Some of the Genetic Evidence for the Evolution of Man

There are multiple lines of evidence that indicates that humans share a common ancestor with the other ape species alive today. I wish to look at some of these lines from genetics.

Often, OE vs YE discussions of genetics descends into an endless discussion of whether the genetic similarity between the many species is due to a common designer or due to common descent. I have issues with why YEers think that a common designer is an adequate explanation once you get away from whatever definiton of "kind" they chose (or not chose usually) to give. But, in the end, those discussions are usually fruitless because there is a convenient out even if calls for evidence are generally lacking.

Instead, I prefer to delve into areas where similar form is no longer expected to yield similar genetics. Some of these still involve coding genes. For exampe cytochrome C seems to work in a myriad of forms, can be successfully transferred across widely varying species, and yet still follows a pattern consistent with common descent. There have been a few other such areas that have been touched upon recently on the sidelines of other threads and I thought it might be useful to bring them into their own thread.

Now this is going to take the form of things such as pseudogenes and retroviral insertions that are non-coding. The most common objection raised is that we might not always know that the gene in question does not actually play a role. And for most of these cases, you can even present a few examples of cases where function has been found for such. For example, in a recent thread on whether new information can arise I gave an example of humans acquring a new gene through a retroviral insertion that proved to be useful. Some pseudogenes have been found to actually have functions. But the key is to not let the few outliers fool us. Giving a use for one or two pseudogenes does not mean that they all have a function.

And often, we can know that they do not have a function. I'll use this as a lead in to my first example: pseudogenes. Most animals make vitamin C through a series of four enzymes. Both humans and the other primates are unable to do this. They all share a very specific mutation in the same gene. This is an example of where we can compare the function of a gene directly in other animals and se that the function has been lost and what mutation caused it to be lost.

My first reference.

"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.

I want to look at pseudogenes 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.

 

The next 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 next subject to look at is retroviral DNA insertions.

"Constructing primate phylogenies from ancient retrovirus sequences," Welkin E. Johnson and John M. Coffin, Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, Issue 18, 10254-10260, August 31, 1999.

Here, about a dozen different retroviral DNA inserts are used to construct the evolutionary tree of human and the other apes and primates. See the following chart to see how closely the different inserts match.
http://www.pnas.org/content/vol96/issue18/images/large/pq1892815002.jpeg

Emphasis added.
http://www.pnas.org/cgi/content/full/96/18/10254

There are many such papers out there using LTRs to trace evolution. Here is another.

Liao, D., Pavelitz, T., & Weiner, A.M. (1998). Characterization of a novel class of interspersed LTR elements in primate genomes: structure, genomic distribution, and evolution. JMolEvol, 46, 649-660.

And another...
"Evolutionary implications of primate endogenous retroviruses," Shih A, Coutavas EE, Rush MG, Virology. 1991 Jun;182(2):495-502.

There are many more that can be found with a little searching.

 

Another example.

"Molecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown," Bailey WJ, Fitch DH, Tagle DA, Czelusniak J, Slightom JL, Goodman M,Molecular Biology Evolution. 1991 Mar;8(2):155-84.

 

Another area that can be used to gain insight into our evolutionary history is to look at genes that have been duplicated. These paralogs can be used to trace our evolutionary history and to identify genes that may have played roles in the evolution of specific lineages. For an example, see the following paper.

"Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution," Andrew Fortna et al, PLoS Biol. 2004 July; 2(7): e207.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=449870

 

There is another complication that arises when looking at these examples. Let me use the retroviral DNA insertions as an example.

As shown above, humans and the other apes and primates share insertions that demonstrate their common ancestry. (The quote is "Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place.") In a young earth hypothesis, this is a major problem. You would have to assume that the humans and all the "kinds" (whatever that may be) of primates and apes were infected by the same combination of virii, that they all inserted the exact same sequence in the same place, and that all these insertions were fixed into the various species.

Furthermore, since these insertions are common between essentially all humans, in a young earth they all must have taken place in the (about) ten generations between the creation and the last common ancestor (Noah) and none have taken place since. Unlikely.

 

There is nothing religious about the DNA studies. There are observable and do not depend on faith in something unseen.

Do you have a logical, empirical explanation of the things listed? Appaerntly not since you did not attempt to address them. Just why do humans and the other apes share the exact same retroviral inserts and at the same locations as the other apes? Did you not read the above references.

When you present your alternate hypothesis, let us know your logic behind it, what empirical evidence you have, and what you think would falsify your hypothesis.

 

There is nothing religious about the DNA evidence. It is not faith in something unseen. It is tangable and testable.

I require no one to accept it. You can accept or reject the truth at your own discretion. BUt if you wish to come in here and say that the evidence is incorrect, then tell us specifically what is wrong with it and what your better explanation is.

Thus far you have rejected out of hand the above lines of evidence without a single factual reason why. Without a why, you have nothing for us to listen to. Examine the evidence. Tell us what is wrong. Tell us your idea of how to better fit the evidence into a young earth scenario. That you cannot do so speaks volumes.

You arfue from assertion, not evidence or logic.

 

Then explain yourself.

You remove DNA from an organism or from the remains of an organism. You sequence it. You compare sequences.

Look above at all the different types of DNA sequences that huamns and apes share. Look for instance at the retroviral insertions that humans and apes share. Have you read it? Just one identical sequence in the same location is plenty of evidence that two creatures shared a common ancestor. Humans and apes share many more than this. How did they get there.

If you think that DNA is not "tangible or testable" as you state above then you better start digging because you have a long row to hoe to prove that.

But, thus far, you do not seem interested in supporting anything. Only in making unsupported and unsupportable assertions.

 

These are not unsupported. Have you even read the thread. I doubt it. There are actual citations and references from peer reviewed journals up there. You know, data that has been put to the rigor of letting your competition look over it and see what they can find wrong with it. Those references make a convincing argument.

Do you have any actual citations and references that are on topic and that contradict what I have said? Or will you play word games and make unsupported assertions in an attept to distract and derail this thread? So far the latter seem to be your modus operandi on all threads.

 

"Peer reviewed journals by geneticists, psychoanalysts, astrologers or theologians don't prove anything other than shared opinions and beliefs about their pet theories. "

Ad hominim. You are attcking them by equating real science to astrology.

Peer reveiw weeds out the weak ideas.

"Since when does one need to resort to arguments based on the authority of some professional practitioner of some art or science in order to post on this forum? I prefer to think and reason intelligently for myself."

Unless you have the training in the fields then your opinion is of no consequence. These people's opinions do matter because they have been trained in the appropriate fields. Unless you can factually show problems, you are wasting our time.

"Evolutionists who don't believe that natural processes and selfish genes are intelligently designed are the ones playing fast and loose with word games. "

You claim this without support. YOu cannot just declare yourself correct.

"Well, what is the intelligently designed "modus operandi" of evolutionism if not the total distraction and derailment of intelligent observations about the creative design of all creatures and processes in nature?"

It does not make a judgement about intelligent or not beforehand. It just looks at the process. So far, no evidence for intelligent design has popped out. Do you have an example? Can you tell us how to tell if something is intelligently designed or not? So far you only seem to declare it so. You make the assertion. You have the burden of proof.

 

Another example of molecular data matching the fossil data for human evolution common with the other apes.

"Molecular phylogeny of the family of apes and humans," Goodman M, Koop BF, Czelusniak J, Fitch DH, Tagle DA, Slightom JL, Genome. 1989;31(1):316-35

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2687100&dopt=Citation