Feature Article - March 2012
by Do-While Jones

Gorilla Genome Sequenced

Gorilla DNA throws a monkey wrench into the theory of evolution.

The gorilla genome reveals that genetic similarities among humans and the apes are more complex than expected, and allows a fresh assessment of the evolutionary mechanisms that led to the primate species seen today. 1

As we expected, comparison of gorilla DNA with human DNA produced results that were unexpected by evolutionists because they aren’t consistent with what the theory of evolution predicted. This “allows a fresh assessment of the evolutionary mechanisms,” which is a polite way of saying that they have to go back to Square One.

Contradictory Phylogenetic Trees

The first problem evolutionists have to face is the fact that analysis of different genes result in different phylogenetic (that is, family) trees.

The standard view of the primate evolutionary tree is that chimpanzees and humans share a more recent common ancestor with each other than either shares with gorillas. Accordingly, the most closely related sequence for any human gene should be found in the chimpanzee. However, Scally and colleagues' demonstrate that, although this is true for most genes, large fractions of the ape genomes contradict this simple pattern. … This process, which leads to conflicting evolutionary trees for different genes, is called incomplete lineage sorting 2

In other words, evolutionists believe that the (unknown) ancestor of modern gorillas split from the (unknown) common ancestor that begat chimpanzees and humans. Therefore, human DNA should be closer to chimp DNA than gorilla DNA. If you use DNA similarities to construct an evolutionary tree, humans and chimps should be more closely related than humans and gorillas. It should not matter what part of the DNA molecule you analyze. The problem (for evolutionists) is that you get different evolutionary trees depending upon which part of the DNA you analyze. They found “large fractions of the ape genomes” in which humans are more closely related to gorillas than chimps.

This is such a common problem that Nature inserted a sidebar article titled, “How incongruities in phylogenetic trees can arise.” According to that sidebar,

Scally and colleagues found that in 30% of the western-lowland-gorilla genome, the DNA sequences are more similar to the corresponding sequences from the human or chimpanzee genomes than the sequences of these two species are to each other — although humans and chimpanzees are expected to have shared a more recent common ancestor with each other than either does with gorillas. Such inconsistencies between evolutionary relationships can result from various processes. 3

In that sidebar they said that the “various processes” that produce incorrect phylogenetic trees are “incomplete lineage sorting” and “gene flow.”

Since these two processes can produce erroneous results, how do you know which phylogenetic tree is correct? It’s simple. If it confirms your prejudice, it is right. If it contradicts your prejudice, it is wrong!

If the theory of evolution were true, that is, if people, chimps, and gorillas really did evolve from a common ancestor, then it would not matter which genes you analyzed. They would all produce the same phylogenetic (that is, evolutionary) trees. But if people, chimps, and gorillas did not evolve from a common ancestor, the differences in DNA would not be the result of genetic mutations over time. The difference would be due to differences in the way the creatures were designed. Certain parts of the DNA molecule would be more similar than others because certain physical features happened to share similar design philosophies.

This certainly isn’t the first time that DNA analysis has produced surprising relationships that aren’t consistent with evolutionary expectations. But even when DNA analysis confirms evolutionary expectations about relationships, it often contradicts the evolutionary timeline.

The Time Problem

For a long time there was a discordance between the fossil evidence and genetic estimates, in the sense that genetic estimates came up with speciation times that were more recent,” says Scally. 4

Moreover, with all the great ape genomes to compare, researchers are better able to assess when gorillas, chimps, and humans evolved—a matter of current debate. The molecular data indicate that humans and chimps went their separate ways only about 4.5 million years ago. But fossils that old and older look either ape or protohuman, so some paleontologists argue for a split as far back as 7 million years ago. Scally's group comes up with a date of about 6 million years ago, adjusting what would have been a more recent estimate by assuming that the mutation rate slowed over time in ape evolution. Another possible complication is that interbreeding may have occurred in the incipient species, slowing the actual separation of the DNA into distinct genomes, Scally points out. The authors suggest that ancestors of the gorilla separated from the human-chimp line about 10 million years ago, consistent with previous estimates.

