Genetic evidence for common ancestry?Or give us a miracle and we'll explain the rest.

Stunning Evidence for Common Ancestry? S. Joshua Swamidass on the Chimp-Human Divergence

Cornelius Hunter

I once had a rare and valuable baseball card I wanted to sell. I placed an ad and was shortly contacted by a collector. But to my dismay he wasn't interested. He had probably looked at hundreds of baseball cards and it only required one look for him to know that my treasured card held no value for him. He did not attempt any negotiating tricks, just a polite "thank you" and off he went. I would have felt better about the encounter if he had tried to haggle with me to lower the price. For I would have had the comfort of knowing my card held at least some value. Apparently it didn't.

I too am a collector of sorts. And like that baseball card collector I have looked at hundreds of specimens. No matter how unlikely the source or the venue, I will go there and have a look. And in short order, I will know exactly what I am looking at, and if there is any value there. But unlike the baseball card collector, I'm not after something you can hold in your hand. 

What I am interested in are the arguments and evidences for evolution. Ever since Darwin, evolutionists have insisted that their idea is undeniable -- beyond all reasonable doubt. I find that complete certainty to be fascinating. So I search out, analyze, and categorize every justification and explanation for that conclusion that I can find.

My goal is to discover the strongest, most powerful, such arguments and evidences, and to understand how thoughtful people can have such certainty. This brings us to S. Joshua Swamidass, a professor in the Genomic Medicine Division at Washington University and author of a recent post at his website, "Evidence and Evolution." Given his credentials, he deserves to be listened to. Swamidass explains that the evidence for evolution is powerful and compelling. This evidence, which he describes as stunning, is definitely a specimen I want to have a look at.

In his post, Swamidass's focus is on human evolution. Evolutionists believe that we humans evolved from a small ape-like creature and that our closest relative on the evolutionary tree is the chimpanzee. The chimpanzee must be our closest relative, they reason, because the chimp's genome is closest to ours, and according to evolution, genetic mutations are the fuel behind evolutionary change.

The problem with this reasoning is that according to many other measures, the chimpanzee is not very similar to humans. There are enormous differences between the two species. Furthermore, in its morphology and behavior, the orangutan is closer to humans than the chimpanzee. Simply put, from an evolutionary perspective the genetic data are not congruent with the other data. Swamidass's evidence will need to overcome this obvious problem.

But that's not all.

The basic idea of humans arising via a long series of genetic mutations is, itself, not indicated by the science and is unlikely to say the least. Remember, the mutations have to be random. According to evolution, you can't have mutations occurring for some purpose, such as creating a design. And natural selection doesn't help -- it cannot induce or coax the right mutations to occur. This makes the evolution of even a single protein, let alone humans, statistically impossible. So this is another enormous problem Swamidass's evidence will need to overcome.

But that's not all.

The incredible designs in the human body are not the only thing those random mutations have to create -- they will also have to create human consciousness. Evolutionists may try to explain consciousness as an "emergent" property that just luckily arose when our brain somehow evolved. Or they may try to explain that consciousness is really no more than an illusion. But these are just more demonstrations of anti-realism in evolutionary thought. By that I mean, evolutionary theory constructs mechanisms and explanations that do not correspond to the real world. So this is another problem Swamidass will need to overcome.

But that's not all.

In recent decades the genomes of humans and chimps have been determined, and in an evolutionary paradigm they make no sense. One of the main problems is that the genes of the two species are almost identical. They are only about 1-to-2 percent different and, if you're an evolutionist, this means you have to believe that the evolution of humans from a small, primitive, ape-like creature was caused by only a tiny modification of the genome.

This goes against everything we have learned about genetics. You can insert far greater genetic changes with far less change arising as a consequence. It makes little sense that tiny genetic changes could cause such enormous design changes to occur. This is yet another problem for Swamidass to overcome.

But that's not all.

Not only is evolution limited to tiny genetic modifications to create the human, but the majority of those modifications would have had to be of little or no consequence. Here is how a 2005 paper on the chimpanzee-human genome comparisons put it:

In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.

The paper is written from an evolutionary perspective, assuming that humans and chimpanzees share a common ancestor. Given that a priori assumption, they were forced to conclude that most of the mutations affecting protein-coding genes led to "neutral and slightly deleterious alleles." So not only are evolution's random mutation resources meager, in terms of both quality and quantity as explained above, but even worse, those mutations mostly led to "neutral and slightly deleterious alleles." This is no way to evolve the most complex designs in the world and it is yet another problem for Swamidass to overcome.

But that's not all.

When evolutionists search for genes in the human genome that do show signs of selection, rather than neutral drift (again, under the assumption of evolution), they find only a limited repertoire of functionality. For example, one study found genes involved in the sense of smell, in digestion, in hairiness, and in hearing. In other words, evolution is suggesting that we differ from the chimp mainly in those functions. It is a silly conclusion and another problem for Swamidass to explain.

