Intelligent Design

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.

256 Replies to “In defense of Swamidass

  1. 1
    DebianFanatic says:

    “Why do humans and chimps share such similar genomes, while the genomes of humans and mice differ so dramatically (see Mouse Genome Sequencing Consortium 2002)?”

    Is that a typo? Shouldn’t it be “genomes of rats and mice”?

  2. 2
    swamidass says:

    Vincent, thank you for actually reading my article and recognizing it for what it was meant to be: an olive branch. I’m not linking back to you from my site, and you have gained a friend. I would also point out that ENV decided to post Dr. Hunter’s further critiques (http://www.evolutionnews.org/2.....02837.html). Maybe they might publish your rejoinder?

  3. 3
    swamidass says:

    And one more thing. Several theologians are thinking of responding to my question. Check out this link. http://swami.wustl.edu/call-response-tree . Is there anyone in your network (or yourself) that would like to respond?

  4. 4
    bill cole says:

    VJ

    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.”

    What does it mean to share a common ancestor? Do you mean that there was a split 6 million years ago and we came about through natural variation. If this is true how would you account for all the novel proteins, epigenetic timing differences and the different alternative splicing sequences. How would you account for the 2500 AA difference in the length of the titan protein?

  5. 5
    Robert Byers says:

    We look exactly like primates. so to not have like genes/dna would be a radical overthrow of genetics surely.
    We look exactly alike because we were given the same body. What other type of body on earth could man be given? A eagle. Not good for driving.
    Hunters criticisms are against the same presumptions we always meet in those defending evolution.
    probably the full stance of the researcher was missed.
    i thought he was just another evolutionist. he is not the same crowd.
    anyways the bible says man was made in gods image. Not our body. that is in the common blueprint for all biology. lips, butt. ears etc.
    God doesn’t have those.
    Seeing our likeness in form/dna is not evidence for common descent.
    its just a line of reasoning because other options were not included.
    what if the bible clearly spelled this out.

  6. 6
    Anaxagoras says:

    I definitely side with Dr Hunter.
    Dr. Swamidass advocates just “common descent” witout clearly stating what kind of process could have led to the existence of humans as we are. What has to be explained are differences.Unless you can provide a sound account of the origin of the traits that make us specificly different beings you are just incurring (as Dr Swamidass does) in the logical fallacy of affirming the consequent. More, Dr Swamidass presents a darwinian gen-centrist explanation of what biological “forms” are that we allready know is far from being appropriate to give account of the true essence of living organisms.

    Dr Hunter criticism points to the fact that gen similarities can not be presented as evidence for naturalistic evolution, and I think his point is not only perfectly legitimate but something that has to be addressed.
    To clarify the debate, I would ask Dr Swamidass.
    Do you mean, when advocating of common descent, that naturalistic unguided occurrences are a sufficient scientific explanation of the evolution of an ape-like ancestor into modern human beings?

  7. 7
    Origenes says:

    Swamidass: A common lawyerly objection to this evidence is that these similarities are “equally” explained by common “design.”

    Swamidass is correct to question the equality of the explanations. For one thing, blind watchmaker evolution has not been shown to be able to produce the kind of information contained in DNA and proteins. Intelligent design is the only known source of this kind of information.
    So, indeed, from a scientific perspective, with respect to explanatory power, common design and common descent — by means of blind watchmaker evolution — are not on equal footing.

  8. 8
    gpuccio says:

    VJ:

    I will not discuss the specifics of Swamidass’ article, Hunter’s criticism, your OP and Hunter’s reply just posted here. I would like just to discuss briefly the real problems which are IMO behind the whole discussion. We have already discussed those points in the past, and you certainly know my position (which is probably similar enough to yours). However, I believe that some aspects need to be restated once in a while.

    The whole problem, as we well know is common descent.

    Now, while trying to respect the positions of all involved, let’s try at least to be clear about the differences.

    1) Common descent in itself means simply that living beings share common ancestors. Universal common descent means that all living beings are supposed to share some common ancestor. The important point is the following: common descent in itself implies nothing about the origin of biological information in living beings.

    2) Neo darwinists usually conflate common descent with the neo darwinian theory about the origin of biological information,which is, according to their theory, RV + NS. In that sense, CD is a necessary part of their theory (it is really difficult to imagine how RV + NS could work without CD). But their theory is:

    CD + RV + NS and nothing else.

    IOWs, as they usually say, descent with modifications. Or, more precisely, descent with random modifications followed by natural selection as the only explanation of all biological information.

    3) The word “evolution” is usually used in the most ambiguous way, on both sides. Usually it means “the whole package” (CD + RV + NS and nothing else). Other times, it is used just to mean CD, or descent with modifications without any other implication. I strongly suggest that we try to avoid the unqualified word “evolution” in our debates, because that is one of the main causes of confusion.

    4) ID is the theory which requires design (the intervention of some conscious intelligent purposeful being) to explain biological information, at least in its complex forms. There may be different ID theories, but they should all include the necessity of design to explain complex functional information.

    5) It is probably true that many, maybe most, in the ID field, at least if we judge from what is posted here, reject both the neo darwinist explanation as a whole (CD + RV + NS and nothing else) and the idea of CD in itself. However, there are many exceptions, Behe and yourself and me among the others.

    6) Whatever position one chooses, the fact remains that ID theory and the rejection of CD are not connected.

    7) While CD is necessary for the neo darwinian theory, its rejection is absolutely not necessary for ID theory. Indeed, I have always stated that CD is not only compatible with ID theory, but also a strong support to it. Indeed, almost all the arguments which I have made here for ID theory are based on the assumtpion of CD.

    8) That said, anyone of free to reject CD. There are certainly possible reasons to do that, and I will not consider those which depend on metaphysical or religious convictions. As usual, I will limit my discussion to the scientific aspect.

    9) The important point, however, is that the arguments against CD are completely different from the arguments against the neo darwinian theory about the origin of information. So much so that, as I have already said, I am firmly convinced that CD is the best assumption to falsify the neo darwinian theory.

    10) My personal opinion, many times expressed here, is that:

    a) The scientific evidence against the neo darwinian theory and in favor of ID is overwhelming.

    b) The scientific evidence for CD (not necessarily universal, and not necessarily in the specific forms which are believed today) is very strong.

    c) There are some scientific arguments against CD, or more probably against universal CD or against specific models of CD, which have some validity. However, IMO, it is difficult to deny that at present the explanatory power for observed data of any theory which completely rejects CD is rather weak.

    11) The really important conclusion is: rejecting CD is not the same thing as defending ID. The two things are not connected, and anyway, the arguments implied are completely different. Conflating the two things can only weaken the ID position: indeed, it’s rather obviously the favorite sport of neo darwinists. Therefore, I strongly invite all those in the ID field to accept or reject CD as they like, and to debate according to their conviction, but possibly not conflating the two problems or the arguments used to discuss each one of them.

  9. 9
    Origenes says:

    Swamidass: 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.

    This fails as a convincing argument for blind watchmaker evolution, because:

    (1). Blind watchmaker evolution cannot produce vitellogenin gene sequences.
    (2). The argument that vitellogenin gene sequences in human DNA are vestigial, is made wrt an area for which a scientific overall concept is lacking: embryo development.
    Sure, some details are discovered, but there is no overall naturalistic bottom-up explanation of embryo development that makes sense. For one thing developmental biologists have shown that membrane patterns, not encoded by DNA, play a crucial role in the embryological development of fruit flies.
    (3). Claims of vestigiality didn’t fare well in the past — e.g. here.

  10. 10
    Andre says:

    Dr Torley and Prof Swamidass

    I have a challenge for you, instead of making a case and explaining the similarities how about explaining the differences?

    Even if our genomes are 99% identical to chimp’s you still have to be able to explain the astronomical 30 000 000 base pair differences that became fixed in a very short 6 000 000 years.

    I am specifically interested in how the sexual reproductive systems managed to cope during these incredibly quick changes in such a short evolutionary timescale.

    Making babies is easy but the systems for sexual reproduction is extremely precise.

    P.S. Dr Torley why is it that these artistic impressions of our supposed ancestors are always created with human eyes? Like the one in your article?

    Here is another example

    http://i.dailymail.co.uk/i/pix.....34x475.jpg

    And another

    http://theresilientearth.com/f.....bustus.jpg

    And another

    http://www.dkfindout.com/us/hi.....ol-makers/

    And another

    http://factsanddetails.com/wor.....m1491.html

    What’s up with that?

  11. 11
    Andre says:

    Dr Torley

    Please don’t tell me it’s gene duplication, because to hold it true you would have to agree with the notion that we are just the result of a huge amount of copy errors. Are we the result of a bunch of copy errors?

  12. 12
    lpadron says:

    I think as or perhaps even more important is the extension of olive branches from Torley to Hunter, Hunter to Swamidass, Swamidass to Hunter, Hunter to Torley, Torley to Torley, Hunter to Torley to Swamidass to Hunter, Swamidass to Ram Dass and Hunter to Swamidass back to Hunter to Torley back to Hunter followed by a swing pass to Swamidass who takes it in for the touchdown….

  13. 13
    Origenes says:

    Gpuccio: I strongly suggest that we try to avoid the unqualified word “evolution” in our debates, because that is one of the main causes of confusion.

    I second that. And I am confused about VJTorley’s position. What is implied when he speaks of an argument in support to the hypothesis of common descent? Does Torley mean in support of unguided blind watchmaker evolution?
    No, Torley does not mean that and that’s why he writes:

    VJTorley: Such a conclusion [common descent] is in no way at odds with Intelligent Design.

    Okay, but why does he write this:

    VJTorley: (…) it would be foolish to deny that the scientific evidence points clearly to our having shared a common ancestor with the chimpanzee.

    If humans and chimpanzees are designed, why would similarities “clearly” point to the existence of a common ancestor? It seems clear to me that it does not. What would prevent a designer from making a human from chimpanzee materials?
    Isn’t it obvious that similarities only point in the direction of a common ancestor if we assume blind watchmaker evolution to be true?
    If so, then why is Torley saying what he is saying?

  14. 14

    Andre,

    Against my better judgement, I will attempt a short reply to your question.

    “Even if our genomes are 99% identical to chimp’s you still have to be able to explain the astronomical 30 000 000 base pair differences that became fixed in a very short 6 000 000 years. I am specifically interested in how the sexual reproductive systems managed to cope during these incredibly quick changes in such a short evolutionary timescale.”

    Out of the gate, in what world is 6 million years a short time? That is an absurdly long time. Our subject understanding of what is short and long, anyways, is besides the point. It is really just a matter of math. Let me show you the formula.

    The basic pattern is that we multiply the number of generations between us and chimpanzees (by way of the common ancestor) times the number of mutations we see per generation along each leg. To be clear, we can directly measure the number of mutations we see per generation in human and chimps as a starting point, so we are not just pulling numbers out of the air. Of course generation time is more complicated, but for most of human history was probably less than 20 years. You get your basic estimates for all of these terms (easily obtained from the literature), and compute how many mutations you expect.

    You can work this the other way around. Using your numbers (which are a bit off), we can see that there are 2 * 6M -> 12M years of mutations between us and chimpanzees. There are 30M mutations, so that means we are seeing about 0.4 mutations per year. For generation times of about 20 years, we get about 8 mutations per generation, which is absurdly close to the experimentally determined generation mutation rate for humans (about 10 per generation). That is absurdly close for a “back of the envelope” calculation. Any discrepancies are easily explained by errors in your numbers, or slight shifts over time. Better formulas only improve on these results. Why did God make us this way?

