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In defense of Swamidass

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After reading Dr. Cornelius Hunter’s panning of Professor S. Joshua Swamidass’s recent article, Evidence and Evolution, I figured the professor must have written a truly awful piece. Nevertheless, I decided to go back and have a look at his article. And I’m very glad I did. Swamidass’s article was irenic in tone, easy to follow, deeply learned, and absolutely right.

Professor Swamidass’s olive branch

What Professor Swamidass was attempting to do in his article was to extend an olive branch to creationists. Nowhere in the article did he belittle or ridicule his opponents, and there was not a trace of the smug superiority which many scientists display, when talking to creationists. Indeed, he bent over backwards to be accommodating:

If we allow for God’s intervention in our history, it is possible we do not share a common ancestor with apes. Adding God into the picture, anything is possible…

Of course, adding God back into the picture, anything could have happened. An omnipotent God could have created us 6,000 years ago…

Of course, the scientific account is not the whole story. It is an open theological question how to complete the scientific account, and theological debate surrounding this question is important and engaging. One thing all should agree on; we humans are certainly more than just apes.

Nowhere in his article did Professor Swamidass argue that evolution is true, or that God made human beings via an evolutionary process. Instead, he attempted to show that the scientific evidence (taken on its own) supports human evolution, before concluding that if humans did not evolve, then theologians need to address this evidence:

Currently, it appears that, for some reason, God chose to create humans so that our genomes look as though we do, in fact, have a common ancestor with chimpanzees

It would have been very easy for God to design humans with genomes that were obviously different than apes, and clearly not a product of evolution. From some reason, He did not. He did not even make us as different from chimpanzees as mice are from rats. Why not?

Let me note for the record that young-earth creationist Todd Wood asked exactly the same question in a recent review of Fazale Rana and Hugh Ross’s revised 2015 edition of their book, Who Was Adam?:

Why do humans and chimps share such similar genomes, while the genomes of rats and mice differ so dramatically (see Mouse Genome Sequencing Consortium 2002)? What is the basis of the pattern of similarity (Wood 2006)?

…Similarity requires explanation, regardless of whether it’s similar genes or similar intergenic DNA.

Professor Swamidass draws no conclusions in his article; he merely poses a legitimate question which creationists have also wondered about. He certainly sounds like a very fair-minded man. I should add that Swamidass is a practicing Christian as well as a trained scientist. At the very least, his article warrants a courteous and carefully argued response. I regret to say that Dr. Hunter’s reply fails on this count: it is misinformed (as I’ll show below), polemical and curtly dismissive in tone, as the following extract shows:

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

This is not science. Swamidass’ claim about what is and isn’t likely “without common descent” is not open to scientific scrutiny…

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.

Like that old baseball card, it’s just another worthless argument.

“Worthless argument”? Professor Swamidass deserves a better hearing than that.

Dr. Hunter’s criticisms of Professor Swamidass’s argument

Dr. Hunter’s failure to address the scientific evidence for common descent

Amazingly, Dr. Hunter manages to completely ignore the scientific evidence for evolution presented in Professor Swamidass’s article. Instead of addressing this evidence, he confines himself to quoting just two sentences from the article. Here’s the scientific evidence for human evolution, summarized by Swamidass, which Dr. Hunter overlooked:

In particular, be sure to check out the links to Dr. Dennis Venema’s more complete explanations of the evidence for the general public: common ancestry and genetic similarity (parts 1, 2, 3, and 4), synteny (parts 1 and 2), pseudogenes (parts 1 and 2), egg yolk (parts 1, 2, 3, and 4) and hominid evolution (hominid genetics and chromosome 2).

Evidence for human evolution: we have remnants of genes for making egg yolks

Here’s just one intriguing piece of evidence for common ancestry, which Dr. Dennis Venema writes about in a series of articles linked to by Professor Swamidass. Unfortunately, this evidence is never even mentioned by Dr. Hunter in his article:

Vitellogenins are large proteins used by egg-laying organisms to provide a store of nutrition to their embryos in egg yolk. Since vitellogenins are so large, they are a good source of amino acids when digested (proteins are made of amino acids linked together). Many of the amino acids in vitellogenins have sugars attached to them as well, so they also serve as a source of carbohydrates. The three-dimensional shape of vitellogenin proteins also acts as a carrier for lipids. As such, vitellogenins can be synthesized in the mother and transferred to the yolk as a ready-made supply of amino acids, sugars, and lipids for the developing embryo.

Placental mammals, on the other hand, use a different strategy for nourishing their embryos during development: the placenta. This connection between the mother and embryo allows for nutrient transfer right up until birth. As such, there is no need for vitellogenins, or storing up a supply in the egg yolk for the embryo to use. Evolutionary biology predicts that placental mammals descend from egg-laying ancestors, however – and one good line of evidence in support of that hypothesis (among many) is that placental mammals, humans included, have the remains of vitellogenin gene sequences in their genomes.

Dr. Hunter: we can’t say what God would or wouldn’t do

Dr. Hunter’s response to such arguments is to cry foul, on the grounds that such an argument involves an appeal to metaphysics:

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.

I disagree. The scientific case for human evolution doesn’t need to specify what a Designer would or wouldn’t do. All it says is that if the Designer of life has no special reason to make X, and we discover X, then X should count as a surprising fact – and hence, a prima facie improbable one. On a special creationist account of human origins, there is absolutely no reason to expect that humans would have what appear to be the remains of genes used for making egg yolks in their DNA – just as there is no particular reason to expect that humans would be more genetically similar to chimps than rats are to mice – or for that matter, than foxes are to wolves, or horses are to donkeys. And let’s remember that most creationists consider horses and donkeys to be members of the same “kind,” just as they consider foxes and wolves to be members of the same kind, and of course, rats and mice as well (see here for a detailed discussion of kinds by Dr. Jean Lightner, from Answers in Genesis. Reasoning on Bayesian grounds, these striking and singular facts have a high probability on the hypothesis of common descent, but are surprising (and hence improbable) on a hypothesis of separate creation. One can only conclude that these facts lend scientific support to the hypothesis of common descent.

Can evolution account for the fact that humans and chimps are genetically much more similar than mice and rats?

Dr. Hunter also faults Professor Swamidass for claiming that the similarity of human and chimpanzee genomes was “predicted by common ancestry,” and that the recent scientific discovery that “humans are about 10 times more genetically similar to chimpanzees than mice are to rats” was “just as predicted by the fossil record.” Hunter replies:

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 than 98-99%…

Second, Swamidass’ claim that mouse-rat divergence, compared with the chimp-human divergence, is “just as predicted by the fossil record” is also blatantly false…

In fact, before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome.

What Dr. Hunter omits to mention is that Professor Swamidass attached a lengthy footnote, which supplies the context for his remarks about rats and mice:

A common lawyerly objection to this evidence is that these similarities are “equally” explained by common “design.” As scientists, our response to this objection is data. Many modern creationists think that the genetic evidence shows that mice and rats share a common ancestor, even though they are 10 times less similar than humans are to chimpanzees. Starting from the genetic evidence, why is it hard to believe chimpanzees and humans are related (less than 1.5% codons different), when we readily accept mice and rats are related (more than 15% different)? Of course, on the outside, not looking at our genomes, humans are very different than chimpanzees, much more different than mice are from rats. Common ancestry predicts this discrepancy between function and genetics by recognizing that genomes are better explained by evolutionary history than readily observable differences between species; mice and rats are more different because they changed more quickly (because of their shorter generation time) for a longer period of time than humans and chimpanzees. What design principle can explain why humans are 10 times more similar to chimpanzees than mice are to rats? No one knows.

