Let us assume that my Maltese Terrier has the same DNA that I do with the exception of one molecular structure.

That certainly doesn't change my opinion of my relationship with my dog.

Genetic Code is probably the closest thing we have to an embedded code from the designer. (Of course, who knows what else we will find in the future that has not even been identified yet.)

It is just like a microcontroller. I change a few lines and I can use it to fly a Cruise Missile into downtown Bagdad. I can change a few more lines and use it to control the anti-lock brakes and save the life of your kids on a wet road. ---certainlly doesn't make the two a result of either design, but it does tell me the designer was probably the same entity.

My point is, you can rattle numbers and data all day long, but it is not making a point---unless your conclusion has already been made.

 

"Let us assume that my Maltese Terrier has the same DNA that I do with the exception of one molecular structure."

You can assume it but it is not true.

"My point is, you can rattle numbers and data all day long, but it is not making a point---unless your conclusion has already been made. "

We are just looking for an alternate explanation that describes the actual details of the observations. Common descent handles the details extremely well. The genome is just what one would expect given common descent.

If you have an alternate explanation, there are many specific details presented here. Pick one, tell us how to explain it, tell us why you would expect things to be that way, tell us how your ideas can be differentiated from common descent and tell us how to test your theory.

These types of genetic studies are being done all the time and are good tests of evolution. So far, the results are in agreement with theory.

Only one conclusion is supported by observation. You make that point by talking about unrelated topics like cruise missles instead of the actual data.

 

Hmmm. The more correct formulation for your statement would be, you can rattle numbers and data all day long and make your point . . . unless the listner has already made up his conclusion and is proof against all evidence.

 

Well, I can guarantee you one thing---there will NEVER be an animal that will evolve to the intelligence of a human who can build a cruise missile. But, of course, we would have to wait three billion years to find out....wouldn't we?

 

Actually Helen the recent estimates lower the figure well below 90% to an approximate 86.7 percent genetic similarity to the chimp (1).

But of course we are 35 percent similar to the daffodil (2), and few would suggest that that makes us one-third narcissus.

Notes for UTE,
(1) Tatsuya Anzai et al., “Comparative Sequencing of Human and Chimpanzee MHC Class 1 Regions Unveils Insertions/Deletions as the Major Path to Genome Divergence,” Procedings of the National Academy of Sciences, USA 100 (2003):7708-7713.

(2) Jonathan Marks, What it means to be 98% Chimpansee: Apes, People, and their Genes (Berkeley: University of California Press, 2002), 29.

Rob

 

Rob

The fact that one theory is attested to by man and the other theory was attested to by God has little significance to those that refuse to believe God.

Wayne

 

I agree that YEC is attested to by man, but I wouldn't say that proponents refuse to believe God.

 

Wayne, you are confusing a THEORY proposed by Young-earth creationist and the revelation given by God.

God's Word is inerrent.

Our theories regarding its proper interpretation are not inerrant.

Rob

 

Rob

I doubt that you had any idea of what I was doing, but thank you for trying.

 

Gold Dragon

What a name you have chosen . . .

 

Of course I was referring to the Dragon in Revelation when I chose it. I must be Satan.