    Does this mean that we have a common ancestor? Not exactly. When you add back in God, anything is possible. Still, somehow, He chose to create so that we look like we have a common ancestor. Why?

  15. 15

    Andre@10: Excellent comment. Whenever Darwinists bring up the genetic similarity between humans and apes (about 97percent), I challenge them to focus on the remaining three percent. That’s where the magic occurs. And, oh, what a difference it makes. Of course, they never have scientific answers for where that massive amount of new information came from, only broad, sweeping statements of faith based upon atheistic philosophical assumptions.

  16. 16
    gpuccio says:

    Origenes:

    I cannot speak for VJ Torley, but I don’t think that he means that CD is unguided. I believe that, like me, he conceives CD as designed CD.

    Why do you think that his sentence:

    “it would be foolish to deny that the scientific evidence points clearly to our having shared a common ancestor with the chimpanzee”

    is not compatible with both chimps and humans being designed? I find no contradiction.

    You say:

    “Isn’t it obvious that similarities only point in the direction of a common ancestor if we assume blind watchmaker evolution to be true?”

    Why? It does not seem obvious to me. A designer who acts on some existing species can certainly modify it by some form of biological engineering transforming it into another, new species. In that case, the new species is designed, but we can certainly say that the original species is an ancestor. IOWs, we have descent with designed modifications. But descent it is, anyway.

    I am always amazed that so many people think that the similarities are the real argument for CD. That’s not really true. Similarities can be explained quite well by both Common Descent and Common Design.

    It’s the differences which are the strongest argument for CD. Not the functional differences, which obviously can and must be interpreted as new design. But the neutral differences, the neutral variation in sequences which retain their functionality.

    That is the true strong argument for common descent. So many proteins remain similar throughout natural history, and yet we can observe growing divergence, neutral divergence, roughly proportional to the chronological separation between species. IOWs, proteins change because of neutral variation, as far as the change does not significantly affect their function.

    We see that happening in human populations. Different sequences which do not affect the functionality can be observed as variation or polymorphisms. Blood groups and HLA antigens are examples of polymorphisms in humans.

    That kind of genetic variation is inherited. Not only in in one species, but apparently also between species. And that is a very strong argument for common descent.

    So, to sum it up, when we compare the genomes, and especially protein sequences, between different species, we can find:

    1) Similarities, which are usually considered as a sign of conserved functionality, and which in principle can be explained as CD or as Common Design.

    2) Functional differences, which IMO are best explained as new design (while neo darwinists will try to explain them as the result of RV + NS).

    3) Neutral variation, which is best explained as CD.

    IMO, CD is very probably true, and the best explanation for what we observe. It is not necessarily universal, and it is probably different from any official model or tree of life. And, above all, it is designed Common Descent: the functional differences, those that make a new species, are designed. The similarities, and neutral variation, and even some forms of “errors” which are transmitted through evolutionary time, are the best signature of the physical connection and derivation of different biological designs.

  17. 17
    Origenes says:

    Gpuccio:

    Origenes: Isn’t it obvious that similarities only point in the direction of a common ancestor if we assume blind watchmaker evolution to be true?

    Why? It does not seem obvious to me. A designer who acts on some existing species can certainly modify it by some form of biological engineering transforming it into another, new species. (….)

    Suppose that here the existing specie is the chimpanzee and the new specie is us humans. That would fit the data, right? No need for a common ancestor.

    Gpuccio: (…) In that case, the new species is designed, but we can certainly say that the original species is an ancestor. IOWs, we have descent with designed modifications. But descent it is, anyway.

    Okay. But my point is that if a specie A has similarities with specie B, then this does not necessarily mean that it “clearly” points to the existence of a common ancestor, as VJTorley claims. Specie B can be an intelligently modified version of specie A, as in your example.

    To be clear, I object against:
    VJTorley: (…) it would be foolish to deny that the scientific evidence points clearly to our having shared a common ancestor with the chimpanzee.

  18. 18
    Cornelius Hunter says:

    gpuccio:

    ========
    It’s the differences which are the strongest argument for CD. Not the functional differences, which obviously can and must be interpreted as new design. But the neutral differences, the neutral variation in sequences which retain their functionality.

    That is the true strong argument for common descent. So many proteins remain similar throughout natural history, and yet we can observe growing divergence, neutral divergence, roughly proportional to the chronological separation between species. IOWs, proteins change because of neutral variation, as far as the change does not significantly affect their function.
    ========

    This point is commonly made in textbooks, and dates back many years. It reflects a theory-laden, evolutionary interpretation of the data, not a theory-neutral view. For example, you may be interested in these:

    https://sites.google.com/site/darwinspredictions/gene-phylogenies-are-congruent

    https://sites.google.com/site/darwinspredictions/the-species-should-form-an-evolutionary-tree

    https://sites.google.com/site/darwinspredictions/similar-species-share-similar-genes

  19. 19
    bill cole says:

    gpucccio

    Origenes:

    I cannot speak for VJ Torley, but I don’t think that he means that CD is unguided. I believe that, like me, he conceives CD as designed CD.

    Why do you think that his sentence:

    Since ID is an inference I think any claim about common decent is beyond the science. Common decent is a claim on how the change occurred i.e. the genome was a modified version of the chimp genome. How would we know this? What we observe is common biochemistry. Anything beyond this is pure speculation without evidence.

  20. 20
    gpuccio says:

    Cornelius Hunter:

    I am aware that there are inconsistencies in different trees. That can be a very good argument against the specific methods and assumptions about those trees, not necessarily against the general concept of CD.

    I agree that many of the concepts that are currently proposed are probably false. My point is simply that we can observe a lot of variation which seems reasonably neutral, and that some form of common descent remains the best way to explain that.

    I don’t know what your position is about that. Do you think that each species appeared designed from scratch? Do you think that neutral variation does not exist? Just to understand. I agree with you on many ideas, but I don’t really understand your position about CD.

  21. 21
    gpuccio says:

    bill cole:

    “Since ID is an inference I think any claim about common decent is beyond the science. Common decent is a claim on how the change occurred i.e. the genome was a modified version of the chimp genome. How would we know this? What we observe is common biochemistry. Anything beyond this is pure speculation without evidence.”

    I am not sure I understand your point.

    ID is an inference. Common descent is an inference. All empirical science is an inference.

    Some inferences are good, some are bad. IMO, ID is a very very good inference. Common descent is probably a good inference, at least with what we know at present. Neo darwinian evolution is a very very bad inference.

    You say:

    “What we observe is common biochemistry.”

    No, what we observe is especially common digital information, common sequences and patterns in sequences, characterized by both similarities and differences. As I have said, similarities and neutral variation are IMO best explained by some form of Common Descent. Functional variation is definitely best explained by design.

  22. 22
    gpuccio says:

    To all here:

    I am not really so motivated to defend Common Descent with all the people here who reject it. However, I have expressed my views and obviously I am ready to discuss them with anyone who is interested in the details.

    My main purpose here was to remind that the arguments for rejecting CD are completely different from the arguments for ID, a concept that many tend to forget.

    Just as an example of how CD is such a strong support for ID, I want to remind that all my examples about conserved function in natural history, and Durston’s method to assess functional information in protein families, all rely on the assumption that proteins undergo common descent and neutral variation. That’s why if a sequence is conserved between distant species we can infer that it is functionally constrained. If we reject CD, all those arguments lose their meaning, which is not good news for ID, IMO.

  23. 23
    bill cole says:

    gpuccio
    Here is what I responded to Joshua on Cornelius blog.
    S Joshua SwamidassMay 12, 2016 at 9:46 PM
    The article I wrote did not make any claims about mechanisms. It did not even argue that evolution was true. VJ get’s my article correctly. He is spot on.

    Bill ColeMay 13, 2016 at 10:01 AM
    Joshua
    Got it. “For me common decent is a misleading term because it came with the theory when the mechanism RMNS was assumed. You are claiming common biochemistry which is true but to round out the article differences must also be clearly examined and hopefully this debate will shake them out. While the DNA similarity is very true the splicing differences are the largest among all vertebrates…abstract below.

    The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
    Nuno L. Barbosa-Morais1,2, Manuel Irimia1,*, Qun Pan1,*, Hui Y. Xiong3,*, Serge Gueroussov1,4,*,
    Leo J. Lee3, Valentina Slobodeniuc1, Claudia Kutter5, Stephen Watt5, Recep Çolak1,6, TaeHyung Kim1,7, Christine M. Misquitta-Ali1, Michael D. Wilson4,5,7, Philip M. Kim1,4,6, Duncan T. Odom5,8,
    Brendan J. Frey1,3, Benjamin J. Blencowe1,4,†
    Author Affiliations
    ?†To whom correspondence should be addressed. E-mail: b.blencowe@utoronto.ca ?* These authors contributed equally to this work.
    ?????????????????????????????????????????????????+
    ??????
    ABSTRACT
    How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species- specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.”

  24. 24
    bill cole says:

    gpuccio

    My main purpose here was to remind that the arguments for rejecting CD are completely different from the arguments for ID, a concept that many tend to forget.

    I think this debate is important and I am grateful for Cornelius, Joshua and VJ engaging. I hope out of this we will get a clear definition of Common Decent because I think it has multiple meanings among those engaged in the ID evolution debates. I had a conversation with Michael Behe this weekend on the subject and am in agreement how he views this. Here is our discussion starting at 1:23. Salvador Cordova is also participating .https://youtu.be/hIy7BhVgPCs

  25. 25
    gpuccio says:

    Origenes:

    “Okay. But my point is that if a specie A has similarities with specie B, then this does not necessarily mean that it “clearly” points to the existence of a common ancestor, as VJTorley claims. Specie B can be an intelligently modified version of specie A, as in your example.”

    I do think that species B is an intelligently modified version so species A. Maybe it’s just a question of words, But let’s say that species A exists at time 1. Then, at some point, because of an explicit design intervention (which could be sudden or gradual, that’s not the point here), species B emerges from some component, or components, of species A. The time passes, and species B goes for its way, up to time 2. Let’s say that species A also go for its way, up to time 2.

    Now, at time 2, we have species B, which is clearly different from species A (because of design), and species A at time 2, which can be very similar to species A at time 1, or maybe have changed in some way (because of design, or simply of natural variation, that’s not important here).

    Now, I think we can correctly say that species A as it was at time 1 is a common ancestor of species B and species A at time 2, however different or similar this can be to the common ancestor.

    I think this is the meaning of “sharing a common ancestor).

    Of course, in many cases, the ancestor could be different from all its progenies, probably because of explicit different designs. For examples, ants and bees and wasps probably share a common ancestor, and it could well be that the old ancestor was neither an ant, nor a bee, nor a wasp, but something a little different, which was then engineered in three different directions.

    Do you have problems with such a scenario?

  26. 26
    gpuccio says:

    bill cole:

    Thank you for your comments.

    I want to be very clear. I absolutely agree that there are huge differences between species, even between those which have many similarities, and probably some common origin. That’s because design is there, everywhere, in huge amounts. Even one single new functional protein is a wonderful example of design, as I have always tried to show with detailed analyses which make a good use (I think) of the concept of Common Descent.

    I absolutely believe that those differences are complex, and that they must be explained by huge differences in information content, be it at genetic or epigenetic level, or anywhere else that we don’t understand.

    In that sense I slightly disagree with VJ that relatively small genetic differences can explain, for example, the differences between humans and chimps. But he is right in requesting that these ideas should find scientific confirmation in new levels if understanding. I am confident that they will.