While Dr. Hunter is correct in pointing out that the hypothesis of that humans and chimps shared a common ancestor, taken by itself, implies nothing about their degree of genetic similarity, he neglects to mention that scientists routinely make use of molecular clocks in order to determine when two species (A and B) diverged, based on their degree of genetic similarity. They do this by using the fossil record to determine independently when two other species (X and Y) diverged, and comparing the divergence between X and Y with that between A and B, in order to calculate the date when species A and B diverged. The basic idea here is that nucleotide sequences in DNA change over time at a rate which is roughly constant across all species, as predicted by Motoo Kimura’s neutral theory of evolution, which, as Professor P.Z. Myers explains in a 2014 blog post, has been vindicated over “selectionist” theories (which categorized mutations as either advantageous or disadvantageous) by the experimental evidence:

First thing you have to know: the revolution is over. Neutral and nearly neutral theory won. The neutral theory states that most of the variation found in evolutionary lineages is a product of random genetic drift. Nearly neutral theory is an expansion of that idea that basically says that even slightly advantageous or deleterious mutations will escape selection — they’ll be overwhelmed by effects dependent on population size. This does not in any way imply that selection is unimportant, but only that most molecular differences will not be a product of adaptive, selective changes…

When comparing the rates of change between homologous genes in different species, we had a bit of a surprise: they are very roughly, sloppily constant. That shouldn’t be true under pure selection theory, but it turns out to make a lot of sense under nearly neutral theory. There is a tradeoff in the rate of mutations occurring, and in becoming fixed in a population. A very large population size will accumulate more mutations purely by chance, but the probability of a single mutation becoming fixed in the population is reduced under large population sizes. When you do the math, you discover that population size cancels out, and the frequency of novel forms becoming fixed over time is dependent solely on the mutation rate.

Think about that. If you compare two species, the number of nucleotide differences between them is basically going to be simply the mutation rate times the number of generations separating them from their last common ancestor. That’s how we can use a molecular clock to date the time of divergence of two lineages.

Professor Soojin Yi (School of Biology, Georgia Institute of Technology, Atlanta) provides a helpful summary of how scientists use molecular clocks and what their limitations are, in a recent article titled “Neutrality and Molecular Clocks,” (Nature Education Knowledge 4(2):3, 2013).

So, what do the fossils show? Sahelanthropus (pictured at the top of this post), who lived around 7 million years ago, is currently considered to be very close to the last common ancestor of humans and chimpanzees (see this family tree for a summary of changes which are believed to have occurred in the human lineage). By contrast, rats and mice appear in the fossil record at least 14 million years ago, according to the Wikipedia article on Murinae (the subfamily comprising Old World rats and mice):

The first known appearance of the Murinae in the fossil record is about 14 million years ago with the fossil genus Antemus. Antemus is thought to derive directly from Potwarmus, which has a more primitive tooth pattern. Likewise, two genera, Progonomys and Karnimata, are thought to derive directly from Antemus. Progonomys is thought to be the ancestor of Mus [the common mouse – VJT] and relatives, while Karnimata is thought to lead to Rattus [the rat] and relatives. All of these fossils are found in the well-preserved and easily dated Siwalik fossil beds of Pakistan.

For more information on the evolution of rats and mice, see here.

Is the chimpanzee really the animal closest to us?

Left: A chimpanzee mother and baby, Baltimore Zoo. Cropped image, courtesy of Wikipedia.
Right: Orangutan, Semenggok Forest Reserve, Sarawak, Borneo, Malaysia. Courtesy of Wikipedia.

Dr. Hunter’s discussion of the difficulties attending the hypothesis of human evolution is even more disappointing. He begins by attacking the claim that the chimpanzee is the creature closest to human beings:

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 the chimpanzee is not very similar to humans according to many other measures. There are enormous differences between the two species. Furthermore, in its morphology and behavior, the orangutan is closer to humans than the chimpanzee.

A quick point about the genetic similarities between humans and chimp DNA: they really are about 98% similar, as I argued in a post last year. What’s more, even alleged de novo genes found in human beings turn out to have 98% similar counterparts in chimps.

As regards Dr. Hunter’s claim that humans are morphologically more like orangutans than chimpanzees, I’m afraid he’s relying on out-of-date information here. Back in 2009, Professor Jeffrey Schwartz and Dr. John Grehan generated a brief flurry of controversy in the scientific world when they published a paper which listed 63 physical characteristics which had been verified as unique to humans and other great apes – chimps, gorillas, and orangutans – and discovered that humans shared no less than 28 of these characteristics with orangutans, but that they only shared two characteristics with chimpanzees, seven with gorillas, and seven with all three apes (chimpanzees, gorillas, and orangutans). Dr. Schwartz has long argued that our closest relative is the orangutan (from whom he says we diverged 12 or 13 million years ago), and he contends that the genetic data don’t tell the whole story, because most human-chimp comparisons only look at the coding region of the human genome. However, in 2010, another team of researchers (Lehtonen et al.) redid the research, using a much larger set of 300 anatomical features, and found (with a 98% degree of confidence) that the ape most similar to human beings was the chimpanzee, after all. Grehand and Schwartz hit back with a paper of their own in 2011, in which they argued that Lehtonen et al. shouldn’t have counted some of the anatomical features listed in their study, but Lehtonen et al. replied with an article showing that Grehan and Schwartz were guilty of logical inconsistencies in their methodology. In other words: evidence purporting to show that humans are physically more like orangutans than chimpanzees turned out to be highly questionable, and there’s no good reason to doubt that chimpanzees are the apes which are closest to human beings – although recent evidence suggests that the common ancestor of humans and chimps may have walked like an orangutan. However, I don’t blame Dr. Hunter for accepting the claim that humans are anatomically closer to orangutans than to chimps: at one point, I was taken in by it myself.

If even the evolution of proteins requires a Designer, how much more so does human evolution

Dr. Hunter continues:

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.

In this passage, Dr. Hunter is alluding to the pioneering work of Dr. Douglas Axe, the author of the 2010 paper, The Case Against a Darwinian Origin of Protein Folds, which I blogged about here. See also here, here and here for follow-up comments by Dr. Axe and Dr. Ann Gauger, in response to criticisms. As far as I can judge, evolutionists have failed to mount a substantial challenge to Dr. Axe’s arguments demonstrating the astronomical improbability of certain protein folds which are essential for all living organisms having evolved by unguided processes. So I am in complete agreement with Dr. Hunter that human beings did not get here by either a chance process or by natural selection.

However, Professor Swamidass never claims in his article that human beings originated via a blind process. As I mentioned above, he’s a scientist who is a Christian. His sole aim, in writing the article, was to show creationists that there is a wealth of scientific evidence supporting the claim that human beings and chimpanzees shared a common ancestor. Nothing in that claim stipulates the mechanism whereby humans arose: it may have been a guided process or an unguided one.

The mystery of human consciousness

Next, Dr. Hunter argues that evolution cannot account for the mystery of human consciousness:

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. Evolutionary theory constructs mechanisms and explanations that do not correspond to the real world. So this is another problem Swamidass will need to overcome.