But that's not all.

That 2005 paper also found a host of chimp-human comparisons that are nonsensical in evolutionary terms. In other words, if you are forced to interpret the genetic comparisons in terms of evolution, you end up with contradictions. For example, if you look at large segments of DNA, corresponding in the human and the chimp, you find unexplainable variations in the chimp-human differences:

Nucleotide divergence rates are not constant across the genome... The average divergence in 1-Mb segments fluctuates with a standard deviation of 0.25%, which is much greater than the 0.02% expected assuming a uniform divergence rate.

To explain these nonsensical findings evolutionists have to resort to a "then a miracle happened" hypothesis. The usual explanatory devices do not work, so they are left only with the claim that local variations in the mutation rate did it -- which amounts to special pleading:

[W]e suggest that the large-scale variation in the human-chimpanzee divergence rate primarily reflects regional variation in mutation rate.

Under evolution there is no scientific reason, beyond hand-waving speculation, for such variations. This is the equivalent of epicycles in geocentrism and so we have yet another problem for Swamidass to address.

But that's not all.

The supposed divergence rate between chimps and humans not only has an unexplainable variation in large, 1-Mb segments of DNA, it also has an unexplainable variation towards the ends of most chromosomes. This is another problem that seems to make no sense under evolution, which Swamidass must explain.

But that's not all.

This supposed divergence rate between chimps and humans also has an unexplainable variation that correlates with chromosomal banding. Again, this makes no sense under evolution. Why should the chimp-human divergence vary with the banding pattern? Evolutionists have only just-so stories to imagine why this would have happened, and it is another problem for Swamidass to address.

But that's not all.

This supposed divergence rate between chimps and humans is not consistent with the supposed divergence rate between the mouse and rat. The mouse-rat divergence is about an order of magnitude greater than the chimp-human divergence. Yet the mouse and rat are much more similar than the chimp and human. It makes no sense under evolution. In fact, before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome. As one paper explained:

Before the launch of the Rat Genome Sequencing Project (RGSP), there was much debate about the overall value of the rat genome sequence and its contribution to the utility of the rat as a model organism. The debate was fuelled by the naïve belief that the rat and mouse were so similar morphologically and evolutionarily that the rat sequence would be redundant.

The prediction that the mouse and rat genomes would be highly similar made sense according to evolution. But it was dramatically wrong.

Another approach is to ignore the morphological similarities and reason from the number of generations available to produce the genomic differences between the mouse and rat. The mouse-rat divergence date is estimated by evolutionists to be older than the chimp-human divergence date. Furthermore, the lifespan and generation time for mice and rats are much shorter than for chimps and humans. From this perspective, and given these two effects, one would conclude that the mouse-rat genetic divergence should be much greater -- at least two orders of magnitude greater -- than the chimp-human genetic divergence. But it isn't. It is only about one order of magnitude greater.

So either way the mouse-rat comparison does not help to explain things and is another problem for Swamidass to explain.

Swamidass Explains?

Under evolution, the science makes no sense. If we begin by assuming chimps and humans share a common ancestor, we end up with all kinds of contradictions and failures. So what exactly are Swamidass's arguments and evidences? How is it that he is so certain? What is it in the data that he finds to be so stunning? And most importantly, how does he resolve the above problems?

Well, he doesn't.

Astonishingly, Swamidass doesn't even mention the above problems. It is as though they don't exist. After some stories and claims of high certainty, here is what Swamidass says:

As predicted by common ancestry, human and chimpanzee genomes are extremely similar (greater than 98% similarity in coding regions), much more similar than we would expect without common descent. Remarkably, just as predicted by the fossil record, humans are about 10 times more genetically similar to chimpanzees than mice are to rats.

First, the high chimp-human genomic similarity was not predicted by common ancestry. No such prediction was made and no such prediction is required by common ancestry. Common ancestry would be just fine with very different levels of similarity from 98-99 percent. In fact, this high similarity makes no sense under evolution, for several of the reasons given above.

Swamidass's claim that this evidence is a stunning confirmation of common ancestry is utterly at odds with the science. It is in stark contrast to the scientific facts.

Second, Swamidass's claim that mouse-rat divergence, compared with the chimp-human divergence, is "just as predicted by the fossil record" is also blatantly false. While evolutionists can always combine various explanatory mechanisms to rationalize just about any comparison, that does not make for stunning evidence that is "just as predicted."

Finally, the real strength of Swamidass's argument lies in its metaphysics. The professor states that the chimp-human genome comparison is "much more similar than we would expect without common descent."

Without common descent?

The evolutionist has just made an unbeatable (and unfalsifiable) argument.

This is not science. Swamidass's claim about what is and isn't likely "without common descent" is not open to scientific scrutiny.

