Human/ape common ancestry has been a subject much discussed recently. A friend wrote me asking for links dealing with human/ape common ancestry. While there are numerous good articles that have talked about this issue from an intelligent design (ID) friendly perspective, I tried to provide him with some helpful links and information.
As a preliminary point, it's important to note that human/ape common ancestry is compatible with ID. Nonetheless, ID proponents are interested in taking a scientific approach to these questions, and the evidence suggests that even modest changes requiring two or more mutations before conferring any adaptive benefit could not arise via Darwinian evolution under any reasonable timescale involving human/ape common ancestry. As a result, questions about human/ape common ancestry should be on the table for people who really want to follow the evidence where it leads.
The basic issue is this: Despite the fact that human/ape genetic similarities are often overstated, YES, in many instances it is true that humans and chimps have very high levels of genetic similarity. Does this functional genetic similarity bolster neo-Darwinian evolution and human/ape common ancestry? Not at all. In fact, we could have predicted these similarities without any knowledge of Darwinian evolution simply by observing that humans have similar body plans to apes. If similar morphology implies similar genetics, then we could predict these high levels of similarities without even thinking about considerations pertaining to common ancestry.
But there's another important point to consider: Functional morphological and genetic similarities between humans and apes could be the result of common design just as much as common descent. That's a good principle to keep in mind as you investigate this issue: functional biological similarity is explained by common design just as well as it's explained by common descent. (In fact, in some cases--such as extreme convergent evolution--such similarity is explained much better by common design.)
There are a lot of good articles out there on this topic, but here is a summary of some articles germane to recent debates:
(1) Casey Luskin and Logan Paul Gage, "A Reply to Francis Collins' Darwinian Arguments for Common Ancestry of Apes and Humans," in Intelligent Design 101: Leading Experts Explain the Key Issues, edited by H. Wayne House (Kregel, 2008), provides a rebuttal to many of Collins' arguments for human/ape common ancestry:
a. This article notes that the evidence for human chromosomal fusion simply shows that our human lineage underwent a fusion event and doesn't say anything about whether our lineage shares a common ancestor with apes. For another good article on problems with the telomeric evidence for human chromosomal fusion, see "Guy Walks Into a Bar and Thinks He's a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity."
b. Collins cites much "junk DNA" as alleged evidence of our shared ancestry with apes, but this DNA turns out to NOT be junk at all.
c. Collins makes weak arguments that a couple mutation in a gene could have produced human cognition--this is an outlandish hypothesis that is easily rebutted.
d. For another recent rebuttal to Collins on the issue of junk DNA and human/ape common ancestry, please see "Francis Collins' Junk DNA Arguments Pushed Into Increasingly Small Gaps in Scientific Knowledge.
e. For background on functions for pseudogenes, see "Et tu, Pseudogenes? Another Type of 'Junk' DNA Betrays Darwinian Predictions".
(2) "Human Origins and Intelligent Design," Progress in Complexity, Information, and Design, Vol. 4.1 (July, 2005).
a. This article reviews the fossil evidence for human/ape common ancestry and finds that it is lacking.
b. There is also a less-technical version of this article here.
a. This article asks whether human/chimp genetic similarities are good evidence for common ancestry. As the journal Science has reported, it notes that human/chimp genetic differences are much more than the "1%" genetic difference we typically hear about.
b. This article also notes that human/ape genetic similarities might result from common design rather than common descent.
c. This piece asks what is the metric for demonstrating Darwinian evolution based upon genetic similarity. There doesn't seem to be one, and the argument often appears arbitrary.
d. In fact there are some parts of our genome, such as the human y chromosome, that are radically different from the chimp genome. For details, see: "Recent Genetic Research Shows Chimps More Distant From Humans, Neanderthals Closer."
e. Geneticist Richard Buggs has an excellent article which argues that the degree of similarity between the human and chimp genome might be as low as 70%:
To compare the two [human and chimpanzee] genomes, the first thing we must do is to line up the parts of each genome that are similar. When we do this alignment, we discover that only 2400 million of the human genome's 3164.7 million 'letters' align with the chimpanzee genome - that is, 76% of the human genome. Some scientists have argued that the 24% of the human genome that does not line up with the chimpanzee genome is useless "junk DNA". However, it now seems that this DNA could contain over 600 protein-coding genes, and also code for functional RNA molecules.
Looking closely at the chimpanzee-like 76% of the human genome, we find that to make an exact alignment, we often have to introduce artificial gaps in either the human or the chimp genome. These gaps give another 3% difference. So now we have a 73% similarity between the two genomes.
In the neatly aligned sequences we now find another form of difference, where a single 'letter' is different between the human and chimp genomes. These provide another 1.23% difference between the two genomes. Thus, the percentage difference is now at around 72%.
We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This "copy number variation" causes another 2.7% difference between the two species. Therefore the total similarity of the genomes could be below 70%.
Be sure to also read Dr. Buggs' follow-up article that answers questions and objections about his argument.
a. This article shows how the genetic data is actually painting a very confusing picture about human common ancestry with apes.
b. The paper reports: "For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee."
c. Another article which elaborates on similar problems is at "Primate Phylogenetics Researchers Swinging from Tree to Tree."
d. Likewise, Jonathan M. recently reported that ERV distributions conflict with the standard phylogeny of human/ape relationships.
(5) In the past few years quite a bit has been written on challenges to widely touted "missing links." Rebuttals can be found in articles like:
a. Lucy: "My Pilgrimage to Lucy's Holy Relics Fails to Inspire Faith in Darwinism."
b. Ardi: "The Overselling of Ardipithecus ramidus."
c. Ida: "The Rise and Fall of Missing Link Superstar 'Ida'."
d. Neanderthals: For a discussion of why Neanderthals don't show anything like human/ape common ancestry, please see: "Does Giberson and Collins' Neanderthal Argument Demonstrate 'Common Ancestry'?"