However, nowhere in his article does Professor Swamidass attempt to argue that evolution can explain human consciousness. All he is endeavoring to demonstrate is that there is strong scientific evidence that humans and chimps had a common ancestor. Remember: the guy is a Christian, not an atheistic reductionist.

Can the relatively tiny modifications of an ape-like ancestor’s genome account for the vast differences between humans and chimps?

Dr. Hunter ridicules the notion that the morphological differences between humans and chimps can be explained by a relatively small number of modifications in their ancestors’genomes, when species that have undergone much greater genetic modification display far fewer morphological differences:

In recent decades the genomes of humans and chimps have been determined, and they make no sense on evolution. One of the main problems is that the genes of the two species are almost identical. They are only about 1-2% 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.

Dr. Hunter’s argument is flawed, because he overlooks the fact that the vast majority of genetic changes are now known to be either neutral or nearly neutral, as explained above: they are product of random genetic drift, and they are mostly non-adaptive. By contrast, morphological changes (including the “design changes” referred to by Dr. Hunter) are often subject to natural selection, which means that they may be either beneficial or deleterious. Consequently, the degree of genetic divergence between two species tells us little or nothing about how different they are, morphologically. That explains how the morphological differences between rats and mice can be relatively slight, even though rats and mice are believed to have diverged long before humans and chimps (which are so morphologically dissimilar that they were placed in separate families until scientists discovered how similar they were genetically).

It has been calculated (Arbiza, 2006; Yu 2006; Donaldson & Gottgens 2006; Kehrer-Sawatzki & Cooper 2007) that a mere 340 beneficial mutations would have been sufficient to transform the common ancestor of man and chimp into a human being, according to biologist Ian Musgrave of Panda’s Thumb. (That’s 240 mutations in protein-coding genes and 100 in regulatory genes.) By contrast, the number of (mostly neutral) mutations occurring in the human lineage is thought to have been about 22.5 million. In other words, the neutral mutations in our lineage outnumber the beneficial mutations by about 100,000 to 1. The vast majority of genetic differences between humans and chimpanzees have nothing to do with survival, or evolutionary fitness.

Could 340 beneficial mutations have been enough to make us human?

Dr. Hunter is aware of this argument, but he doesn’t find it convincing:

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…

…[The authors of a 2005 paper on the chimpanzee-human genome comparisons] 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.”

That’s right. According to current evolutionary thinking, most of the mutations separating us from chimps were inconsequential, from a survival perspective. A relatively small number of changes – in fact, a mere 340 – made all the difference.

Now, you might be inclined to say: “That’s ridiculous!” Fine. My response is: prove it. You can’t just rely on intuition, because intuition is not infallible. To illustrate my point, consider a transition which dwarfs even the metamorphosis from an ape-like creature to a human being: the transformation from a land animal to a whale. Ask yourself: how many steps would have been required to accomplish this change? Biochemist Larry Moran has an answer for you: “Evolutionary biologists who have spent their entire careers studying evolution, genetics, and developmental biology are comfortable with a few thousand mutations causing the transformation from land animals to whales.” Crazy? That’s what I thought too, when I saw the figure. But if you do the calculations, it turns out that a few thousand mutations might be enough after all, for reasons I discussed in a recent post.

Is there any evidence for natural selection operating on the human brain?

Next, Dr. Hunter argues that the only evidence for natural selection in the human genome relates to relatively trivial functions like smell and hearing, and that there’s no evidence for natural selection operating on the human brain:

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.

Dr. Hunter neglects to inform his readers that the study he cited is a very old one: it goes back to 2003. What’s more, the study included an important disclaimer: “This study has focused only on protein-coding genes, and it will require examination of regulatory sequences to determine the contribution of regulation of gene expression to the evolutionary divergence between humans and chimps.” A more recent paper by Capra et al., published in the Philosophical Transactions of the Royal Society B in 2013, reveals that out of the 2649 non-coding human accelerated regions (ncHARs) which they analyzed in the human genome, about 30% (or 773) function as developmental enhancers, and that using a prediction tool known as EnhancerFinder, the scientists predicted that “251 of the 773 ncHAR enhancer candidates are active in brain development, 194 are active in limb development and 39 are active in heart development.” It turned out that among the validated enhancers, brain enhancers were actually the most common. So much for Dr. Hunter’s claim that the functions identified by scientists in which humans differ from chimps mainly relate to the sense of smell, digestion, hairiness and hearing.

A molecular clock that ticks at different rates in different regions of the human genome

But Dr. Hunter has more up his sleeve. This time, he quotes from a paper dating back to 2005, which found that nucleotide divergence rates are not constant across the human genome. In other words, the molecular clock ticks at a different rate at different places:

That 2005 paper also found a host of chimp-human comparisons that are nonsensical on evolution… For example, if you look at large segments of DNA, which are corresponding in the human and the chimp, you find unexplainable variations in the chimp-human differences…The usual explanatory devices do not work, so evolutionists are left only with the claim that local variations in the mutation rate did it—which amounts to special pleading…

Hang on a minute. How big are the differences we’re talking about here? Are we talking about a ten-fold difference between divergence rates across the genome? Nope. Not even close. A five-fold difference, perhaps? Wrong again. To see what Dr. Hunter is talking about, take a look at this graph. It shows that the overall difference between human and chimp DNA is about 1.2%. If we compare different chromosomes, we find that the difference is slightly higher on some chromosomes than others. And that’s all. If we look at the median figures for chromosome pairs 1 to 22, we find that the genetic difference between humans and chimps varies from about 1.1% to a little under 1.4%. The authors were a little surprised that there was even that much variation, and they wrote: “The average divergence in 1-Mb segments [of the genome – VJT] fluctuates with a standard deviation of 0.25%, which is much greater than the 0.02% expected assuming a uniform divergence rate.” To recap: the study’s authors reported that the mean divergence between human and chimp DNA is 1.2%, and if the molecular clock ticked at a uniform rate across the genome, then the authors would have expected relatively slight variations in this divergence. Instead, they found fluctuations with a standard deviation of 0.25%, which is still insignificant compared to the mean divergence of 1.2%. In other words: so what? Dr. Hunter is making a mountain out of a molehill.

Local variations in the genetic divergence rate between humans and chimps

Dr. Hunter continues:

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 on 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 on 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.

So, how much of a variation are we talking about here? If we look at the graph provided by the authors of the study, we see that even near telomeres (the ends of chromosomes), the level of divergence between human and chimp DNA never gets above 2.1%, and elsewhere in the genome, it never falls below 1.0%. In other words, we’re talking about a two-fold variation in the rate at which the molecular clock ticks, in the worst possible case. Earth-shattering, isn’t it?

Dr. Hunter wonders why the level of chimp-human genetic divergence would vary with the chromosomal banding pattern, and why it would be higher near the ends of chromosomes, if humans evolved. Short answer: I don’t know, and neither do the study’s authors. But I’d like to ask Dr. Hunter a question: can he account for these facts, on a creationist account of origins? He can’t. In other words, what we have is a curious fact which neither evolution nor creation explains well, and which is fatal to neither theory – or putting it more succinctly, much ado about nothing.

Can evolution account for the dissimilarities in rat and mouse genomes?

But Dr. Hunter thinks he has another ace up his sleeve: the fact that the genetic difference between mice and rats is about 10 times greater than that between humans and chimps.