"I am very happy to see the authors conclude [with] divergence dates that are consistent with both the fossil and genetic records," Begun says. "Usually one line of evidence is used to discredit the other." 5

Yes, geneticists usually insist that their dates are correct, and paleontologists insist that their dates are right. Scally, to the great joy of Began, was willing to go out of his way to fudge the genetic data to agree with the paleontologists. Here’s how Scally says he did it.

Two issues need to be addressed in interpreting the results from CoalHMM (Supplementary Table 4.2). First, the results themselves are obtained in units of sequence divergence rather than years, and so need to be scaled by an appropriate yearly mutation rate. Second, as with any model, CoalHMM makes several simplifying assumptions whose consequences we need to understand in the context of realistic demography. We discuss these issues in turn.

Using a rate of 10-9 mutations per bp per year, derived from fossil calibration of the human–macaque sequence divergence and as used in previous calculations, CoalHMM’s results would correspond to speciation time estimates THC (for human–chimpanzee) and THCG (for human–chimpanzee–gorilla) of 3.7 and 5.95 Myr ago, respectively (Fig. 1b). These dates are consistent with other recent molecular estimates, but are at variance with certain aspects of the fossil record, including several fossils which have been proposed—though not universally accepted—to be hominins, and therefore to postdate the human–chimpanzee split (Fig. 1b). Indeed, the relationship between molecular and fossil evidence has remained difficult to resolve despite the accumulation of genetic data. Direct estimates of the per-generation mutation rate in modern human populations, based on the incidence of disease-causing mutations or sequencing of familial trios indicate that a lower value of (0.5–0.6)×10-9 bp-1 yr-1 is plausible (based on average hominine generation times of 20–25 yr). This would give substantially older estimates of approximately 6 and 10 Myr ago for THC and THCG, potentially in better agreement with the fossil record.

However, this timetable for hominine speciation must also be reconciled with older events, such as the speciation of orang-utan, which is thought to have occurred no earlier than the Middle Miocene (12–16 Myr ago), as fossil apes before that differ substantially from what we might expect of an early great ape. This is possible if we allow for mutation rates changing over time, with a mutation rate of around 1×10-9bp-1yr-1 in the common ancestor of great apes, decreasing to lower values in all extant species (Fig. 1b). … However we note that Sahelanthropus and Chororapithecus remain difficult to incorporate in this model, and can be accommodated as hominin and gorillin genera only if most of the decrease occurred early in great ape evolution.

An alternative explanation for the apparent discrepancy in fossil and genetic dates (leaving aside the issue of whether fossil taxa have been correctly placed) is that ancestral demography may have affected the genetic inferences. Certainly CoalHMM’s model does not fit the data in all respects. Perhaps most importantly, it assumes that ancestral population sizes are constant in time and that no gene flow occurred between separated populations, approximations that may not hold in reality. 6

Scientists now have the technology to accurately compare DNA molecules and compute the number of differences. The (erroneous) assumption evolutionists use is that the species being compared came from a common ancestor, and the differences are due to mutations that occur at some rate. But mutations occur so slowly that it takes many generations for enough mutations to build up to be measurable. They estimate, “1×10-9bp-1yr-1”, which is a mathematical way of saying, “one in 1,000 million per base pair per year.” (A DNA molecule is made up of a long twisted string of pairs of bases.) They divide the number of differences by this estimated rate to determine how long it has taken for this many differences to accumulate.

The “rate of 10-9 mutations per bp per year” is “derived from fossil calibration of the human–macaque sequence divergence.” In other words, “knowing” (from the fossil record) how long ago humans and macaques had an unknown common ancestor, and measuring how many differences there are in (at least some portion) of their DNA molecules, they can compute how many mutations there were over many millions of years.

The irony is that even though the “molecular clock” is calibrated using certain fossil data, it still doesn’t agree with other fossil data very often!