    I absolutely agree that the concept of CD has been almost always conflated with the idea of unguided evolution, and that the consequences for science of that kind of ideological application have been and still are tragic. That’s probably the reason why so many feel the need to reject CD together with the theory of unguided evolution. That’s exactly the reason why I think it is really important to distinguish between the two things.

    You say:

    “I think this debate is important”. I think so too. And I am grateful for your very balanced contribution. I have not the time now, but I will certainly look at the discussion you linked. I am really interested.

  27. 27
    Cornelius Hunter says:

    gpuccio:

    ===========
    I am aware that there are inconsistencies in different trees. That can be a very good argument against the specific methods and assumptions about those trees, not necessarily against the general concept of CD.
    ===========

    If they are not good arguments against CD, then the question arises, does CD have any empirical content? More below …

    ===========
    I don’t really understand your position about CD.
    ===========

    Well it seems pretty clear to me that there are big scientific problems with CD. I’m talking about things like lineage-specific biology. Biology is loaded with one-off designs, all over the place. Species that otherwise are similar and adjacent on the evolutionary tree have all kinds of unique designs under the hood. CD just doesn’t work. If CD was vulnerable to the empirical evidence it would have been dropped, or at least acknowledged to be problematic. But CD does not seem to be vulnerable to the empirical evidence. The evidence has been viewed as rare anomalies and not normative.

  28. 28
    Origenes says:

    Gpuccio, thank you for the explanation. I have one more question wrt ‘common ancestor’.

    Gpuccio: Of course, in many cases, the ancestor could be different from all its progenies, probably because of explicit different designs. For examples, ants and bees and wasps probably share a common ancestor, and it could well be that the old ancestor was neither an ant, nor a bee, nor a wasp, but something a little different, which was then engineered in three different directions.

    Suppose that a sudden explicit design intervention takes place and a new specie, the sawfly, emerges from some components of the wasp. Suppose further that the implementation of this sawfly in nature is instant. Would you then say that ants, bees, wasps and sawflies share a ‘common ancestor’? Or would you argue that wasps and sawflies share a ‘common ancestor’, namely the wasp?

  29. 29
    Andre says:

    Thank you to all the people participating hopefully we can slug this out and everyone will walk away a little bit richer in understanding.

    I think I need to define my terms clearly, I am not opposed to CD but I simply do not find the evidence convincing enough and here is why.

    Firstly CD is a general assumption in biology that life arose on earth once, and that all organisms are related in some way. All good and well except; assumptions are not scientific evidence is it? Dr Craig Venter in his infamous video where he denied common descent said;

    “The tree of life is an artifact of some early scientific studies that aren’t really holding up…So there is not a tree of life.”

    The entire world has been trying to verify and acknowledge Darwin’s Tree of life which was his assumption in the first place!

    CD is evolutionary biology’s sacred cow or as William Dembski once said on these very same pages of Uncommon Descent

    “Common descent is the sanctum sanctorum of evolutionary biology.”

    I simply cannot help in remaining skeptical, because I don’t accept Darwin’s assumption.

  30. 30
    gpuccio says:

    Origenes:

    “Suppose that a sudden explicit design intervention takes place and a new specie, the sawfly, emerges from some components of the wasp. Suppose further that the implementation of this sawfly in nature is instant. Would you then say that ants, bees, wasps and sawflies share a ‘common ancestor’? Or would you argue that wasps and sawflies share a ‘common ancestor’, namely the wasp?”

    Well, I would say that wasps and sawflies share a common ancestor in the wasp (as it was at the time of the split, even if instantaneous).

    And if that “ancient” wasp was itself derived from a common ancestor of bees, wasps, and ants, then the sawfly too would have some connection with that older ancestor.

    You see, I look at the problem not so much from the point of view of species, but rather from the point of view of information and sequences. The important point is that sequences “travel” through different species retaining a physical continuity.

    Now, let’s say that some protein A, which was already present in the common precursor of ants, wasps and bees, is passed finally to the sawfly. The point is, neutral variation can happen in the sequence at different times. So, specific variations which were present in the wasp from which the sawfly derived will probably be observed in the sawfly and in wasps, but they could not be present in ants and bees. While other neutral variations which were already present in the common ancestor could be observed in all the lines derived from it.

    Of course it is not so simple, and there are problems, exceptions and often true enigmas. That’s why I think that the really important thing is not so much to have a final “tree of life”, but rather to understand the pathway of information in sequences. For us in ID, that is specially important, because what we really want is to understand when and how new functional information is added to the existing pool of genomes and proteomes. Our best chance to distinguish between non relevant (neutral or quasi neutral) digital information and functional digital information (designed information) is in comparing sequences between species and trying to understand their history.

    If we reject all forms of common descent, then how do we explain the differences in similar molecules in different species? I am convinced that some of them are functional, and I have defended that idea many times here. But frankly, I cannot accept the idea that all differences in similar sequences are functional, which is the extreme consequence of trying to explain everything by common design.

    We know that errors happen in biological reproduction. We know that mutations and variation are a constant component of the biological world. We know that many forms of variation are neutral. We know that many proteins are rather tolerant to many forms of variation, while others are not. We cannot deny those things, because we can observe them happening. And if neutral variation happens daily, then it must generate diversity in functional sequences.

    Therefore, part of the differences we observe must be due to neutral variation. And if those differences are grossly proportional to chronological separation between species (and believe me, that is generally true) how can you explain that simple fact, if not by the accumulation of neutral variation throughout natural history, by a physical continuity of species?

  31. 31
    gpuccio says:

    Cornelius Hunter:

    Thank you for clarifying better your position. I appreciate it.

    I have tried to detail better my ideas on the subject in my posts in this thread. However we may differ, believe me, my convictions are in no way due to any “acceptance” of traditional darwinian ideas. I think I can safely state that I am at least as critical of darwinism as you are, but sometimes in different ways. 🙂

  32. 32
    gpuccio says:

    Andre:

    I am not a fan of any tree of life, and even if a tree of life is accepted in principle, we are certainly very far from having any credible model for it. Even darwinists have completely different ideas about the tree of life and especially its rooting.

    I don’t even believe that life necessarily originated once. I have said many times that, while I accept the general principle of Common Descent, there is really no evidence that it need be universal. We know too little about OOL. My current idea is that life originated with some form of prokaryotes. I have said many times that in my opinion LUCA was also FUCA. But that is only a conjecture at present. We need more facts, and I am confident that more facts will come. But even darwinists accept that LUCA was not necessarily a single type of organism. A multicentric OOL, and multicentric development of species are a possibility, especially in a design paradigm. However, some form of Common Descent is IMO always a necessary inference, with the facts that we have at present.

    I respect your skepticism, even if I am not a great fan of the word, given the way it has been used in our recent culture. Regarding Darwin’s assumptions, I am not only skeptical about them: I reject them completely. As I have tried to explain, my acceptance of Common Descent is purely empirical and based on molecular data, and has really nothing to do with Darwin and his ideas.

  33. 33
    Eric Anderson says:

    gpuccio:

    Are you familiar with Paul Nelson’s analysis of the common descent issue, in particular his 2005 presentation in Helsinki, Finland?

    I’d be curious to know your thoughts about his approach.

  34. 34
    Cornelius Hunter says:

    gpuccio:

    In my experience, it is not that CD advocates are unaware of the contradictory evidence, it is that that evidence doesn’t matter. This raises the question of what exactly is their line of reasoning, such that they are not vulnerable to such evidence?

  35. 35
    vjtorley says:

    Hi everyone,

    I’m off to work in a few minutes, so I’ll have to be brief.

    First, I’d like to thank Professor Swamidass for his kind comments on my post. I appreciate his confirmation of the fact that he was extending an olive branch to the creationist community.

    Second, I’d like to point out that common descent is simply a hypothesis about ancestry. It does not say anything about the processes whereby we diverged from our ancestors. If Dr. Hunter wishes to point to unique designs found in various lineages, then he is welcome to do so. But that’s an argument for Intelligent Design, not an argument against common ancestry.

    Third, I do in fact believe that the process whereby humans arose from a chimp-like ancestor was an intelligently guided process. You just can’t get a magnificent organ like the human brain via a process of random mutations and natural selection.

    Fourth, I strongly believe that if you’re going to argue against common descent, then you need to make sure your arguments are up-to-date and scientifically watertight, and that they are telling arguments. Some readers have written about conflicting genetic trees. But if you look at the big picture, the vast majority point to us having the chimp as our closest relative. A few trees which focus on particular genes point to it being the gorilla instead of the chimp, but that’s hardly surprising, if gorillas diverged from the line leading to humans and chimps only a short time before humans and chimps split off from one another.

    Got to go now. I’ll be back later.

  36. 36
    vjtorley says:

    Hi everyone,

    Back again. For those who would argue that rates of fixation in the human line can’t be explained by the neutral theory of evolution, I should say that this was once my view, by I was forced to revise it when I examined the evidence. I discussed this on UD a couple of years ago in a series of posts. Here they are, from latest to earliest:

    http://www.uncommondescent.com.....-im-wrong/
    http://www.uncommondescent.com.....sor-moran/
    http://www.uncommondescent.com.....-fixation/
    http://www.uncommondescent.com.....-us-human/
    http://www.uncommondescent.com.....lles-heel/
    http://www.uncommondescent.com.....rry-moran/

    Enjoy!

    Re the white of the eye, or sclera: no-one is sure when it evolved, although some have suggested that it appeared when Homo ergaster/erectus arose in Africa.

    See this discussion:
    http://boards.straightdope.com.....p?t=427666

  37. 37
    Mung says:

    gpuccio:

    My main purpose here was to remind that the arguments for rejecting CD are completely different from the arguments for ID, a concept that many tend to forget.

    The arguments for accepting CD are metaphysical, while the arguments for ID are scientific.

    🙂

  38. 38
    mike1962 says:

    Interesting and thought provoking OP, Dr Torley. Thank you.

  39. 39
    Mung says:

    Just so we all know what we are debating:

    Joshua Swamidass

    Before summarizing the evidence supporting the common descent of man, I want to start with a story. This story is meant to reduce the fear some feel when encountering evidence that might contradict their understanding of the Bible.

    What does the Bible say about the origin of man?

    How does “the scientific consensus” differ from what the Bible says about the origin of man?

    How does “common descent ID” differ from what the Bible says about the origin of man?

    How does Swamidass address and resolve these questions?

  40. 40
    Mung says:

    Genesis 1:26-27 (ASV):

    And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the birds of the heavens, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth.

    And God created man in his own image, in the image of God created he him; male and female created he them.

    No mention of how man was created or from what materials man was created. So why are so many people opposed to the common descent of man?

  41. 41
    Peter says:

    I know the primary motivation in these blogs is just to talk ad nauseum, but truthfully, there is absolutely no evidence for any form of evolution. Evolution is the theory that every creature transformed from an earlier one. No one has ever evolved a species B from species A using random processes. No circumstantial evidence has ever been shown to do this either. So obviously, primate to human evolution is just speculation. There is no valid scientific reason to argue it.

    Also, VJ, you can’t hold a candle to Cornelius. He is the world greatest evolutionary expert. He understands the science, philosophy, and flawed human nature. You are not fit to clean his sandals.

  42. 42
    Mung says:

    Swwamidass:

    Let us imagine that God creates a fully grown tree today, and places it in a forest. A week later, a scientist and a theologian encounter this tree. The theologian believes that God is trustworthy and has clearly communicated to him that this tree was created just a week ago. The scientist bores a hole in the tree..,

    Why on earth would the theologian believe that God has communicated to him that this tree was created just a week ago?