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. And yet the mouse and rat are much more similar than the chimp and human. It makes no sense on evolution. In fact, before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome…

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

Dr. Hunter is right on one point: scientists were at first surprised to discover that the genetic difference between rats and mice was so large. That’s because they based their prediction on the morphological differences between rats and mice, which are relatively small, and inferred that the genetic difference would be small, too. That was a big mistake, for reasons explained above: the vast majority of the genetic differences between any two species are neutral or near-neutral mutations, which dwarf beneficial mutations by a factor of about 100,000 to 1. However, the fossils tell a different story: rats and mice diverged at least 14 million years ago, compared with 6 or 7 million years for humans and chimps. And when scientists calculate the time of divergence using genetic differences, they arrive at a median figure of 17.9 million years ago for the date when rats and mice diverged, versus 6.2 million years ago for the split between humans and chimps, according to timetree.org. I’d say that tallies reasonably well with the fossil record. And I don’t say that lightly: I have in the past been highly critical of inconsistencies in the molecular clock, which I highlighted in a post written four years ago. There is still a lot we don’t know, and alert readers will have noticed that current estimates of the date when humans and chimps diverged vary considerably, as this graph reveals. Nevertheless, the vast majority of the estimates lie between four and nine million years ago, so we’re talking about a two-fold variation, which is still far less than even one order of magnitude. That’s annoying, but scientists can live with it, just as astronomers back in the 1970s and 1980s were able to live with the fact that the age of the universe lay somewhere between 10 and 20 billion years, depending on the method you used to measure it. (They’ve now concluded that it’s 13.8 billion years old.)

Dr. Hunter’s last stand

But Dr. Hunter believes he has one more argument that will demolish the case for human evolution:

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.

Wrong. As we’ve seen, mice and rats diverged around 18 million years ago, compared with around six million years ago for humans and chimps. That’s a three-fold difference. What about the effects of generation time on the molecular clock? Soojin Yi addresses this point in her 2013 paper, “Neutrality and Molecular Clocks,” which I cited above:

Wu & Li (1985) were the first to test the generation-time effect hypothesis using DNA sequence data. They used data from 11 genes of primates and rodents. Since primates have a much longer generation time than rodents do, the molecular clock should be faster in rodents compared to primates. Indeed, they found that for synonymous sites, rodents show approximately two times the rate of molecular evolution when compared to primates (Wu & Li 1985). For nonsynonymous sites however, such an effect was not found. In other words, the neutral molecular clock, but not the amino acid molecular clock, ticks faster in the rodent lineage compared to the primate lineage, which fits well with the idea of a generation-time effect.

So the neutral molecular clock ticks twice as fast for rats and mice as it does for primates. Multiply that by the three-fold difference between the 18-million-year-old mouse-rat divergence date estimated by evolutionists and the 6-million-year-old human-chimp divergence date, and you get an expected level of genetic divergence which is just six times greater – and not two orders of magnitude (or 100 times) greater, as calculated by Dr. Hunter. This figure of a six-fold difference comports well with the ten-fold genetic divergence reported by Professor Swamidass in footnote 2 of his article: at least 15% of the codons in rats and mice are different, compared with less than 1.5% in humans and chimps.

Conclusion

There is a lot that we still don’t know about human origins. I accept that. But it would be foolish to deny that the scientific evidence points clearly to our having shared a common ancestor with the chimpanzee. Such a conclusion is in no way at odds with Intelligent Design.

What do readers think?

UPDATE:

Readers may wish to peruse the following articles, written in response to my post and to Professor Swamidass’s article, “Evidence and Evolution”:

A Response to VJTorley by Dr. Cornelius Hunter.
One Long Argument — Responding to VJ Torley on Human-Ape Common Descent by Dr. Cornelius Hunter.
Of Tree Rings and Humans by David Klinghoffer.
Debating Common Ancestry by John West.

Professor Swamidass has also written a follow-up article:
Call for Response to the Tree.

I also wrote a short comment in response to Professor Swamidass’s article, “Evidence for Evolution”, which has recently been updated with an FAQ section:

Hi Dr. Swamidass,

Thank you very much for your kind remarks about my post on Uncommon Descent.

I’d just like to comment briefly on what you said about Dr. Hunter in the FAQ:

“Third, I do believe that Dr. Hunter is not being intentionally deceptive or manipulative. I believe he is making a good faith effort, to the best of his abilities, to engage the evidence I have raised.”

I would like to endorse what you said. I pulled no punches in my post, and on a few occasions, I did criticize Dr. Hunter for relying on flawed arguments. I also wrote that he “neglects to inform” his readers on a couple of basic points. For the record, I wish to make it quite clear that I am not accusing Dr. Hunter of being intentionally deceptive. All of us are, at times, guilty of an unintentional bias towards arguments that we personally favor, and it is all too easy to ignore what we might perceive as very minor or trivial problems in these arguments, when presenting them to an audience. That was what I had in mind when I wrote about Dr. Hunter’s “neglect.”

Despite my differences with Dr. Hunter, I have the greatest respect for him as a Christian, and I would like to thank him for his forbearance and courtesy.

Likewise, when I referred to Dr. Hunter in my post as believing he had an ace up his sleeve, I was not implying that he was resorting to any sleight-of-hand or trickery. Rather, I was using the term in the sense in which the Cambridge English dictionary defines it: secret knowledge or a secret skill that will give you an advantage.

For the record, I believe Dr. Hunter to be an honest man. And I apologize for any pain or distress suffered by Dr. Hunter as a result of reading my post. I wish him well.