Scientists, qua scientists, do not have knowledge of all possible explanations for the origin of life. This is why scientists, qua scientists, make statements about theories, not about the complement of a theory. A scientist cannot know that something is unlikely "without" his theory. That implies knowledge of all other possible theories. And that knowledge does not come from science.

This is the strength of Swamidass's argument. Notice that with this metaphysical knowledge, all of the scientific problems melt away. No wonder he does not address them. They are inconsequential. At worst, they are simply interesting puzzles. The truth of the matter is already known.

If Swamidass is correct then, yes, of course, the genomic data must be strong evidence for common ancestry. But it all hinges on his metaphysics. This is not about science. It never was.

As 'Just so' as it gets II

Rafting Monkeys "Fill a Gap" in Evolutionary Theory?

David Klinghoffer 

Among evolutionary icons -- peppered moth, Darwin's finches, Haeckel's embryos -- arguably the most risible is the rafting monkey. Even Darwinists seem to understand this.

A Washington Post article includes an interview with an author of a new Science paper, "Oligocene primates from China reveal divergence between African and Asian primate evolution," that once again renews the demand for belief in seafaring monkeys. We've covered this paradox before -- monkeys can't swim much less sail. Just last month evolutionary theorizing dodged a bullet by avoiding the spectacle of rafting foxes on the world's oceans.

The researcher, Christopher Beard, explained to reporter Sarah Kaplan how it must be the case that tarsier-like monkeys, evidenced by fossil teeth found in China, sailed on clumps of earth and felled trees, 30-40 million years ago, across an aquatic void separating Asia from Africa, which was then an island:

"It's a little complicated," Beard said, almost sheepishly.

You don't say.

This more convoluted version of our history begins in the Eocene, some 40 million years ago. At this time, Earth's climate was hot and humid, and the continents were just beginning to move into the positions they hold today. India was zooming headlong toward the bottom of Asia (the inevitable collision would one day give rise to the Himalayas). An inland sea flooded the center of the Eurasian land mass. And Africa was an island continent, separated from Asia and Europe by a narrow stretch of ocean.

Early anthropoid (humanlike) monkeys were flourishing in Asia at that time. But they also, somehow, found a way to migrate across the watery barrier to Africa. And since monkeys don't really swim, scientists' best theory about their migration is -- I kid you not -- that they sailed across on rafts made of trees.

"You're laughing," Beard said, "but it's now known that this happened repeatedly. Because of the greenhouse conditions, a lot of monsoons were hitting Asia at the time. When that happens, rivers would flood, riverbanks erode. A half an acre of land with a bunch of trees growing out of it falls into a river and floats out to sea."

"And if there are a bunch of monkeys hanging out in the trees when that happens," he continued, "suddenly those monkeys become sailors."

"I kid you not." "You're laughing, but it's now known that this happened repeatedly." It is "known" not because anyone can picture the scenario without cracking up or feeling "sheepish" but because the theory demands it. See here for Casey Luskin's earlier comments on the "biogeographical conundrum" posed by these Chinese monkeys.

And look here for pictures of how the drifting continents were disposed in the relevant time period between the Oligocene and the Eocene. From Asia to Africa by sea was a considerable distance, and monkeys are supposed to have accomplished this feat while clinging for dear life to bits of earth and tree debris? On Lake Washington near our home, I beg my wife and kids not to row out even close to shore on a store-bought inflatable raft!

Science Daily has additional thoughts from Dr. Beard on the "'mother lode' of a half-dozen fossil primate species." A half-dozen is a "mother lode"? More:

These primates eked out an existence just after the Eocene-Oligocene transition, some 34 million years ago. It was a time when drastic cooling made much of Asia inhospitable to primates, slashing their populations and rendering discoveries of such fossils especially rare.

"At the Eocene-Oligocene boundary, because of the rearrangement of Earth's major tectonic plates, you had a rapid drop in temperature and humidity," said K. Christopher Beard, senior curator at the University of Kansas' Biodiversity Institute and co-author of the report. "Primates like it warm and wet, so they faced hard times around the world -- to the extent that they went extinct in North America and Europe. Of course, primates somehow survived in Africa and Southern Asia, because we're still around to talk about it." Because anthropoid primates -- the forerunners of living monkeys, apes and humans -- first appeared in Asia, understanding their fate on that continent is key to grasping the arc of early primate and human evolution.

Sarah Kaplan's article in the Post speaks more than once of the fossils as "fill[ing] in the gaps":

The fossils "fill a gap," in our understanding of our evolutionary history, Stony Brook University primatologist John Fleagle, who was not involved in the study, told the Christian Science Monitor. They illustrate "a whole aspect of primate evolution that wasn't clearly documented before."

But the value of "filling a gap" lies in reducing the distance you have to leap in order to believe something seemingly far-fetched. More about rafting animals surely makes the challenge for evolution tougher, not easier. I would have said reducing, not increasing, the number of such unlikely sailors would "fill a gap."