    Why would the theologian not take the same approach as the scientist?

  43. 43
    Mung says:

    Swamidass:

    The scientist bores a hole in the tree, and counts its rings. There are 100 rings, so he concludes that the tree is 100 years old. Who is right? In some senses, both the scientist and the theologian are right. God created a one week old tree (the true age) that looks 100 years old (the scientific age). Moreover, it would be absurd for the theologian to deny the 100 rings that the scientist uncovered, or to dispute the scientific age of the tree. Likewise, the scientist cannot really presume to disprove God. Instead, the theologian should wonder why God would not leave clear, indisputable evidence that this 100 year-old tree is just a week old.

    Did God reveal to the scientist that one ring means one year? Why would the theologian deny that there were 100 rings?

    Likewise, the scientist cannot really presume to disprove God.

    Great! The tree is one week old, God said so.

    Instead, the theologian should wonder why God would not leave clear, indisputable evidence that this 100 year-old tree is just a week old.

    The evidence indicates the tree is 1 week old. 100 rings = 1 week. The question is, what would leave clear, indisputable evidence that this 100 year-old tree is just a week old?

    Does Swamidass answer this question?

  44. 44
    Mung says:

    Swamidass:

    Let us imagine that God creates a fully grown tree today, and places it in a forest. A week later, a scientist and a theologian encounter this tree…the theologian should wonder why God would not leave clear, indisputable evidence that this 100 year-old tree is just a week old.

    Huh? It’s only a week old. God created this one week old tree with 100 rings.

  45. 45
    Andre says:

    Gpuccio

    So are we then in full agreement that CD is first and foremost an assumption?

  46. 46
    Andre says:

    Dr Torley

    I saw your short reply but please help me understand why apes in these artistic impressions have human eyes? How can we accept this assumption or speculation as true?

  47. 47
    Andre says:

    Gpuccio

    I just want to highlight that my use of the word skeptical must please not be conflated with the materialist version of intellectual dishonesty. Like I said I am not opposed to CD, I am not convinced by it. Our material friends use of skeptical is not the same.

  48. 48
    Andre says:

    Dr Torley

    What is meant by when Homo Ergaster arose? Is this via the process of gene duplication, aka copy errors?

  49. 49
    Origenes says:

    Gpuccio: You see, I look at the problem [common ancestry] not so much from the point of view of species, but rather from the point of view of information and sequences. The important point is that sequences “travel” through different species retaining a physical continuity.

    This interpretation of common ancestry appeals to me and it makes perfect sense to say that, those retained sequences you speak of, have ancestors. However, by the same logic, newly introduced sequences do not have ancestors — they are orphans. How does one square such unrooted new information with common ancestry?
    VJTorley doesn’t see it as a problem:

    If Dr. Hunter wishes to point to unique designs found in various lineages, then he is welcome to do so. But that’s an argument for Intelligent Design, not an argument against common ancestry.

    I don’t understand how unique designs are “not an argument against common ancestry”, because, by definition “unique designs” do not have an ancestral design. If common descent is to be taken as a context in which all sequences, designs and information make sense, then ‘orphan’ sequences, designs and information should not exist.

  50. 50
    gpuccio says:

    Mung:

    As you can easily see, I have not commented on what Swamidass says, because I am not really interested in arguments about how religious people should see this or that. I see little of scientific relevance is such discussions.

    Frankly, I am also not interested in olive branchs of any kind or in relational adjustments. I am only interested in science. ID theory is tha best explanation for biological information, period. The only olive branch I can conceive of is an admission of that simple fact.

    My only interest here was to clarify some aspects about the Common Descent issue, which as you can see remains a very “hot” issue for ID people. That I have tried to do.

  51. 51
    gpuccio says:

    Andre:

    “So are we then in full agreement that CD is first and foremost an assumption?”

    I think we can agree, if I specify better the meaning of words in my epistemological views about science.

    In brief, I believe that all empirical sciences are made of inferences about observed facts. We can call them hypotheses or theories, but inferences they are anyway. Only darwinists are so crazy to think that inferences can magically become facts.

    So, Common Descent is IMO an inference which can in some measure explain some oberved facts, and I have also tried to explain briefly what those facts mainly are (if I have time enough, I shall post something more detailed about that).

    Inferences can be good or bad, but they are never definitely true. All scientific inferences, even the best, can in principle be falsified by new facts.

    An inference is good when it explain rather well observed facts, and when at presnt there is no better inference to explain those facts. IMO, CD is at present the best explanation for those fcats I have mentioned, but no one is obliged to think so.

    In my view of science, no scientific theory, even the best, must necessarily be accepted by all scientists. There are physicists who don’t agree with the Big Bang theory, or even with quantum mechaniscs (Einstein was an example). They have their arguments, and they could be right. But at present, I would say that the Big Bang and quantum mechanics remain by far best explanations for many things.

    Science is not about final truths. It is about theories. Each person can and must decide for himself what theories he accepts as best.

    In that sense, constructive skepticism (IOWs, the faculty of motivated doubt) is a precious resource in science. Unfortunately, as you well understand, today the word skepticism has come to mean biased dogmatism (its logical opposite). But constructive doubt is a very good thing.

    But what do we mean with the word “assumption”?

    My answer is rather simple. Let’s take the example of CD. For me, CD is a reasonable inference, not as strong as ID, but rather good. Others can obviously disagree.

    Now, when we want to make new inferences, we often take some previous inferences and consider them as established (at least tentatively), so that we may base new reaosning and inferences on those premises. That is an “assumption”.

    For example, I assume CD when I make inferences about the functional information in proteins by their conservation through species. I have argued many times that the alpha and beta chains of ATP synthase are wonderful examples of functionally constrained sequences, and thereofer of design.

    Why? Because they are strongly conserved from bacteria and archaea to humans.

    The reasoning assumes CD and neutral variation, and very simply says: if these sequences have remained strongly similar throughout about 3.5 billion years of CD, during which they have been exposed, like any other sequence, to neutral variation, the only possible explanation is that they cannot change more than that, because changes are eliminated by negative selection.

    Therefore, they have a very high content of functional information (in the order of thousands of bits), and the oonly possible explanation of their existence is design.

    This whole reasoning has no meaning if I don’t assume CD and neutral variation.

    Again, I have tried to explain my views as clearly as possible.

  52. 52
    vjtorley says:

    Hi Origenes,

    Thank you for your comments. You write:

    I don’t understand how unique designs are “not an argument against common ancestry”, because, by definition “unique designs” do not have an ancestral design. If common descent is to be taken as a context in which all sequences, designs and information make sense, then ‘orphan’ sequences, designs and information should not exist.

    I understand “common descent” as a hypothesis about organisms, not as a hypothesis about genes or complex structures. I do not think that all of the complex structures found in the human body are necessarily modifications of structures found in other animals. And I do not think or all of the genes in our DNA are necessarily modifications of genes found in other animals. I find it quite plausible that the Designer (whom I believe to be God) created some new genes and some new structures in the human lineage, although I’m a lot more certain about us possessing new structures than I am about us possessing new genes. Most of the so-called “orphan genes” described in the literature are nothing of the sort, since they have 98% similar counterparts in chimps, as I discovered last year:
    http://www.uncommondescent.com.....an-beings/

    However, I’m quite sure that the human brain, which is the most complicated machine known to exist in the universe, was designed.

  53. 53
    vjtorley says:

    Andre,

    I believe that the ancestral species in the line leading to modern humans were designed by the Creator. That includes Homo ergaster. At least some of the beneficial mutations which led to this species were engineered. New information was thus inserted into the ancestral human genome by the Creator.

  54. 54
    vjtorley says:

    Andre,

    I suspect that artists paint our hominin ancestors with whites in their eyes (sclera) in order to make them look more intelligent (and more human-like) than they actually were.

  55. 55
    bill cole says:

    VJ

    Second, I’d like to point out that common descent is simply a hypothesis about ancestry. It does not say anything about the processes whereby we diverged from our ancestors. If Dr. Hunter wishes to point to unique designs found in various lineages, then he is welcome to do so. But that’s an argument for Intelligent Design, not an argument against common ancestry.

    We need a very clear definition of common decent. This idea is very fuzzy without RMNS as a mechanism.

  56. 56
    bill cole says:

    VJ

    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.

    I think your conclusion here is because you do not understand the complete biochemical picture, based on available evidence today. I believe that Cornelius does.

    IF YOU LOOK AT THE GENE TIMING AND SPLICING DATA YOU WILL SEE DIRECT CONTRADICTION OF YOUR CONCLUSION. MAKING YOUR CONCLUSION FROM DNA COMPARISON ALONE NOT COMPETENT SCIENCE.

  57. 57
    Eric Anderson says:

    bill cole @55:

    We need a very clear definition of common decent. This idea is very fuzzy without RMNS as a mechanism.

    Good point.

    When 99% of evolutionary scientists use or hear “common descent” it is understood to mean — assumed to mean — something that occurred by purely undirected natural and material processes.

    If someone is proposing “common descent” that does not occur by purely undirected natural and material processes, then fine. But they need to be clear about what they are proposing.

    As I understand gpuccio, for example, he proposes that there are infusions of information at various stages along the way — meaning, design interventions in the history of life — while there is some continuity of descent preserved.

    Fair enough.

    But, as you say, common descent without a proposed mechanism is “very fuzzy.”

    We might, for example, look at something like the Intel Pentium II processor and the Pentium III processor and note a lot of similarities, including a nice, obvious temporal development over time. We could rationally say that there is a “descent” relationship from II to III. But the key — where the rubber meets the road — is that there was an additional infusion of information, additional architectural parameters, additional functional integrated specified complexity that allowed II to “descend” and turn into III.

    In other words the Pentium III processor came about by design, not by “common descent,” at least not as that term is generally understood.

  58. 58
    vjtorley says:

    Hi Bill Cole,

    I’ve just had a look at the paper, The Evolutionary Landscape of Alternative Splicing in Vertebrate Species by Nuno L. Barbosa-Morais et al. (Science Vol. 338, 21 December 2012), which you cited above in support of your claim that gene timing and alternative splicing data contradicts common descent. A few excerpts:

    AS [Alternative splicing] detection is approximately twice as frequent in all analyzed primate organs as in the equivalent organs from mouse and other species (Fig. 1A and fig. S1). Moreover, there is an overall decline in AS frequency as the evolutionary distance from primates increases. These differences are significant (P < 10^?10, Mann-Whitney U tests), are robust to different methods of AS frequency detection, and are independent of the variability in AS detection rates between individuals within the same species (Fig. 1A and fig. S1). Genes with the highest AS complexity in human are significantly enriched in cytoskeleton-associated functions (P < 0.03) (table S1), which suggests that AS-directed diversification of the cytoskeleton may have been a driving force in the evolution of increased cellular complexity in vertebrate species…

    We next investigated the relative rates at which AS and GE [gene expression] have evolved. From pairwise comparisons of PSI values in homologous tissues, we observe an overall increase of PSI divergence from human with evolutionary time (Fig. 2A)…

    However, the overlap between sets of splicing code features used in a given pair of species decreases with increased evolutionary distance (Fig. 3C and fig. S12; see also below)…

    However, because our results also indicate that vertebrate splicing codes diverged with increasing evolutionary distance, and because specific subsets of AS events could not be reliably predicted using the splicing code, changes in trans-acting factors likely also contributed to evolutionary differences in AS.

    Exactly how does this falsify the hypothesis of common descent?