Comments
Professor Swamidass: Thank you again for your efforts in the discussion -- I know it take a lot of time from a busy schedule to follow and participate in even one thread. I appreciate your willingness to politely and humbly acknowledge how your comment may have been misinterpreted. That is very gracious of you and speaks to your good character, even if we disagree on some of the issues. I wish more ID critics demonstrated similar class. While we are at it, please also forgive any harsh or insensitive comments from our side. It is certainly easy in the heat of debate to harshly attack another's position, especially with the relative anonymity of the internet separating us as actual individuals -- with our unique individual capabilities and flaws and personalities somewhat distorted or hidden from view. Thanks again for participating. Best wishes with your new book and other work, and hopefully we can have you back again before too long.Eric Anderson
May 19, 2016
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Please forgive my blindness. It's not the blindness, it's the unbelief. :)Mung
May 19, 2016
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vjtorley @253 As far as I'm aware of, no one made any unfair accusation in this case. Professor Swamidass himself admitted having written statements that did not sound humble at all and could be easily interpreted as arrogant. Truth is never unfair. Lack of humility is part of our human nature, hence it is encountered everywhere we look, including the academic/scientific community and ourselves too. Hence, I would not have brought it up to professor Swamidass' attention if he had not claimed being a Christian. That was the trigger, the game changer. Whoever claims to be a follower of Christ must be aware of the responsibility such a claim implies. According to the Bible NT every Christian is a priest and a saint, i.e. a forgiven sinner whose life purpose is to give glory to God and enjoy Him forever. That's why Johann Sebastian Bach signed his musical compositions with the Latin phrase "Soli Deo Gloria" even though few mortals in music history could be compared to Bach. That's how we want our attitude to be always. I will be very thankful to anybody who alerts me after noticing something I've written that may sound arrogant. As I told professor Swamidass, whoever publicly claims being a Christian must realize that he/she is seen as an ambassador of the King of kings in this world, hence it must do everything in such a way that could be stamped Soli Deo Gloria.Dionisio
May 19, 2016
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Hi everyone, I would like to thank Professor Swamidass for his comments on this thread. Discussion is still continuing over here at https://uncommondescent.com/intelligent-design/bakers-dozen-thirteen-questions-for-dr-hunter/ and I welcome further contributions. Let me add that Professor Swamidass is a highly qualified scientist, and I think that for that reason, his arguments warrant a certain degree of respect. Readers are welcome to disagree with him, but accusing him of arrogance is rather unfair. At any rate, it has been an interesting exchange of views.vjtorley
May 19, 2016
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Prof. S. Joshua Swamidass @250 If you're truly a follower of Christ, you must know that I have to forgive you, because God forgave me much bigger sins and graciously gave me eternal life through saving faith in the redemptive power of Christ's death on the cross and His resurrection. BTW, if you ever find time to look at my questions, please pay careful attention to every word. They all have meaning. I look forward to reading your answers someday. Thank you. Soli Deo Gloria Rev. 22:21 PS. You may find a few interesting papers referenced in the following discussion threads: https://uncommondescent.com/intelligent-design/mystery-at-the-heart-of-life/ https://uncommondescent.com/evolution/a-third-way-of-evolution/Dionisio
May 19, 2016
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Swamidass: It [naturalistic macroevolution] provides a coherent explanation of Biology (not invoking God, so not violating methodological naturalism).
I take it that you mention "not invoking God" for the specific reason to contrast ID with science. You seem to think that ID does invoke God. This misunderstanding explains why you continually write things like:
Swamidass: As philosophical and theological exercises, the best ID arguments make sense to me.
You are mistaken about ID. To be clear, ID does not invoke God.Origenes
May 19, 2016
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@249 I am sorry. What I said was not humble. I hope you guys will forgive me. I did not intend to be rude. I see why you feel comment was arrogant, which is why retracted it. I am sorry. I certainly do not compare with the King of Kings. I am not worthy to untie His shoes. I try hard, but fall short. Look to Him not me. I'm sure I will be back someday. Keep asking your questions Dionisio. I promise I will answer more of yours next time. I like you. Okay? And gpuccio's example is good. I'm sure he will serve you well until I return. Peace.Prof. S. Joshua Swamidass
May 19, 2016
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Prof. S. Joshua Swamidass @244
I was just hoping to explain how I see it, because it seemed that you wanted to know. I can clearly see how that came off as arrogant.
arrogant? That's an understatement. Note what you wrote earlier: Prof. S. Joshua Swamidass @237
You forget with whom you are speaking. This is my area of expertise. I do not assess the field by reading pop culture books. I read the primary literature. I have 20 years of experience in science and have read thousands of papers on this topic, from every viewpoint and side of the issue. If I say something exists that you do not know about, maybe, just maybe, I am right.
What saddened me more is that you publicly claimed to be an ambassador of the King of Kings. Someone who claims to be Christian must be truly humble and a servant of all. If I write something that sounds arrogant here, I want someone to bring it up to my attention right away so I correct the error. A true Christian has God's spirit dwelling within, making it unbearable painful to look down on others, just because they may know less about certain topics or for any reason. Grace, love, compassion, patience, respect, humility, are some of the attributes that should be easily visible in Christians. Christians are not better persons than non-Christians. They are just forgiven sinners, justified by their saving faith in Christ. All human beings are created with dignity. Our Lord of Lords asks us to love other people, even if they disagree with our principles. Here's an example for you to imitate if you change your mind and decide to come back to discuss in this site: gpuccio knows a lot more biology than I do and perhaps theologically speaking we're on different pages, but still he answers all my questions, even the dumb ones respectfully and clearly. A couple of years ago, when one of gpuccio's interlocutors in a discussion thread suggested I better refrain from commenting in this blog, because I'm too ignorant of biology, gpuccio encouraged me to keep commenting and asking questions in this site. Since then he has indicated -with his refreshing sense of humor- what he considers important areas of biology. I encourage you to learn from gpuccio's example how to explain things clearly, paying attention to important details, and treating others with much respect. BTW, just in case you change you mind and want to do some damage control, here's a reminder I wrote to you @224 and @233 about the questions you had chosen to skip: https://uncommondescent.com/intelligent-design/in-defense-of-swamidass/#comment-607486Dionisio
May 19, 2016
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bill cole #242, Well spotted. Common descent is a full-blown inference — see GPuccio #21 — yet Swamidass considers it to be 100% science. However, he somehow feels that design inferences are outside of science.Origenes
May 19, 2016
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Prof Swamidass, I suggest you read my description of what interests ID at @216 which you mocked but never answered. All the links you provide fall into tier 5 or what ID is not interested in. Then maybe you will start to understand why you seem to not understand ID. All your examples are focused on things ID accepts and are not that interested in and you ignore what they are interested in using derisive comments.jerry
May 19, 2016
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common decent requires inference
Common descent is a possible conclusion or as you say inference from the data but there is no way to prove it. It is a possibility. The data does not comes close to supporting UCD but it certainly is consistent with a lot of the fossil record. People who claim UCD or even a lot of common descent are essentially begging the question. So it is consistent with a lot of the data but that is the best one can say about it. So is design. The only reason to stick one's neck out about common descent or UCD is because it supports the atheist position that every new species was the result of naturalistic evolution and originated from just one place. So anyone who pushes UCD has an agenda. Many TE's also support it because they hold that all evolution is naturalistic. Which is why they hate ID. It is not inconsistent with ID because new species could have happened through some design process or a naturalistic process from a previous species. ID does not dispute all species that have happened through naturalistic processes. It may be how most species originate but it cannot explain the overall gene pool for the various orders.jerry
May 19, 2016
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@232: Eric Anderson I am willing to continue this conversation over email or phone with you. I'm easy to find online. Send me a note please.Prof. S. Joshua Swamidass
May 19, 2016
