I found the following section, from the ARJ article referenced in my prior post, illuminating.

In general, creationist research into the area of human-chimp genome similarity has been largely limited to the interpretation of claims made in evolutionary research without fully addressing the highly selective methods used or the non-alignable data that is often omitted. Nevertheless, many important points and discoveries have been brought to light.

Prior to the completion of the chimpanzee genome project, molecular biologist David DeWitt points out that despite the supposed high DNA similarity between human and chimp, significant differences exist in cytogenetics, types and numbers of transposable elements, insertion and deletion events, gene expression patterns and mRNA splicing (DeWitt 2003). In a later report, DeWitt also demonstrates that if a 5% genome-wide difference is accepted, this level of similarity is still insufficient to support various hypothetical models for selection and common ancestry consistent with evolutionary timelines (DeWitt 2005). The rate of mutational buildup in the genome of humans was further tested in computer simulations by Sanford et al. (2008) and found to represent a serious challenge to Darwinian evolutionary timelines irrespective of reported human-chimp genome differences.

Many mutations (DNA sequence differences) separating human and chimp from a common ancestor are thought to take place in regions where the genome is non-coding, a finding recently confirmed by an evolutionary report (Polavarapu et al. 2011). While evolutionary reports of non-coding DNA differences between humans and chimps continue to emerge, the logical association between these differences and the now well-documented functional and feature-rich nature of the entire non-coding region of the human genome is dramatically down-played. The wide diversity of research into the Encyclopedia of DNA Elements (ENCODE) has spectacularly confirmed the many critical features of non-coding DNA (The ENCODE Project Consortium 2011). In the area of creationist research, biologists Woodmorappe and Batten were some of the first creationist authors to illustrate how a diversity of data in the field of non-coding DNA provided support to the genome-wide function of a wide variety of important non-coding sequence classes and DNA features (Batten 2005; Woodmorappe 2004). In a recent comprehensive review that discusses a wide variety of design features in non-coding DNA, molecular biologist and intelligent design proponent Jonathan Wells thoroughly debunks the fraudulent concept of junk DNA (Wells 2011). For a brief review on the subject associated with a summary of Wells’ book see the recent article by Tomkins (2011b).

Perhaps the greatest ongoing discrepancy between human and chimp that does not fit with the so-called high similarity claims, is the marked differences in behavior and anatomy as summarized by creationists Anderson (2007), Purdom (2006) and Wieland (2002). These obvious differences between human and chimp do not seem to correlate with the supposed claims of nearly identical DNA similarity between the taxa. In fact, a secular science writer for the BBC has recently published an entire book documenting this paradox titled Not a chimp (Taylor 2009).

While many creationist authors tentatively accepted the standard evolutionary claims regarding human chimp DNA similarity, a number of reports indicated that the “nearly identical” dogma was not as clear-cut as it seemed to be. In fact, it was indicated that evolutionary data reports on human chimp DNA similarity largely represented pre-screened data that is already know to be homologous (similar in sequence) at some level, such as highly similar protein coding sequences shared among the taxa (Tomkins 2009a, 2009b). In addition, a recent literature review combined with a bioinformatics research project, evaluated the hypothetical fusion of two chimp-like chromosomes (2a and 2b) to form human chromosome 2. This project showed that the evolutionary primate fusion paradigm was seriously flawed in a number of key respects, further discounting nearly identical DNA claims (Bergman and Tomkins 2011; Tomkins 2011c; Tomkins and Bergman 2011).