    You also write:

    What does it mean to share a common ancestor? Do you mean that there was a split 6 million years ago and we came about through natural variation. If this is true how would you account for all the novel proteins, epigenetic timing differences and the different alternative splicing sequences. How would you account for the 2500 AA difference in the length of the titan protein?

    No, I don’t think we came about through natural variation. Where did I ever say that? I’m quite happy to acknowledge that novel human proteins were engineered. All I’m saying is that the Engineer modified the genes of an apelike creature in order to produce us.

  59. 59
    vjtorley says:

    Hi everyone,

    As I see it, common descent is a hypothesis about material causes, not efficient causes. What it tells us is that whatever process gave rise to us and the information in our genome, the material which that process worked on and modified was the genome of an apelike creature. Simple as that.

  60. 60
    vjtorley says:

    Hi Eric Anderson,

    You write:

    When 99% of evolutionary scientists use or hear “common descent” it is understood to mean — assumed to mean — something that occurred by purely undirected natural and material processes.

    That’s not how I mean the term “common descent.” What I mean by the term is that humans and chimps share a common ancestor. That’s all.

    You write that common descent without a proposed mechanism is “very fuzzy.” It is vague, in the sense that it does not specify the source of new information. That vagueness is intentional: it’s a hypothesis about material causes, rather than efficient causes.

    You also write:

    We might, for example, look at something like the Intel Pentium II processor and the Pentium III processor and note a lot of similarities, including a nice, obvious temporal development over time. We could rationally say that there is a “descent” relationship from II to III. But the key — where the rubber meets the road — is that there was an additional infusion of information, additional architectural parameters, additional functional integrated specified complexity that allowed II to “descend” and turn into III.

    In other words the Pentium III processor came about by design, not by “common descent,” at least not as that term is generally understood.

    I entirely agree with your point about the infusion of information, and I believe this is what happened in the human line. But where your analogy breaks down is that computers don’t have babies, and primates do.

  61. 61

    Hello, a FAQ has been added to my original article that includes a response to Michael Behe’s contribution to this conversation. I hope this helps address your questions. In particular, thank you Bill Cole for raising this to Michael Behe’s attention.
    http://swami.wustl.edu/evidence-for-evolution

  62. 62
    Origenes says:

    VJTorley, thank you for your response.

    Torley: I understand “common descent” as a hypothesis about organisms, not as a hypothesis about genes or complex structures.

    It seems to me that common descent is foremost a hypothesis about how new species are introduced by the designer of life. According to this hypothesis, new species do not go directly from the designer’s lab to earth, but are instead introduced by being born out of somewhat similar species. An example of this is “the process whereby humans arose from a chimp-like ancestor”. How does one picture such an event? Am I correct to say that, according to this version of the common descent hypothesis, there were once at least two unfortunate human beings with chimp-like parents?

  63. 63
    bill cole says:

    VJT
    ,Thank you for your comments here. I truly appreciate them.

    Exactly how does this falsify the hypothesis of common descent?

    The alternative splicing differences makes new proteins which can account for the dramatic phenotypic differences. This shows a large biochemical divergence between man and chimps. Way beyond the differences between rats and mice. When you compare DNA sequences you are unconsciously spinning because that is just part of the story. I agree that if you define common decent as the change from one specie to another via a directed mechanism then we are in sync, but honestly I think that claiming knowledge of the design mechanism is wild speculation at this point. As Michael Behe said in our conversation the “how” of the design is beyond our current understanding at this point and he avoids these conversations.

  64. 64
    bill cole says:

    VJT
    Here is the other paper I discussed with Michael Behe.
    Evolutionary dynamics of coding and non-coding transcriptomes.

    Necsulea A1, Kaessmann H2.
    Author information

    Abstract

    Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.

  65. 65
    gpuccio says:

    Origenes:

    “This interpretation of common ancestry appeals to me and it makes perfect sense to say that, those retained sequences you speak of, have ancestors. However, by the same logic, newly introduced sequences do not have ancestors — they are orphans. How does one square such unrooted new information with common ancestry?”

    New genes arise in species. They are obviously designed. We still don’t know much on their origin, but it seems that at least in a number of cases they can arise from non coding DNA sequences.

    That is a very good argument for design and for CD at the same time. Let’s say that you have some non coding sequence in primates, and that in humans, through a final mutation, it becomes an ORF (and therefore a protein coding gene) with a specific function for the protein. There are examples like that.

    Now, is a sequence in an ancestor species has already much of the potential for the future protein coding gene, but still it is non coding, no kind of gradual RV + NS can be invoked: a sequence which is non coding cannot be selected for the functions of a protein which is still non existent. So, if the sequence of the non coding DNA gradually acquires the correct configuration to be able to code for a functional protein, and then, in a new species (for example humans) it is finally “released” as a protein coding gene by the final addition of a start codon, only design can explain that process. At the same time, CD between the ancestor and the final species must be true too, so that the sequence can be prepared in the ancestor and activated in the final species.

    New genes can also arise by transposon activity. Many genes have that kind of signature. Many times I have argued that transposons are perfect potential tools for protein engineering by a biological designer.

    Of course new genes could be written also “from scratch” in the new species. Even in that case, CD can still be true for the rest of the genome (the genes which are shared between the ancestor and the final species), while new genes can simply be added during the engineering process.

    In general, I prefer the scenario where new genes derive from existing non coding sequences, either by simple directed mutations or by transposon activity. There is already some evidence for that kind of process.

    For a recent paper about de novo genes, you can look at this:

    http://rstb.royalsocietypublis.....8/20140332

  66. 66
    mk says:

    hi guys. the vitellogenin protein have other function then making yolk. so even if it was functional in the human past it cant be evidence for a commondescent.

    the mice-rat different is also very easy to explain. we know for example that chimp is closer to human then orngutan from genetic prespective. but actually the orangutan is the closer to human from morphological prespective:

    http://news.nationalgeographic.....lated.html

    so closer genetic similarity doesnt mean a close morphology. ther is a different between variation and function.

  67. 67
    Eric Anderson says:

    vjtorley @60:

    What I mean by [common descent] is that humans and chimps share a common ancestor. That’s all.

    Share a common ancestor in the sense that they both descended from the common ancestor through a natural process of generation-to-generation reproduction and random chance changes accumulating over time? That would be the normal understanding of common descent.

    I agree with you that there must have been some outside infusion of information and, I would argue, not just a nucleotide tweak here or there, but some really fundamental complex specified changes. That is where the shorthand term “common descent” starts to break down, because presumably we would then mean that humans descended from some ape-like creature by the normal pathways of common descent, plus new information-directed design.

    But where your analogy breaks down is that computers don’t have babies, and primates do.

    Certainly no analogy is perfect, but it still raises an important concept. What is it that you image having babies brings to the table? What is it about having babies that can turn an ape-like creature into a human?

    Unless we are falling back on the tired evolutionary assertion that copying errors, mutations, random changes creeping in during reproduction, and the like can produce new functionally-integrated, information-rich organisms, then there is nothing special about ape-like creatures having babies that helps turn them into a human.

    Bear with me a moment while I try to better understand your position:

    Maybe what you are saying is that the claim of an unbroken chain of reproduction from an ape-like ancestor can help explain the similarities between chimps and humans, and at the same time we need an outside infusion of information to explain the significant characteristics that make us human?

  68. 68
    gpuccio says:

    To all:

    OK, here is a very simple example of what I mean by differences in similar proteins as evidence of common descent.

    Let’s take myoglobin, a globin with a definite function. Let’s look at it in vertebrates.

    The human protein is 154 AAs long. Here are the results of blast with 4 vertebrates which can be reasonably considered at increasing chronological proximity with humans in natural history. I am not assuming any refined tree here, just the simple fact that bony fish and birds and mammals and primates are in some gross sequence if compared to humans. Humans are primates, and primates are mammals. Both bony fish and birds are vertebrates but not mammals, and it is perfectly reasonable that bony fish are more ancient than birds.

    Now, let’s look at the blast results:

    Best hit in bony fish: Sarda chiliensis:

    bitscore 131;
    expect 5.00E-38;
    identities 71 (48%);
    positives 90 (60%);
    length 147;

    Best hit in birds: Acanthisitta chloris

    bitscore 248;
    expect 2.00E-82;
    identities 118 (77%);
    positives 135 (87%);
    length 154;

    Mouse:

    bitscore 264;
    expect 1.00E-89;
    identities 129 (84%);
    positives 141 (91%);
    length 154;

    Chimpanzee:

    bitscore 310;
    expect 3.00E-110;
    identities 153 (99%);
    positives 153 (99%);
    length 154;

    OK, I think that’s enough. The problem is, how can you explain the relative diversisty between fish myoglobin and human myoglobin (only 48% identity), and the gradual increasing similarity to the human form, up to the almost identity in chimpanzee?

    One could say that all those differences are due to functional restraint, but that is really unlikely: after all, the protein remains rather similar for structure and function. OK, there can certainly be some functional adjustments from species to species, and part of the diversity can be functional, but all of it? I really don’t think so.

    The best explanation is: the split between fish and mammals is older, and the protein we find in fish and the protein we find in humans have been subject to neutral variation for more than 400 million years. The functionally constrained part of the sequence has remained similar (which explains the strong 48% identity), but what could change has changed, in such a long divergence time.

    Compare that with the 84% identity with the mouse protein. The split between rodents and the ancestors of primates is probably about 80 million years ago.

    And, obviously, chimpanzee has a protein which is almost the same as humans.

    I insist that common descent and neutral variation remain the best explanation for such a pattern, in a protein which retains essentially the same structure and function. I am ready to discuss other explanations, if you have them.

    For clarity, I must say that I remain convinced that part of the observed diversity can be explained functionally, and can be designed. But definitely not all of it.

  69. 69
    gpuccio says:

    Eric Anderson:

    “Maybe what you are saying is that the claim of an unbroken chain of reproduction from an ape-like ancestor can help explain the similarities between chimps and humans, and at the same time we need an outside infusion of information to explain the significant characteristics that make us human?”

    I definitely agree with this statement.

    I would add the the claim of an unbroken chain of reproduction from an ape-like ancestor can help explain not only the similarities between chimps and humans (or any other couple of related species), but also the differences due to neutral variation.

    It is absolutely true that we need an outside infusion of information (explicit design) to explain the significant characteristics that make us human (or that make any species what it is).

  70. 70
    Eric Anderson says:

    gpuccio @65:

    Let me start off by saying that I know you have looked into this issue in more detail than I and, coupled with the fact that I have a great deal of respect for your opinion, my inclination is to defer to you on this issue.

    If I may, however, perhaps I can articulate just a couple of points of intellectual unease.

    First, if new genes arise from non-coding sequences, are you suggesting that the nucleotide-to-amino acid sequence was already there and just became activated, or are you suggesting there was some kind of natural process whereby the coding sequence somehow came into proper formation (concatenation, accidental nucleotide changes, etc.)?

    Second, and more importantly, I think we all recognize that the traditional evolutionary story of random changes to DNA nucleotide sequences won’t cut it when it comes to turning an ape-like creature into a human. The idea that some new genes might suddenly arise is interesting, to be sure. But it is only one step removed from the old Darwinian storyline and, importantly, doesn’t address all the other required aspects. Having a new gene-coding sequence pop into my DNA is indeed impressive, but it won’t get me anywhere on the path to functionality.

    Specifically, I still need to have mechanisms that decide when to activate that gene, how much to produce, where to chaperone it to, how it will be used in the cell, and on and on. Furthermore, many (perhaps most) gene-products are primarily used in concert with others in larger complexes (one of the things Behe has been exploring the past decade).