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I said it would be my last comment, but apparently that did not go over well. I meant no disrespect. Maybe you are right. Maybe there is just something obvious that I am blind to see. Please forgive my blindness. I just don't get it. Reading the books, looking at the math, talking to the theorist, I'm just not convinced. I want to be. I am not. I was just hoping to explain how I see it, because it seemed that you wanted to know. I can clearly see how that came off as arrogant. Sorry about that. Once again, I meant no disrespect. We just see things differently. I'm fine with that. I see things in a certain way, informed by my theology and the rules of mainstream science. That is powerful but it has its limits. Maybe you see something here more correctly than me. If that is the case, I sincerely hope you are able to make a more effective case for yourselves in the future. The current argument loses me. Even if we disagree on this, there is, I hope, a place to focus on our common ground. We don't have to agree on everything to agree on somethings. Right? So...hopefully this is the last comment.Prof. S. Joshua Swamidass
May 19, 2016
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Very interesting debating technique by Swamidass: **tell your opponent that he is completely wrong and then let him sort out why this is so.** — First example:
Swamidass: So let me start with the ID work I found highest quality in this genre. This is is a paper published by Behe in 2004 (…) As a trained computational biologist, I spent 15 minutes reading the paper, about 2 hours thinking about it, and identified two clear errors.
Let me guess, you won’t point out those “clear errors”, but we have to sort it out ourselves?
Swamidass: Of course, I am not so stupid as to try and litigate technical details of stochastic differential equations on a blog comment. I leave it to you to find the errors. If you can’t, maybe you are not an expert here.
Aha. Well, of course you won’t name those errors. The best(!) ID paper contains two clear errors, but you won’t tell us which they are and if we cannot find them we are stupid. Okay, got it. - - - - - — Second example:
Swamidass: (on SETI vs. ID): Of the top of my head, I can come up with about five material differences.
Five(!) material differences in methodology no less! Let me guess, you won’t point out any of those five material differences, but we have to sort it out ourselves?
Swamidass: Now you try. What are the differences? For each difference, why do you think they are immaterial or material? After a few people post on it, I’ll show you why I think the differences are so substantial as to make the original argument unconvincing.
StephenB: ID’s methodology is formulated to detect physical patterns in nature that appear to have been arranged for a purpose. SETI uses the same methodology. (…) ID, does, indeed, use the scientific method: Observation>>Hypothesis>>Experiment>>Conclusion. If that isn’t the scientific method, then what is? Please be specific.
Upright BiPed: SETI’s methodology uses an operational definition of intelligence based on a measurable artifact of intelligence. The exact same methodology is available to ID, and is valid for the same reasons. Your comment is mistaken.
Swamidass: (…)
Origenes
May 19, 2016
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Eric Dr Swamidass VJT
1. First, you suggest multiple times that inferences lie outside of science. Why do you think that? What definition of “science” are you using, and why is the idea of the design inference being “science” a concern?
When I asked Dr Swamidass can common decent answer the how question he replied.
Of course, the inference to naturalistic macroevolution is leap from here. In contrast with design, it provides a framework from which to generate new testable hypothesis without “toeing the line” on methodological naturalism. That is why macroevolution works in science. It is really useful as a framework for proposing testable hypotheses
Do you see the inconsistency in the argument? What Dr S is stating IMHO is that common decent requires inference yet to you he states inferences lie outside of science. This says that common decent lies outside of science. Without inference there is no theory of common decent according to his statement. How macroevolution can generate testable hypothesis is a mystery to me.bill cole
May 19, 2016
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Professor Swamidass
You will certainly have grown the ID culdesac into a community of researchers larger than you can count. I’m sure, at this point, you protest. This seems hard. And difficult. And long. Yes. It is. Science is hard, difficult, and long. But it is grand. Come meet me here.
One of the most arrogant comments I have ever seen here. I would not want to have made a similar comment. This is right up there with the "overwhelming" information is support of Darwin and evolution which people would use when they couldn't back up what they say and try to put people down because they are obviously dumber and clueless. The interesting thing is none of the links you provide support your position:
I do not think atheists have an indisputable case against. Though, to be honest, there math is usually more solidly worked out
None of the studies would be disputed by ID people as having any effect on what they believe so how they support atheism is beyond me. As I said you do not understand ID and this just reinforces that point of view. The fact that you do not know this and make such an arrogant statement is problematic at best.jerry
May 19, 2016
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Professor Swamidass: Thank you for the additional mathematical information you provided in response to jerry's comment. Do you happen to have handy a link or a brief explanation of the two errors you noted in Behe's paper? Also, do the two errors you noted fundamentally change Behe's conclusion in that paper? What about the more basic probability approach that is central to the design inference? After all, that is the principal context of the discussion here. ----- BTW, it is wonderful that you think so highly of your field. No doubt you should. Computation is indeed important and critical. Let's keep in mind, however, that biology is first and foremost about engineering. Yes, math can help with the engineering and our understanding of the engineering and to implement the engineering. But at the end of the day how organisms function in the real world is a matter of engineering. :)Eric Anderson
May 19, 2016
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Dr Swamidass
Any one of these papers, ID theorists could: 1. Get the same data as the paper (it usually all freely available). 2. Build an alternate, precise mathematical model for design. 3. Fit the data (using less parameters) better than the current evolutionary models. 4. Test the implications of that model on the behavior of biological systems today. 5. Instead of a book, publish two or three papers on that effort (I do not care the reputation of the journal if the actual science is good).
Has there ever been a mathematical model published that supports a natural path of a genome converting from on kind to another?bill cole
May 19, 2016
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Professor Swamidass @232: Thank you for taking time to share your detailed and thoughtful comments. I think there are many things we can all agree on, and your willingness to engage in discussion is both refreshing and helpful. jerry has already responded to a number of details, so I won't rehash his excellent points, but I just wanted to flag a couple of issues that jumped out at me. 1. First, you suggest multiple times that inferences lie outside of science. Why do you think that? What definition of “science” are you using, and why is the idea of the design inference being “science” a concern? Also, if you are being logically consistent, presumably you would also then acknowledge that an inference to a multiverse is outside of science? And someone inferring that life began by purely natural process is outside of science? And someone inferring that organism A turned into organism B through a process never-before witnessed (but inferred) is outside of science? 2. Second, you have made several references in this thread to the incorrect math employed by ID proponents. I realize you don’t have time to give us a dissertation, but it would be very helpful to understand your issue with two aspects: (a) the design inference generally, meaning, the concept of using probability calculations to determine the odds of a system arising through chance processes, and (b) one or two specific examples of the “equations that are so far off” that you can use them as a teaching tool. Incidentally, it would seem that the basic ID approach of analyzing probabilities is applicable to design inferences across the board in all relevant disciplines, including the ones I’ve mentioned. Ironically, no-one ever seems to have an issue with it until it comes to biology and then all heck breaks loose. And it isn’t helpful to respond to the design inference, as you have implied more than once, that we can’t apply normal principles to biology because biology is unique or because biology is non-intuitive and so on. An objective outside observer might be forgiven for thinking that such an approach is actually an attempt to isolate biology, and the Darwinian storyline, from criticism. 3. Finally, you focus on the fact that there is still much we do not know. That is absolutely correct, and you won’t get any disagreement from me on that front. But you need to turn the lens of scrutiny the other way around. Specifically, nearly everything we have learned about biology over the last century has made the Darwinian storyline less credible, not more. It was very easy for Darwin to gaze around in nature and imagine that “slight successive modifications” could turn organism A into organism B. After all, he hadn’t a clue about DNA, digital code, sensors, feedbacks, concatenation algorithms, or anything else going on in the cell. The more we learn, the more clear it becomes that the Darwinian storyline is lacking. So, yes, it is very true there is much we don’t know. Including first and foremost on that list, we should note, how in the world a long string of accidental particle collisions could lead us to the complexity and diversity of life we see around us today. But despite what we don't know, the trajectory of the evidence is quite clear: the naturalistic storyline is the wrong place to look for answers to most of what we see in biology, and design is more and more the most likely explanation.Eric Anderson
May 19, 2016
