Gorilla, Orangutan, Chimp and Human Genomes: Population Genetics and Intelligent Design

Living things are largely made of proteins.  A simplified definition of a gene is that it is a segment of DNA that codes for the synthesis of one or more particular proteins. A more complete definition is given by Wikipedia:

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a polypeptide or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism’s cells and pass genetic traits to offspring, although some organelles (e.g. mitochondria) are self-replicating and are not coded for by the organism’s DNA. All organisms have many genes corresponding to various biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

A modern working definition of a gene is “a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions “.

What concerns us here is that in any sizeable population of a species, there can be more than one form of a gene. These different forms are called “alleles.” Dennis Venema explains,

Populations have genetic diversity – not all members of the population are genetically identical. For any particular gene, then, a population may have several slightly different forms present within it. These different forms are called alleles. An example in humans that is fairly well-known is the different alleles that control blood types: one allele gives rise to the A type, another to the B type, and a third allele the O type. Individuals may be either blood type A (either two A alleles or A + O); blood type B (either two B alleles or B + O); type AB (one A allele + one B allele) or type O (two O alleles). Any one individual can have only two alleles of this gene (one from mom, the other from dad), but as a population we collectively maintain all three. Other human genes have many more alleles than three (for example, some genes of the immune system have hundreds of alleles) despite the fact that any given individual can have at most two. The larger a population is, the more alleles of a given gene it can maintain.

There are many lines of evidence, which we will not rehearse here, that humans and chimpanzees split from a common ancestor around 6 million years ago, gorillas split off about 10 million years ago, and orangutans split off around 14 million years ago. A key point is that when we speak of splitting from a common ancestor, that common ancestor was not a single individual or breeding couple, but a whole population.  Among all the individuals that made up that ancestral population, there would be a hodgepodge of various forms (alleles) of each gene.

For the sake of simplicity, suppose that 10 million years ago, half of the existing great ape population packed up, moved 500 miles east, and evolved separately to become today’s gorillas. Meanwhile, the remaining population split four million years later to eventually become today’s chimps and humans. On average, we would expect the gene forms (alleles) in humans to more closely resemble the alleles in chimps than the forms found in today’s gorillas.

However, straightforward population genetics says that we would NOT expect that to be true for every single human gene. Out of the mix of genes in each population at each stage, some alleles will get lost and others survive. The basics of this “Incomplete Lineage Sorting” were worked out in the 1980s and 90s.   One can estimate statistically what percentage of human genes will have forms closer to gorillas or to orangs than to chimps. And indeed, this is what has been found recently as the genomes of the great apes have been sequenced.

For orangs, Dennis Venema at BioLogos reviewed the results of a 2011 study by Holborth, et al.  These researchers predicted that about 0.9% of the human genome would most closely match orangutan, rather than chimp. The actual value derived from the orang genome was 0.8%, which is pretty close. This helps demonstrate the self-consistency of evolutionary genetics. Venema includes a clear layman’s explanation of gene distributions among populations that split into different species, using color-coded figures.

The gorilla genome was more recently sequenced, and analyzed here by Scally, et al. (Nature 483,169–175, 08 March 2012).  Their first figure (below) illustrates the possible fate of various gene forms (alleles). The numbers at the bottom (1.37%, etc.) are average nucleotide divergences between human (H) and chimp (C), gorilla (G), and orangutan (O).

The gray lines within this figure denote how, for a particular gene, chimps can end up with a form that is closer to the gorilla form than the human form, even though the gorilla speciation split came earlier than the chimp-human split. While that is true for some genes, the statistical probability is that the majority of chimp genes will most closely resemble the human forms, and vice versa.

And again, this is what the researchers found from the actual genome. From the Abstract:

We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression.

As expected, for the majority (70%) of the genome, humans and chimps are closer to each other than to gorilla, but for 30% of the genome, the opposite is true. As the researchers point out, this is consistent with other genetic and fossil evidence, subject to various reasonable assumptions on mutation rates, etc. Joe Felsenstein has provided a back-of-the-envelope calculation method which demonstrates that the observed 30% figure squares with what would be expected for this situation (see the Appendix to this post).