    As a thought experiment, let’s make the conservative assumption that at least one difference between humans and chimps requires a molecular machine as complex as a bacterial flagellum. Even if all the 40+ proteins popped into the DNA all at once, there is still an incredible amount of coordination, orchestration, planning, timing, and so on that are required before the morphological result can be realized (and before the molecular machine can be visible to natural selection).

    Just as horizontal gene transfer, co-option, and similar theories don’t help much to explain the origin of new organisms, the idea of new genes arising within an organism, from non-coding regions or otherwise, suffers a similar limitation.

    —–

    I agree there are some interesting data points in all of this and that we are just scratching the surface. I respect the viewpoint of those, including Behe, who argue for “common descent.” I try to pin down exactly what they mean, because based on the evidence I have seen to date, I remain highly skeptical that anything close to a purely natural process can be responsible for turning an ape-like creature into a human.

    Might there be some continuity across generations and even across species? Perhaps.

    But the need for design to get from A to Z is clear.

  71. 71
    mk says:

    hi gpuccio. you said:

    ” OK, there can certainly be some functional adjustments from species to species, and part of the diversity can be functional, but all of it? I really don’t think so.”-

    first. the histone h4 protein sequence havent change for about 1 bilion years. so it may be true that most of the aa sequence is functional. even in the dna level we know that a codon that code for the same amino acid can have other result in the protein regulation.

    2)the chytochrome b sequence have an absurd phylogeny that doesnt fit with evolution history. so does it mean that evolution isnt true in this case?

  72. 72
    bill cole says:

    VJT Eric Gpuccio

    THIS IS THE REAL ISSUE:

    http://www.ncbi.nlm.nih.gov/pubmed/15716009#

    Abstract
    The chimpanzee is our closest living relative. The morphological differences between the two species are so large that there is no problem in distinguishing between them. However, the nucleotide difference between the two species is surprisingly small. The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species. Still, the number of proteins responsible for the phenotypic differences may be smaller since not all genes are directly responsible for phenotypic characters.

  73. 73
    vjtorley says:

    Hi mk,

    Thank you for your posts. You suggest that the orangutan is closer to human beings than the chimp is, morphologically, citing this article in support of your claim:

    http://news.nationalgeographic.....lated.html

    However, the article you cite dates back to 2009. More recent research with a much larger dataset of morphological characters indicates that the chimpanzee is the species most similar to human beings, morphologically speaking:

    http://onlinelibrary.wiley.com.....354.x/full
    http://onlinelibrary.wiley.com.....759.x/full

  74. 74
    vjtorley says:

    Hi Eric Anderson,

    Thank you for your post. You ask:

    Maybe what you are saying is that the claim of an unbroken chain of reproduction from an ape-like ancestor can help explain the similarities between chimps and humans, and at the same time we need an outside infusion of information to explain the significant characteristics that make us human?

    Yes. That is indeed my position. May I add that 22.4 million neutral mutations are believed to have taken place in the human line since it diverged from the line leading to chimps. These would on my account be entirely natural changes, and they represent 99.999% of the mutations that were fixed in the human line.

    The 340 beneficial mutations that are believed to have taken place in the human line during the same period represent only a tiny fraction (0.001%) of the mutations that were fixed in the human line, but it is these mutations that explain the important physical differences between humans and chimps. As I envisage it, many (but not all) of these mutations would have been intelligently directed.

    I would also wholeheartedly concur with gpuccio’s comments in #68 and #69 above.

  75. 75
    vjtorley says:

    Hi Bill Cole,

    Thank you for your post, citing an article by Glazko, G., V. Veeramachaneni, M. Nei, and W. Maka?owski, “Eighty percent of proteins are different between humans and chimpanzees” (Gene 346 (2005 Feb 14): 215-9).

    I googled its title and came across a commentary on the article at the pro-evolution Website:

    http://www.evolutionarymodel.c.....oteins.htm

    The commentary makes a couple of important points:

    The publication does not say that “80% of our [proteins] do not exist in apes;” rather it says that 80% don’t have identical sequences of amino acids (big difference)…

    But the question that some creationists hope you won’t ask is how much different did they find those 80% of proteins to be? Answer: unexpectedly little…

    [The commentary includes a table showing the percentage of proteins showing 100%, 99%, and 98% sequence identity
    between humans and chimps for different functional categories. It appears that many chimpanzee proteins are at least 98% similar to human proteins – VJT.]

    So not only are 20% identical, but the 80% that are different are still so similar that much of the genetic basis for the phenotypic differences must be due to regulatory sequences and/or genes that have major effects.

    I hope that helps.

  76. 76
    Andre says:

    Wait a minute. … only 340 beneficial mutations explain the difference? I am not buying that. I am basing that on the Sexual reproductive systems alone. Try as I might to conceive of the posssiblity, it falls flat and again it’s because the Sexual reproductive systems, even those of our last common ancestor would have been too precise to allow what people are assuming. If I had a single example of a crockoduck I would be convinced.

  77. 77
    bill cole says:

    VJT I concur with you analysis

    So not only are 20% identical, but the 80% that are different are still so similar that much of the genetic basis for the phenotypic differences must be due to regulatory sequences and/or genes that have major effects.

    If there is only an average of 4aa differences per protein that is about 64000 adaptions. (.8x 20000×4) Lynch’s mathematical model runs out of adaptive resources at about 6 for neutral theory.
    ?
    I think the differences may be due to different splicing where exons are changed. It appears that phenotypic changes may be driven by splicing codes. The origin of these codes are unknown at this point. So if exons are shuffled the proteins may look similar but molded for different tissue types.
    Attached an article about splicing and its impact on evolution from MIT.

    Evolution: It’s all in how you splice it
    MIT biologists find that alternative splicing of RNA rewires signaling in different tissues and may often contribute to species differences.
    Anne Trafton, MIT News Office December 20, 2012
    ?

  78. 78
    gpuccio says:

    Eric Anderson:

    All that you say is very reasonable, and in no way it seems different to me from what I think.

    I will try to clarify better.

    “First, if new genes arise from non-coding sequences, are you suggesting that the nucleotide-to-amino acid sequence was already there and just became activated, or are you suggesting there was some kind of natural process whereby the coding sequence somehow came into proper formation (concatenation, accidental nucleotide changes, etc.)?”

    In the model I am proposing, and which already has some empirical support, what happens is exactly that at some point the nucleotide-to-amino acid sequence is already there, but is not translated because there are still a couple of adjustments missing, for example a start codon at the right place. IOWs, we have in some species a sequence of nucleotides which is non coding, probably not functional, but has the information potential to become an ORF if a couple of final “switches” are adjusted.

    In another species, which appears some time later, and which is “derived” from the ancestor species, that sequence appears as an ORF, is translated and generates a functional protein.

    Now, you ask: how could that sequence of nucleotide reach the information to become a functional protein coding gene, before it even could be translated?

    And the answer is: by design. A more or less gradual design prepares sequences in the non coding DNA so that in a future time they can become functional genes.

    This is a very strong model for design, if as I think it will become ever more supported by observations. Indeed, in such a model, NS cannot be invoked at all, because the sequence reaches its informational content before being even translated. Therefore, the right nucleotides must be in place before they can act through a symbolic correspondence to aminoacids through the genetic code. Therefore, to explain the functional information in the sequence, we have only two possibilities:

    1) Design

    or

    2) RV + sheer luck (Remember, NS cannot be invoked here).

    Guess which is the best explanation? 🙂

    Now, how can a non coding sequence be designed? My favourite possible mechanisms, as already said, are:

    a) Guided mutations

    b) Guided transposon activity

    Let’s go now to the problem of how we get to be humans. I perfectly agree with you. Humans certainly have some new genes, but IMO they cannot explain the huge informational jump in human organization, especially at the brain level.

    The problem here is that we understand so little of those famous “procedures” which, through complex epigenetic regulations, guide cell developmnent and the organization of cells, tissues, organs and body plans.

    The information for those procedures certainly exists, and in some way it is transmitted from cell to cell, from being to being. But where and how is it written?

    I insist that such information:

    1) Is certainly very complex. Neo darwinists love to believe that very complex functional arrangements, like a working nervous system of about 10^11 neurons and about 10^14 neuron connections, of which we understand almost nothing at present, can come out of a few simple mutations. I happily leave that kind of folly to them. I am certain that very complex procedures are necessary to organize such a result.

    2) Is certainly written somewhere in the cell, in some way. Otherwise, how could it be transmitted from cell to cell and from being to being?

    So, I believe that humans have a huge amount of new and specific procedural information in their cells (in the genome, or epigenome, or anywhere else). I believe that we still don’t understand where that information is written, and how, and therefore we cannot really understand what makes the difference between humans and chimps (or simply between any couple of different species).

  79. 79
    Origenes says:

    Gpuccio: Of course new genes could be written also “from scratch” in the new species.

    Those new genes won’t fit well with common descent (CD).

    Gpuccio: Even in that case, CD can still be true for the rest of the genome (the genes which are shared between the ancestor and the final species), (…)

    Of course. However the obvious problem is that CD is not true for new genes. CD as a context in which all sequences make sense fails — it simply cannot accommodate new sequences. And, mind you, the infusion of new sequences must have been MASSIVE since LUCA.

    Gpuccio: Let’s say that you have some non coding sequence in primates, and that in humans, through a final mutation, it becomes an ORF (and therefore a protein coding gene) with a specific function for the protein. There are examples like that.

    If I understand you correctly, the reasoning goes like this: the sequence was infused as non coding in an ancestor, so it doesn’t really count as infusion of new information and therefore we won’t have to reject the concept of CD. Please correct me if I’m wrong, but such attempts to push the problem back one step, seems to me like an elaborate attempt to square infusion of new information with CD.

  80. 80
    Andre says:

    Gpuccio

    Now, how can a non coding sequence be designed? My favourite possible mechanisms, as already said, are:

    a) Guided mutations

    And on that statement we are are in full agreement, this paper; http://www.ncbi.nlm.nih.gov/pubmed/22522932 has identified that there is evidence that mutations are not random, I particularly like the heading of the paper

    Evidence of non-random mutation rates suggests an evolutionary risk management strategy.

    Wallace was of course right and Darwin, clueless and if the mutation rates are not random its highly likely that the mutations themselves are guided as well.

  81. 81
    gpuccio says:

    mk:

    I will try to answer your two questions:

    1)

    “the histone h4 protein sequence havent change for about 1 bilion years. so it may be true that most of the aa sequence is functional. even in the dna level we know that a codon that code for the same amino acid can have other result in the protein regulation.”

    Histones are among the most conserved sequences in eukaryotes. That means that functional constraints here are extremely strong. IOWs, almost all the sequence is functional. But most proteins are much less conserved. Look for example at my nunbers for myoglobin, in post #68.

    It is true that synonimous mutations can sometimes have functional consequences, but that is not the general rule. Most synonimous mutations are neutral, and that’s why you find them in conserved proteins, and when you compute the ka/ks ratio in a very conserved protein, its value is very low.

    2)

    “the chytochrome b sequence have an absurd phylogeny that doesnt fit with evolution history. so does it mean that evolution isnt true in this case?”

    I have not studied that particular case, but I am sure that there are many molecules that contradict current models of evolutionary history. That can simply mean that current models of evolutionary history are wring under many aspects. I would not be surprised. Most “evolutionary histories” are built by assuming not only CD, but a lot of other things derived from the idea that unguided evolution is the origin of biological functional information. IOWs, they do not include design in their reasoning.