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@236 I think this will be my last post with you guys for a while. Thanks for being kind hosts. I appreciate that, and will remember this fondly. I'll look forward to the next interaction too. Feel free to stay in touch with me over email, and I'll try and keep you abreast of my future work. I will comment finally on a quote that brought a smile to my face, and spring to my step. "Swamidass: I do not think atheists have an indisputable case against [ID]. Though, to be honest, [their] math is usually more solidly worked out" "Jerry: This is nonsense. I am sorry. They have no math!! If they do then present it or at least describe it and its logical implications. I would be very interested in that. You would be the first person to ever try that here." You forget with whom you are speaking. This is my area of expertise. I do not assess the field by reading pop culture books. I read the primary literature. I have 20 years of experience in science and have read thousands of papers on this topic, from every viewpoint and side of the issue. If I say something exists that you do not know about, maybe, just maybe, I am right. It turns out that there are hundreds of mathematical modeling papers published each month that are directly relevant to this discussion. This is vast area of work, that is mathematically rigorous and has consistently produced knowledge about how biological systems function in the present, not just the past. My specific expertise, by the way, is just one relatively small subfield in a gigantic discipline. I can only smile when you say: "This is nonsense. I am sorry. They have no math!!" My meta-question is, how is that you do not know about a vast body of work that is directly relevant to the questions you find most important in science? Remarkably, I linked directly to several papers in this area in my article, and so did VJ, but somehow you missed them. My best guess is that only a tiny tiny fraction of this work has made its way into pop culture, and the part that has is very watered down and simplified. If this is your only way of thinking about science, through the processed and prepackaged thoughts of Dembski, Meyers, Axe, Behe, and Denton, of course you would not know about this world. Perhaps, you are in a fishpond. Science, however, is a vast ocean of adventure and discovery. Come join me over here. The water is great. I encourage you to actually click through the links on VJ and my posts to get to the primary literature. Then start looking at the references in these papers. Then start look at the papers that reference these papers. You will see more math than you will be able to keep up with, and you still will not have scratched the surface. In this exchange, I found these three the most helpful, but there are many more: http://www.nature.com/ng/journal/v47/n7/full/ng.3292.html http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329511/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396900/ So let me start with the ID work I found highest quality in this genre. This is is a paper published by Behe in 2004 (in the lead up to the Dover Trial). The story here is interesting. He got it published, but ID became so toxic that he was forced to retract the paper. I disagree with that btw. I think it would be helpful if more work like this was done by ID people. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2286568/ This article works because it puts his rhetoric down into actual formulas that we can objectively assess. It turns out that his math is inadvertently wrong, in a very subtle way. As a trained computational biologist, I spent 15 minutes reading the paper, about 2 hours thinking about it, and identified two clear errors. Moreover, I identified at least 2 ways to experimentally validate his model, which he apparently did not think to do. I don't think the article should have been retracted. Rather, it should been built upon and figured out precisely. Of course, I am not so stupid as to try and litigate technical details of stochastic differential equations on a blog comment. I leave it to you to find the errors. If you can't, maybe you are not an expert here. So here is the deal. If you want ID to be taken seriously. You need end the silly polemics. This is not an argument to be won with words. It is an exposition of mathematics. Any one of these papers, ID theorists could: 1. Get the same data as the paper (it usually all freely available). 2. Build an alternate, precise mathematical model for design. 3. Fit the data (using less parameters) better than the current evolutionary models. 4. Test the implications of that model on the behavior of biological systems today. 5. Instead of a book, publish two or three papers on that effort (I do not care the reputation of the journal if the actual science is good). Now you have one story. Get your friends together. Multiply this times 1000, so there is a body of rigorous work full of interesting stories. Police yourselves, and shoot down the bad models that fail, and come to a consensus together about what consistent design principles (mathematically speaking) explain the data with fewer parameters than strictly evolutionary models. At this point, maybe 10 years from now if you begin in haste, and are fortunate enough to be right, you might then have the seed of scientific argument. Of course, if you are right, it will grow even further from there. You will certainly have grown the ID culdesac into a community of researchers larger than you can count. I'm sure, at this point, you protest. This seems hard. And difficult. And long. Yes. It is. Science is hard, difficult, and long. But it is grand. Come meet me here.Prof. S. Joshua Swamidass
May 19, 2016
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Prof. Swamidass, I still maintain you do not understand ID. You mis-state a lot of what ID is about. Now given that there are hundreds of persons on this site who comment, one can hardly expect everyone to have the same understanding. I am sure many would have issues with my understanding.
The simplest way to put it is that ID is trying to make a “strong” proof instead of a “weak” proof. The weak proof is what we have, and it is very hard to turn into a strong proof.
I have no idea what this means. But ID never claims certainty but only that evidence points to a design conclusion and not to a naturalistic conclusion in many cases. In most research studies I have seen there are four parts, 1) background 2) methodology 3) results and 4) conclusions. It is in part 4 that ID comes into play. If one does a million studies in science based on this paradigm, only a handful will need to consider a design inference in the conclusions. It is rare in science that ID has a place. No one is making what you call a “strong proof.” So this criticism is inappropriate.
Take the fine tuning argument. I find it compelling. I think it is probably right (though I do not think the inference itself is in science).
No it is more than science. It is an argument that uses science and logic.
At the same time, there is a reasonable (though unproven) argument against it: the Multiverse. This counter argument has some weak support.
Yes, the argument is very weak. Why won’t scientists admit it and just let the two arguments stand up side by side. They won’t and that is the heart of the issue in our world. Why won’t scientists let an honest debate take place. That is a major criticism of the science community to which you belong. Just as an aside, how many universes are there in the Multiverse? If there is a finite number the argument falls apart from lack of sufficient resources to explain our universe. If there is an infinite number of universe then there is no universe that is impossible and we get absurdities such that our universe has happened an infinite number of times and so has every other possible universe.
I am skeptical that the first life was produced by natural causes. We certainly do not have a strong scientific case for it.
There is no case for it at present. Absolutely none let alone a strong one.
But we also do not have a rock solid case against it.
No but logic says that it was either natural or it wasn’t. If the case against natural is strong because it seems to be impossible, then the case for the other gains acceptance. Not certainty but it strengthens the argument against naturalistic origins which supports a design argument. That is not science but logic.
We are talking about a very very rare and localized event in the distant past.
Now you are starting to understand ID and why it cannot be treated as science in the usually way. It is a series of one time events. The questions is the number of the one time events. Is it zero as the materialist claim or could it be millions or somewhere in between. I have seen some claim that it was only once or a couple times, first in the creation of the universe and then in some important but very limited interventions. But we are taking theology here and this is probably the root cause of the disagreements with ID by some theists. I have seen some theists who try to limit the interventions to creation and in Christian theology to just the birth and resurrection of Jesus. We do not know the number. ID tries to point out when there may have been an intervention by some unknown entity. Never a certainty but a possible inference that should be allowed based on the evidence and mathematics. As I said above in nearly all research studies this is rarely a conclusion.
To be clear, I think the inference to design is reasonable (and outside science), but it is not as rock solid as we want it to be
Nobody says it is.
For evolution, the arguments are much weaker still.
Depends what you mean by the word evolution. If you just mean the appearance of new life forms over 3.5 billion years, you will get no objection from most ID adherents except for the YEC’s.
The pattern is just that we do not know enough about the biology to make reliable mathematical claims about biological systems. Computational biology has just not come far enough. We do not understand enough.
Yes, with all the math and computers there is no evidence of new species development except at the lowest level. And never an instance of the development of complex functional novelties. Not one. So Biology is very limited in this area. Why cannot biologist admit this. And possibly conclude the reason for it may be that it is extremely unlikely.