So far, this is unremarkable, maybe even boring: evolutionary genetics, in the form of incomplete lineage sorting, predicts that although chimp is our closest living relative species, some significant fraction of the human genome will more closely resemble gorilla or orangutan than chimp – – and this is confirmed by the actual genome sequencing. Where it gets sadly entertaining is in the deceptive spin that so-called Intelligent Design advocates put on these findings.

When the orangutan sequence was published, showing that for ~0.8% of our genome, humans are more closely related to orangutans than to chimpanzees, the Discovery Institute’s Casey Luskin blogged,

Since humans are typically said to be most closely related to chimps, this data conflicts with the standard supposed tree…the basic problem is that one gene (or portion of the genome) gives you one version of the tree, while another gene (or portion of the genome) gives you a very different version of the tree. This leads to discrepancies between molecule-based trees, wherein DNA data fails to provide a consistent picture of common ancestry… In the end, molecular trees are based upon the sheer assumption that the degree of genetic similarity reflects the degree of evolutionary relatedness…. Clearly this assumption fails when different genes paint contradictory pictures of evolutionary relationships.

For the recent gorilla sequencing,  Luskin’s post leads off, “A whopping 30% of the gorilla genome — amounting to hundreds of millions of base pairs of gorilla DNA — contradicts the standard supposed evolutionary phylogeny of great apes and humans.”  He further states, “The standard evolutionary phylogeny of primates holds that humans and chimps are more closely related to one-another than to other great apes like gorillas. In practice, all that really means is that when we sequence human, chimp, and gorilla genes, human and chimp genes have a DNA sequence that is more similar to one-another’s genes than to the gorilla’s genes. But huge portions of the gorilla genome contradict that nice, neat tidy phylogeny.”

Luskin here generates verbiage that is virtually guaranteed to give the layman the impression that something is deeply wrong with standard evolutionary theory: “contradicts”; “conflicts”; “discrepancies”; “fails to provide a consistent picture of common ancestry.” The reality is, as we described above, is that these results completely confirm the consistency of evolutionary theory. So Luskin is being deeply deceptive in his treatment of the subject.

This is a typical example of the half-truths which are the hallmark of “Intelligent Design.” Luskin could claim that he was merely repeating what the research showed. He is indeed correct in stating that “one gene (or portion of the genome) gives you one version of the tree, while another gene (or portion of the genome) gives you a very different version of the tree.” But it is inexcusable to omit the fact that this pattern is predicted by elementary population genetics, and thus poses no problem for standard evolution.

Luskin descends into outright falsehood when he claims that the concept that the degree of genetic similarity among species reflects the degree of evolutionary relatedness “fails when different genes paint contradictory pictures of evolutionary relationships.” We discussed above why it is completely expected that a certain percentage (though less than half) of human genes will be closer to gorilla or orang than to chimp. (I’m sorry to have to critique Luskin so severely; he is a nice guy in person, and perhaps he simply doesn’t understand what he is writing about).

In his post on the gorilla genome, Luskin makes an attempt to dismiss scientists’ explanations of their findings:

…their explanation is that interbreeding between populations of chimps, humans, and gorillas after the initial splits of these lines caused different genes to become fixed in different lineages at different times. Called incomplete lineage sorting, it provides a convenient after-the-fact explanation for why different genes carry different phylogenetic signals. Of course, this is merely an ad hoc hypothesis invoked to explain away inconvenient data which contradicts the standard phylogeny.

First, Luskin here shows he doesn’t understand that incomplete lineage sorting (which takes place at the time of species splitting and has been the focus of discussion here) is a completely different phenomenon than interbreeding of species (which by definition can only take place after species splitting). Second, it is gross misrepresentation to describe incomplete lineage sorting as “after-the-fact” and “ad hoc invoked to explain away inconvenient data.” As we noted, this population genetics theory was worked out many years ago, and yields straightforward predictions for the statistics of allele distributions in speciated populations. It was not cobbled together to explain away these recent genome sequences.