    I am certain that design is the principle behind all complex functional information in biology. Therefore, there is no surprise that theories which assume no design in biology reach wrong conclusions. But it’s not the assumption of CD that is wrong, IMO. It’s rather the assumption of unguided evolution.

  82. 82
    mk says:

    hi vjtorley. there is several problems with their paper. for example:

    “However, it cannot be denied that there are numerous similarities between Homo and Pongo in morphological, life history, physiological, behavioural and cultural traits If the currently accepted hypothesis of hominid evolution is correct, these similarities must either be symplesiomorphies (shared primitive characters), convergences, or erroneous observations”

    so when we see a phylogenetic-morphologic contradiction they may solve this by “convergent evolution”.

    they also cant explain other thing. for example:

    ” Grehan & Schwartz (2009) demonstrated that the human–orangutan hypothesis provides a more parsimonious biogeographical scenario than the human–chimpanzee hypothesis, and argued that this provides external support for their phylogeny”

    so it isnt so simple.

    more then that: we know that both gorila, chimp and orang are apes. when human isnt. so in general morphological terms chimp need to be more close to gorila or orang then human.

    even if we ignore all this points its still doesnt evidence for a commondescent. its just mean that similar morphology=similar genome.

  83. 83
    gpuccio says:

    Origenes:

    “If I understand you correctly, the reasoning goes like this: the sequence was infused as non coding in an ancestor, so it doesn’t really count as infusion of new information and therefore we won’t have to reject the concept of CD. Please correct me if I’m wrong, but such attempts to push the problem back one level, seems to me like an elaborate attempt to square infusion of new information with CD.”

    No, no! I must miss something about what you think. Why do you believe that “Those new genes won’t fit well with common descent”? I don’t understand. And why do you say that:

    “the sequence was infused as non coding in an ancestor, so it doesn’t really count as infusion of new information and therefore we won’t have to reject the concept of CD”

    No. It certainly counts as infusion of new information. The information will be activated later, but it is certainly infused before the activation.

    My simple point is that CD remains true. Windows 10 is “descended” from Windows 8, for example, even if massibe new information has been infused in the new version. But still, the programmers did not write everything from scratch. They took Windows 8 and re-wrote parts, and added new parts. But, for example, if there was a bug in some part of the software and it was not corrected or re-written, then you can find the same bug in Windows 10. That’s how you distinguish between two software products which are derived one from the other, and two which have been written in a completely independent way.

    CD just means that the designer works starting from what already exists, and re-uses part of what already exists, while transforming the rest, or just adding new parts. If the engineering takes place “in vivo”, by intervention on existing beings that reproduce, you have descent anyway, but it is guided descent.

  84. 84
    gpuccio says:

    Andre:

    I am happy that we agree on that. I love the idea of guided mutations, but I love even more the idea of guided variation through guided transposon activity. There is increasing evidence of transposon signatures in new genes.

  85. 85
    gpuccio says:

    bill cole:

    I am puzzled like anyone else by the apparent contradiction between phenotypic differences between humans and chimps (which are huge) and the small differences at nucleotide level. I have tried to comment on that in the last part of my post #78.

  86. 86
    gpuccio says:

    VJ:

    We have been making parallel discussions here, but I think we agree on many things. 🙂

    Just a question. I see from your post #74 that you accept the idea that 22.4 million mutations have probably taken place in the human line since it diverged from the line leading to chimps (and I can agree). But you also accept that these would mostly be entirely natural changes. So, you restrict the beneficial (functional) mutations to about 340.

    I ask: why? Isn’t it more credible, if we accept the intervention of design, that many more mutations are functional?

    After all, those numbers are derived assuming that no design intervenes. If you consider design as a true factor, then everything changes.

    Most of designed mutations would naturally be in regulatory networks, IOWs, in those parts of the genome that control epigenetic procedures. As we don’t know what those parts are, and how they work, those highly functional mutations would easily be classified as “neutral”, simply because they take place in parts of the non coding DNA whose function we don’t understand.

    I believe that many more mutations in humans are functional. And still even that is not enough, IMO, to explain the huge functional information which makes humans different from chimps.

    One of my recurrent points is that current theories definitely underestimate the diversity between species which is functional. Almost all diversity which is not in protein coding genes is usually interpreted as neutral.But species which are different must have different epigenetic procedures. And those procedures must be written somewhere. Information does not appear by magic out of thin air!

  87. 87
    Origenes says:

    Gpuccio: No, no! I must miss something about what you think. Why do you believe that “Those new genes won’t fit well with common descent”? I don’t understand.

    Because those new genes — genes written “from scratch” — don’t have ancestral genes.
    Are we talking past each other?

  88. 88
    gpuccio says:

    Origenes:

    Yes, maybe it’s only a verbal misunderstanding. For me CD means only that engineering happens in existing living beings, and that what is not re-engineered is transmitted from one species to another. That is more than enough to explain the molecular data I have mentioned.

    Of course, new information is added when the engineering takes place, either as transformation of what exists or as addition of new content. That new information can be added gradually or suddenly: that is not really relevant, and only future data could help answer that. However, when it is added, it becomes part of what is transmitted from that point on.

    So, we share genes with bacteria (for example the components of ATP synthase), and some of them retain high identity. Other genes appear in eukaryotes, and we share them with fungi, for example. Other genes appear for the first time in vertebrates. And so on.

    The point is: our beta chain of ATP synthase, 529 AAs, shares 334 identities with the corresponding molecule in E. coli, for a total of 663 bits of functional information conserved for billion of years. I don’t believe for a moment that the molecule has been re-written from scratch for each new species in 4 billion years. I believe that the molecule, with its functional information, has simply passed from one species to the other.

    The same comparison, made with S. cerevisiae (yeast), an eukaryote, gives 476 identities, 958 bits.

    The point is, even these extremely conserved molecules change a little with time, while retaining their function. And the change is grossly proportional to the separation in time between species, Isn’t that perfectly compatible with CD and neutral variation in time? How can we explain that differently?

    Of course, histone H3 appears in eukaryotes, and remains strongly stable up to humans:

    Histone H3 (136 aas): human to S. cerevisiae: 121 identities, 248 bits.

    Myoglobin, instead, as explained, changes very much just in vertebrates.

    Functional constraint and neutral variation are two forces constantly opposing each other. The field for that opposition is offered by some physical continuity of living beings (Common Descent).

  89. 89
    gpuccio says:

    mk:

    In my answer at post #81 I write:

    Histones are among the most conserved sequences in eukaryotes. That means that functional constraints here are extremely strong. IOWs, almost all the sequence is functional. But most proteins are much less conserved. Look for example at my nunbers for myoglobin, in post #68.

    It is true that synonimous mutations can sometimes have functional consequences, but that is not the general rule. Most synonimous mutations are neutral, and that’s why you find them in conserved proteins, and when you compute the ka/ks ratio in a very conserved protein, its value is very low.

    To prove my statement with facts, I have blasted Histone H3 human against yeast. Both molecules are 136 AAs long. As already said in post #88, the AA sequence in the two molecules is almost identical: 121 identities, 248 bits.

    I have performed a computation of the Ka/Ks value between the two molecules: the result is 0.009766106.

    Now, as you may know, a Ka/Ks ratio around 1 points to neutral variation. A lower value points to purifying (negative) selection: IOWs, the sequence is conserved, and synonimous mutations are more frequent than non synonimous mutations, because non synonimous mutations have probably been eliminated ny negative selection, while synonimous mutations, being usually neutral, are tolerated.

    Here the value is 0.0097, a very low value: that confirms that the sequence is highly conserved, as we already knew.

    But it also confirms that even in such a conserved molecule, synonimous mutations have indeed taken place: that’s why the value of Ka/Ks ratio is so low.

    In detail, the rate of non synonimous mutations (Ka) is 0.09766105, while the rate of synonimous mutations (Ks) is 9.999999.

    Those numbers prove that synonimous mutations go on even in extremely conserved sequences. That can be explained only by the fact that they are usually neutral.

    Remember, human vs yeast, we are discussing a probable time split of at least 1 billion years.

  90. 90
    Mung says:

    How does one picture such an event?

    How does one picture the subsequent diversification of life from a few animals which came off an ark after a global flood?

    Most creationists I know of accept at least some form of common descent even if they reject the idea that man and apes share a common lineage.

  91. 91
    Mung says:

    gpuccio:

    I insist that common descent and neutral variation remain the best explanation for such a pattern, in a protein which retains essentially the same structure and function. I am ready to discuss other explanations, if you have them.

    How can we test the claim that the differences are due to neutral mutations and that the identities are due to selection?

  92. 92
    Mung says:

    Perhaps we should cease to speak of common descent and speak of descent with modification. That might help distinguish the arguments, whether they are against shared descent or whether they are concerned with the means of modification.

  93. 93
    bill cole says:

    gpuccio VJT

    bill cole:

    I am puzzled like anyone else by the apparent contradiction between phenotypic differences between humans and chimps (which are huge) and the small differences at nucleotide level. I have tried to comment on that in the last part of my post #78.

    How much of a role do you think alternative splicing may play in this. According to the paper I recently attached the splicing codes were 30% different between the lowest level vertebrates and chimps and a 50% jump between chimps and man. Alternative splicing is an interesting “design” strategy to make large changes to proteins with a lot less code.

  94. 94
    bill cole says:

    Mung

    Perhaps we should cease to speak of common descent and speak of descent with modification. That might help distinguish the arguments, whether they are against shared descent or whether they are concerned with the means of modification.

    Very good point 🙂

  95. 95
    gpuccio says:

    bill cole:

    Alternative splicing is certainly an important factor. But the problem is: what controls alternative splicing?

    We often take alternative splicing for granted, but we need to understand how different forms of s proteins can have different functions, what guides cells to effect the correct splicing at the correct time, and so on.

    IOWs. the problem is always: what information guides alternative splicing, or other epigenetic strategies, like histone modifications, DNA methylation, and so on?

    In the end, most differences must explain how cell behave, how they differentiate, how they find their place and role, how they build macroscopic forms and body plans. And we still understand very little of all that.

  96. 96
    mk says:

    hi again gpuccio

    you said:

    “It is true that synonimous mutations can sometimes have functional consequences, but that is not the general rule. “-

    first- how we can be sure?

    secondly- about the h4 protein. i know about one experiment showing that we can delete a big part from the protein and it still remain functional. so it may not be conserve after all.

    3-i think about this example: according to evolution fly and mosquito split off about 250 my ago. fly generation is about less than one month. so even if one generation mean only 1 new mutation we will need only 10^8 month to change his entire genome. or about less than 10^7 years. so fly and mosquito are suppose to be different in about their entire genomes from each other. far from reality. it may be evidence that most of the dna sequence is functional and not neutral.

    last problem is that we cant know for sure how the original sequence look like. so we cant know what is the real Ka/Ks ratio unless we assume that evolution is true.

    also remember that about 30% of the genes between gorila and human are closer then chimp and human.

  97. 97
    gpuccio says:

    Mung:

    “How can we test the claim that the differences are due to neutral mutations and that the identities are due to selection?”

    The Ka/Ks analysis is a way. Look at my post #89.

    It is generally true that in functional protein coding genes non synonimous mutations are rarer than synonimous mutations.

    The classical explanation is that non synonimous mutations are “antagonized” by negative selection, at least when they affect the function of the protein. On the other hand, synonimous mutations are apparently mostly unaffected, and they are grossly proportional to the time separation between the molecules.