So, to keep the paleontologists happy (and to prevent creationists from pointing out yet another inconsistency), they fudged the data. They “allow for mutation rates changing over time.” In other words, they suggest that mutation rates might have been about half of the nominal rate, which would make the DNA dates agree with the accepted evolutionary dates.

They also suggest that their own model might not be correct because it “assumes that ancestral population sizes are constant in time and that no gene flow occurred between separated populations,” which are “approximations that may not hold in reality.” That is just a polite way of saying that they are using a model that isn’t worth a darn!

But even if they fudge the mutation rate to make their data match some fossil data, it still doesn’t match other evolutionary beliefs. We “note that Sahelanthropus and Chororapithecus remain difficult to incorporate in this model, and can be accommodated as hominin and gorillin genera only if most of the decrease occurred early in great ape evolution.”

“Acceleration” is a Code Word

Whenever there are more differences in the DNA than evolutionists expect, it is because something (unknown) “accelerated” the rate of evolution. Watch out for paragraphs like this one:

We also identified cases of pairwise parallel evolution among hominines. Human and chimpanzee show the largest amount, with significantly more shared accelerations than expected by chance, whereas gorilla shares more parallel acceleration with human than with chimpanzee across a range of significance thresholds (Supplementary Fig. 8.3). Genes involving hearing are enriched in parallel accelerations for all three pairs, but most strongly in gorilla–human (Supplementary Table 8.4d–f), calling into question a previous link made between accelerated evolution of auditory genes in humans and language evolution. It is also interesting to note that ear morphology is one of the few external traits in which humans are more similar to gorillas than to chimpanzees. 7

Since there are so many genetic differences, something (but we don’t know what) MUST have caused much more rapid evolution in certain parts of the DNA than in other parts. Not only that, whatever it was that caused the rapid evolution, caused it to happen in both species (that is, “in parallel”).

The Tragedy

It would be funny if it wasn’t such a tragedy. The real tragedy in this entire article is the waste of time and talent. If Scally and his associates had been creationists instead of evolutionists, they could have learned so much more.

Because of their religious bias, creationists look for God’s wisdom in the design of the DNA molecule. For example, creationists would have realized that gorillas are stronger than people. By comparing gorilla DNA with human DNA, one might determine what it is in the DNA that makes gorilla muscles stronger. That knowledge could lead doctors to find genetic treatments for diseases that weaken muscles in humans.

But since Scally and his associates are evolutionists (or funded by evolutionists), they wasted all their time trying to figure out how long ago gorillas and humans diverged from a common ancestor. The bulk of their work was wasted figuring out how to fudge the raw data to make it produce conclusions consistent with fossil data. Even if evolution were true, there would be no medical advantage to knowing when humans and gorillas parted evolutionary company.

It really is a tragedy.

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1 Richard A Gibbs & Jeffrey Rogers, Nature, 8 March 2012, “Genomics: Gorilla gorilla gorilla”, pp. 164-165, http://www.nature.com/nature/journal/v483/n7388/full/483164a.html
2 ibid.
3 Richard A Gibbs & Jeffrey Rogers, Nature, 8 March 2012, “Genomics: Gorilla gorilla gorilla”, pp. 164-165, “Box 1: How incongruities in phylogenetic trees can arise”, http://www.nature.com/nature/journal/v483/n7388/box/483164a_BX1.html
4 Kerri Smith, Nature Podcast, 7 March 2012, “Sequencing of gorilla genome adds to understanding of our evolutionary path”, http://www.nature.com/news/gorilla-joins-the-genome-club-1.10185
5 Elizabeth Pennisi, Science, 7 March 2012, “A Little Gorilla in Us All”, http://news.sciencemag.org/sciencenow/2012/03/gorilla-genome-sequenced.html
6 Aylwyn Scally, et al., Nature, 8 March 2012, “Insights into hominid evolution from the gorilla genome sequence”, pages 169-175, http://www.nature.com/nature/journal/v483/n7388/full/nature10842.html
7 ibid.