Unfortunately, this is pretty standard fare for Intelligent Design writers. They continually take genuine scientific findings, or not-so-solid scientific speculations, pull out some half-truth that fits their anti-evolution agenda, and serve it up to their gullible readers while withholding the full story. Their lack of integrity may well drive any educated person away from consideration of the truth-claims of Jesus Christ.

I hold an alternate view of reality which integrates God’s revelation in His Word and in His works, engaging the full sweep of the physical evidence. We can posit “intelligent design”, not of one species at a time, but of the entire universe, with its physical constants exquisitely tuned to allow carbon-based life-forms. Furthermore, we can rest in God’s providential, though invisible, guidance of the world. Jesus said that every hair on our heads is numbered, and not a single sparrow falls apart from the Father, so it is no great stretch to regard mutations and differential selection as just another aspect of His providence. (I understand that the obvious suffering and cruelty in the world seems at odds with divine providence; the guest post Lucky To Be Alive  has some thoughts on that subject).

*****  APPENDIX: Comments On a “Panda’s Thumb” Post on Gorilla Genome *****

In response to a young earth creationist butchering of the gorilla genome story, P.Z. Myers posted a short entry on the subject on The Panda’s Thumb. Myers’ article pretty much says what I just wrote above, though with more rigor. What I found interesting were the comments made on his entry. Various readers sound off their opinions, such as “Once again, creationists display nothing but distortion and misrepresentation. They take clear evidence for evolution and in direct opposition to creationism and try to pretend that just the opposite is true. And these are the same guys who try to get scientific respectability by holding fake ‘conferences’!. Man, these guys are pathetic.”

On a more constructive note, Joe Felsenstein (Comment posted 3/12/2012 7:02 AM) provided a short-but-sweet way to calculate backwards in time to estimate what fraction of human and chimp genes should be more similar to each other than to gorilla. This is the “coalescence” approach. He made assumptions like a population size of 100,000 and a differential speciation time of 2 million years. These can obviously be adjusted, and he notes that this does not take into account things like recombination or selective sweeps. Note Felsenstein’s 3/15/2012 1:05 PM comment where he corrects an arithmetic mistake he made in his 3/12 comment. With that correction, his calculations yield the result that some 60% of genes would be closest in humans and chimps, while 20% would be closest in humans and gorillas and the remaining 20% closest in chimps and gorillas. While this is only semi quantitative, it shows that the experimental finding that 70% of the genome is closest between humans and chimps (compared to gorillas) is the order of magnitude that population genetics would predict.

Thomas Mailund, a Danish senior author of the research articles on the orang and gorilla genomes, weighs in with comments such as, “It boggles my mind that it [this genome research] can be interpreted as a failure of our theory of evolution.” The Intelligent Design controversy is literally foreign to Mailund. This is not just because the evangelical anti-evolution movement is largely a North American phenomenon, but also that religion of any sort is not a part of his world as a professional in Scandinavia. He notes that, “I can count on one hand the number of religions people I have ever known, so there is a cultural aspect here… the whole religion discussing is something that is a bit alien to me since I never have to deal with it in my own life.”

Dennis Venema adds a couple of hopeful comments on the state of North American evangelicalism, “I do think we are seeing improvement, though. Ten years ago accepting evolution was exceedingly rare in evangelical circles. Now it is not uncommon for folks in the pew to accept it, and we’re seeing more and more pastors coming around to the notion. They are still the minority, but they’re there. It’s like a selective sweep – these things take some time… My approach over the last few months has just been to try teach basic evolutionary concepts to Christians, little bit by little bit. Feedback I get seems to suggest it is working. Ten years ago there wasn’t an identifiable position/organization that was overtly evangelical and accepted evolution. Nowadays BioLogos will often get invitations to present alongside YECs and OECs as another ‘acceptable Christian position’ on origins. That’s real progress, in my mind.”

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