Furthermore, many of the “mathematically” inclined ID theorists (I won’t name names here), make very bad assumptions in their math.
I suggest you name “names” and how their math is deficient. Remember most of the math is just showing that the anti-ID’s mathematical argument are specious. So it is the math of biology that is suspect and not ID’s math.
With all due respect, I do not see this restraint often in the ID community.
I have to disagree. What ID is confident about is that the naturalistic point of view has no mathematical support. That is the confidence I see. It is confidence that the arguments underlying atheism or naturalistic evolution are fallacious not that there arguments are rock solid. But if you discredit the other side, you support your side a little more.
I do not think atheists have an indisputable case against. Though, to be honest, there math is usually more solidly worked out
This is nonsense. I am sorry. They have no math!! If they do then present it or at least describe it and its logical implications. I would be very interested in that. You would be the first person to ever try that here. So please try to understand what ID is about. You claim you do but your statements indicate otherwise.jerry
May 19, 2016
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Andre @ 234 Is that "generous" ? You definitely have a good sense of humor. :)Dionisio
May 19, 2016
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I'll be even more generous and say.... We give you fermions, bosons, amino acids all the proteins and materials you need and all you have to demonstrate is how this.... http://www.fairviewebenezer.org/fv/groups/public/documents/images/141030.jpg or this.... http://www.kidport.com/reflib/science/humanbody/skeletalsystem/images/HipJoint.jpg built itself........Andre
May 18, 2016
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Prof. S. Joshua Swamidass Please, don't forget to answer the questions @224: https://uncommondescent.com/intelligent-design/in-defense-of-swamidass/#comment-607486 Thank you.Dionisio
May 18, 2016
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@221 Next one... "I am, however, sincerely interested in your claim to have found that the design inference fails in biology. I would not wish to proceed down a path that is intellectually problematic, so please share with us your understanding so that we can avoid such a mistake. I am not being sarcastic — if you can help us avoid going down the wrong path with Dembsik, Behe and other ID proponents, I would like to know sooner, rather than later, in my life." This is a very very wise request. So I will take it seriously. The simplest way to put it is that ID is trying to make a "strong" proof instead of a "weak" proof. The weak proof is what we have, and it is very hard to turn into a strong proof. The issue is, because of our lack of knowledge in science, strong proofs are very hard. We have to make claims about things we do not know, which are always fraught. Take the fine tuning argument. I find it compelling. I think it is probably right (though I do not think the inference itself is in science). I think this is a reasonable place to explain that "As a Christian I think this might be evidence that God created our world." At the same time, there is a reasonable (though unproven) argument against it: the Multiverse. This counter argument has some weak support. (1) we know of a mechanism (spontaneous symmetry breaking) that could, by analogy, explain how physical constants are randomized, (2) some versions of the Multiverse are, in principle, detectable though this hasn't happened yet, (3) most mathematical models of inflation that take quantum uncertainty into account (i.e. the Big Bang) induce a multiverse (ironically, it takes fine tuning to extinguish this behavior). None of this evidence strong, it is very weak, but it does make the multiverse claim a plausible (internally consistent) alternative to fine tuning. So what do we make of this? I'm comfortable with the weak argument.I don't need to force it into a strong argument (that disproves or denies the Multiverse). So that is fine tuning. The origin of life is very similar. I am skeptical that the first life was produced by natural causes. We certainly do not have a strong scientific case for it. But we also do not have a rock solid case against it. It is certainly reasonable to believe God make the first cell. The hard proof that this happened though? I am very skeptical. We are talking about a very very rare and localized event in the distant past. We do not even know what the first life was like, or how many other planets like the Earth exist in the Galaxy. To be clear, I think the inference to design is reasonable (and outside science), but it is not as rock solid as we want it to be. There are just too many unknowns to make a reliable calculation. For evolution, the arguments are much weaker still. I've already been explaining some of their deficiencies. The pattern is just that we do not know enough about the biology to make reliable mathematical claims about biological systems. Computational biology has just not come far enough. We do not understand enough. Furthermore, many of the "mathematically" inclined ID theorists (I won't name names here), make very bad assumptions in their math. Their equations are so far off that I can use them as a teaching tool with PhD students, asking them to point out the errors in socratic dialogue. What is needed here is some appropriate epistemological humility. Biology is much much harder than people imagine. We should have doubt of everyone's strong claims here, not just the people we disagree with. Modeling biology is very hard. With all due respect, I do not see this restraint often in the ID community. The answer to overconfident atheism, is not overconfidence on the opposite side. A better approach is arguing clearly that science is profoundly limited (it is), and it is ill-advised to make the far reaching claims of the overconfident theorists. This of course cuts both ways. In the same way I do not think ID theorists have a credible mathematical case for design, I do not think atheists have an indisputable case against. Though, to be honest, there math is usually more solidly worked out. Still, biology is hard, and some of the most important features of biology (e.g. how many possible solutions to a specific problem are there?) we just have no idea at this point. For now, evolution works as an explanatory framework in science, but the exact role of God in this story is unfathomable. I have my guesses. I'd love to have clarity here. However, we just do not know enough to make strong claims. I think there is a real place for design arguments. I am not hostile to them. I recommend, however, that you look at the whole picture. ID right now is loathed by scientists, philosophers, and historians alike (including Christians). Some of that is earned. Some of that is unearned. At the same time, the ID movement is not the only option. Why not work with the American Scientific Affiliation (ASA)? They are well respected in most academic quarters, have a thriving community of Christian scientists, philosophers and historians (of science of course). Associating with them will not get you kicked out of science. They are also thinking about design inferences too, but in (I find) a much more grounded way. I encourage you to check them out, and maybe even go to the conference this summer. You won't regret it.Prof. S. Joshua Swamidass
May 18, 2016
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Okay, I'll weigh in again here on a few points... "Over the years there have been many high level anti-ID pro natural evolutionists who have commented here. None of them had the confidence you seem to exhibit that the process is well understood and the mathematics of it explain evolution." To be clear, I do not think that naturalistic evolutionists have a rock solid case that evolution makes mathematical sense. I find that absurd, as I am sure you do too. At the same, I do not think that ID theorists have a rock solid case that evolution does not make sense. We just do not know enough about biology to make a believable case for or against it. It is foolhardy to think we can. And, for that reason, I argue both against atheists and ID theorists here. The strongly convinced ones both have too much confidence in simplistic mathematical models, and do not have appropriate humility. Biology is just very difficult to model well. I am so convinced of this, that (even as a computational biologist) I am very skeptical of all the hard and strong claims coming from both camps. Based on my expertise in biology and modeling, I have a very confident and comfortable agnosticism here. Frankly, it is easy to poke holes in both sides arguments (i.e. their math). It is also easy to see how both sides could be right. The case is just not definitive. To me the psychology here is remarkable. Why do I get "otherized" when I agree with your larger point, but think your proof is bad? Someone explain that to me.Prof. S. Joshua Swamidass
May 18, 2016
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5. I do not understand why #4 is necessary. Why is #2 not enough? Why do you need the label “science?” Why not just make a solid and sound philosophical argument based on scientific knowledge? This respectable, and would end like 90% of the conflict.
Because the common atheist is philosophically ignorant. Many a visitor to UD has been banned for arguing against ID while also arguing against basic logic.Mung
May 18, 2016
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I am not ignorant. Please, stop arguing my ignorance is the problem. Ok, your ignorance is not the problem. ;) But we're not ignorant either. Many of us are dedicated Christians who have consistently examined through constant study what we believe and why we believe it, in particular with regard to creation and evolution.Mung
May 18, 2016
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It seems clear to me that the good Professor thinks that "design inference" means "goddidit."Mung
May 18, 2016
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Prof. S. Joshua Swamidass:
Then I got a PhD in computational biology and learned how far off the math I was taught in ID was from the actual biology.
I'd be interested to hear your comments about: Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of EvolutionMung
May 18, 2016
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