    I find that explanation perfectly reasonable, and I accept it. I am not aware of any convincing alternative explanation for that pattern.

  98. 98
    gpuccio says:

    Mung:

    Of course, I do believe that some of the differences are due to different functional requests. That is exactly what is usually overlooked in traditional evolutionary reasoning.

    So, IOWs, when we compare two homolog proteins in two distant species, we can find:

    1) Identities and similarities, which must be interpreted as conservation of information due to functional constraints (negative, purifying selection).

    2) Neutral differences, which can be generically divided into:

    2a) Synonimous mutations in the gene, which do not modify the AA sequence in the protein, and are assumed to be neutral (with some exceptions)

    2b) Mutations which do affect the AA sequence in the protein, but which are probably neutral because they do not really affect the structure and function of the protein itself.

    3) Differences which correspond to different functionalities in the two species.

    Now, while it is certainly easy to evaluate 1) and 2a), it is really difficult to differentiate between 2b) and 3). IMO, most of 3) is usually conflated with 2b), as I have tried to argue in my post #86 to VL.

    In my past OPs, I have also tried to argue that regulatory proteins, or regulatory parts of proteins, are more likely to change greatly even between not so distant species, and probably contribute to different regulatory procedures: see for example my OPs about prickle protein.

    Proteins which have more a “final effector” role are more likely to remain similar for the functional part, and to change mainly because of neutral variation (2b). That should be the case for myoglobin, for example.

    You can easily understand that I believe that variation of the 3) kind is the most interesting for us, and is very reasonably designed.

  99. 99
    bill cole says:

    gpuccio

    We often take alternative splicing for granted, but we need to understand how different forms of s proteins can have different functions, what guides cells to effect the correct splicing at the correct time, and so on.

    IOWs. the problem is always: what information guides alternative splicing, or other epigenetic strategies, like histone modifications, DNA methylation, and so on?

    Yes:-) The codes are not well understood and therefore this transition is not well understood yet we claim common decent? Aside from DNA similarities this is looking like the most dramatic transition if you look at alternative splicing data and timing data in all vertebrate evolution.

  100. 100
    gpuccio says:

    mk:

    I appreciate your arguments. Here are my answers:

    “first- how we can be sure?”

    In science we are never sure. We just try to choose the best explanation with what we know. That is an essential part of my scientific epistemology. See my post #51.

    “secondly- about the h4 protein. i know about one experiment showing that we can delete a big part from the protein and it still remain functional. so it may not be conserve after all.”

    I definitely disagree with that conclusion. I know that paper. You cannot really evaluate functionality in those terms. True functionality is proven in the wild, and in long times. The paper you refer to, IMO, does not prove in any way that the conservation of histone sequence is not due to functional constraints. If you give me the reference for it again, we can discuss the paper in more detail.

    “3-i think about this example: according to evolution fly and mosquito split off about 250 my ago. fly generation is about less than one month. so even if one generation mean only 1 new mutation we will need only 10^8 month to change his entire genome. or about less than 10^7 years. so fly and mosquito are suppose to be different in about their entire genomes from each other. far from reality. it may be evidence that most of the dna sequence is functional and not neutral.”

    I definitely agree with you on that. I do believe that most of the genome is functional. But, at the same time, much of the functional genome is tolerant to some variation. We have good evidence of that in proteins, even in human proteins, for example in polymorphisms which do not affect function or cause disease, which are very frequent.

    Neutral variation exploits that tolerance.

    In functional non coding DNA, that tolerance could even be greater.

    “last problem is that we cant know for sure how the original sequence look like. so we cant know what is the real Ka/Ks ratio unless we assume that evolution is true.”

    This reasoning is not epistemologically correct, IMO. I would reason this way.

    We have a definite pattern of Ka, Ks and Ka/Ks ratio. That is an observable fact, and we have to try to explain it. That’s what science is about.

    Now, we look at the relationship between that pattern and other observable facts, or other reasonable inferences, like the classification of biological beings and what we reasonably know about natural history. We are making no special assumptions here.

    Then, we observe definite relations between the pattern of Ka/Ks and other informations, like the chronological times of appearance of species, or their collocation in some reasonable classification of species.

    To explain the data I have mentioned, we propose Common Descent and neutral variation. We are not “assuming” evolution, whatever you mean by that word. We are explaining observed facts with a theory. Which is exactly what science should do.

    “also remember that about 30% of the genes between gorila and human are closer then chimp and human.”

    I have no special idea about the relationship between gorilla and humans as compared to chimp and humans. I don’t even consider it a very important issue, and it is certainly an issue about which I know very little.

    I know form my experience at blasting proteins that primates have definitely the highest protein homologies with humans. That is very difficult to deny. I accept that we are more related to primates than, say, to rodents, or even more to bony fishes, because the molecular evidence is overwhelming. And each time I have tried a Ka/Ks analysis, I have found results perfectly compatible with the gross natural history as we understand it.

    I have no doubts that if one tries to go more into details, more difficulties arise. That is perfectly natural.

    But, to prove my point, I only need the results that I can get from scenarios where the difference is more significant and easy to observe. Remember, my purpose is to show the reasons to believe in Common Descent and neutral variation in a strong ID perspective, not to build a precise tree of life. I am not interested in that.

  101. 101
    gpuccio says:

    bill cole:

    I have tried to explain why I accept CD (not “claim” it) as a reasonable explanation. The transition from apes to humans is certainly one of the most difficult issues. For me and my arguments, it is not more important than any other transition in natural history, but I can understand the importance it has for other reasons.

    If you prefer to think that the apes-humans transition is special, I have no problem with that. I think that too, but the “special” for me is linked to other considerations, and not in particular to the problem of CD.

    However, my reasonings about CD are motivated by the whole scenario of genomes and proteomes throughout natural history, and they do not depend particularly on the apes-to-human transition. If it were shown that for some reason that transition is an exception, I would still accept CD as a general principle of biological design.

  102. 102
    gpuccio says:

    Mung:

    Descent with designed modifications is very good for me! 🙂

  103. 103
    bill cole says:

    Hi gpuccio

    If you prefer to think that the apes-humans transition is special, I have no problem with that. I think that too, but the “special” for me is linked to other considerations, and not in particular to the problem of CD.

    I am trying to get scientific clarification. The public has been lead to believe that this transition by understood natural means is a fact. Based on our discussion I think that you agree this is not at all a fact and almost certainly wrong. I think CD became a confusing term once we no longer considered RMNS the driver of evolutionary change.
    I applaud Mung’s attempt to clarify and your subsequent agreement 🙂

  104. 104
    gpuccio says:

    bill cole:

    I agree. Please, consider that I am a convinced defender of biological ID in its strongest form: for me, RV + NS cannot explain even a single functional protein, least of all a new species, least of all humans! 🙂

    Anything which exhibits more than 150 – 500 bits of digital functional information (we can discuss the safest threshold) is IMO designed.

  105. 105
    Dionisio says:

    Very interesting discussion.
    Keep it up!
    🙂

  106. 106
    Dionisio says:

    gpuccio @95

    Alternative splicing is certainly an important factor. But the problem is: what controls alternative splicing?

    We often take alternative splicing for granted, but we need to understand how different forms of s proteins can have different functions, what guides cells to effect the correct splicing at the correct time, and so on.

    IOWs. the problem is always: what information guides alternative splicing, or other epigenetic strategies, like histone modifications, DNA methylation, and so on?

    In the end, most differences must explain how cell behave, how they differentiate, how they find their place and role, how they build macroscopic forms and body plans. And we still understand very little of all that.

    Excellent point.

  107. 107
    Dionisio says:

    gpuccio @100

    True functionality is proven in the wild, and in long times.

    Yes, for example, as I’ve mentioned this before, if they’d get rid of all the small TV screens attached to the back of the seats in economy class in some airliners long routes, the airplanes will still fly well.
    Hence, one could safely conclude that those TV screens are completely unnecessary to fly the airplanes. But do they make a difference in the airliner’s business regarding the services and conveniences they offer compared to their competition?
    Those TV screens have no functionality as far as the airplanes’ flying mechanisms are concerned, but they make a difference in the airliner’s business.
    However, how can we test that? Definitely not by just flying the airplanes. Maybe they would need to see how business goes during some time after the removal of that stuff from the cabin seats? Hence the test would have to be done in the real environment and for some time. Maybe then the experts could see if the removed artifacts were functional or not for the passenger’s comfort and satisfaction, specially compared to the competition.

    Could we draw some analogies with the biological systems?

  108. 108
    mk says:

    1)first about the histone protein. dr hunter post about this here:

    http://darwins-god.blogspot.co.....tones.html

    and if its true then why its so conserve?

    2)if we found that even synonimous mutations can effect the protein function- then the whole Ka/Ks ratio is in doubt.

    3)if most of the mutations are functional (like in my fly example)- then we cant consider those as neutral.

    4)you said:

    “We have a definite pattern of Ka, Ks and Ka/Ks ratio. That is an observable fact”

    again- how its a fact if we assume that the sequence have been changed during milion of years?

    5)you said:

    “I have no special idea about the relationship between gorilla and humans as compared to chimp and humans. I don’t even consider it a very important issue, and it is certainly an issue about which I know very little.”-

    its very important because its mean that many genes contradict the ka\ks ratio. if its was true that most of the bases are neutral then we predict that all the chimp genes need to be closer to human then gorila. because they represent the time they split off (aka neutral clock).

  109. 109
    gpuccio says:

    mk:

    I am not sure I understand all your points. Briefly:

    1) I have read that post by Cornelius Hunter. In this particular case, I really disagree with his conclusions. As said, if you are interested we can discuss the issue in more detail.

    2) No. The cases where synonymous mutations have detectable effects are rare, and the effect can be explained because of alterations in the translation rate. There is really no doubt that most synonymous mutations are neutral. They are so common: if they were not neutral, nothing could work in the protein world. They are common exactly for that reason: they are invisible to negative selection.

    3) It’s not that most of the mutations are functional. It is true that probably most of the genome is functional. Mutations are usually either neutral or deleterious. We know that well, even form human data. As I have tried to explain, neutral mutations are perfectly possible in functional DNA, because most of functional DNA has some tolerance to sequence variation, which is different from gene to gene.

    4) You ask:

    “again- how its a fact if we assume that the sequence have been changed during million of years?”

    I don’t understand what you mean. Ka/Ks is a measure that is done on existing protein coding genes, comparing their nucleotide sequence. It is an objective result, and as such it can be observed, The general pattern of those measures in the existing proteome is, again, an observable fact. There is no assumption here: you take the sequences, input them in your statistical software, and you get the numbers. What is your problem?

    You can debate the meaning of that pattern, not the pattern itself. If you have reasonable arguments about how to explain the pattern differently, I am here to listen.

    5) You say:

    “its very important because its mean that many genes contradict the ka\ks ratio. if its was true that most of the bases are neutral then we predict that all the chimp genes need to be closer to human then gorilla. because they represent the time they split off (aka neutral clock).”

    I have never said that most of the changes between chimp and humans, or gorilla and humans if you prefer, are neutral. Indeed, if you read my post #86, you can see that I argued with VJ, saying clearly that IMO many of those changes can be designed, and can affect regulatory procedures.

    The Ka/Ks ratio can be computed only in protein coding genes. Protein sequences are very similar in primates. In short evolutionary times (a few million years) even synonymous mutations are rare. I have not computed any Ka/Ks ratio between chimps, gorillas and humans. Have you any data about that which contradict the meaning of the ration itself? Can you give the references?

  110. 110
    mk says:

    about point 1)if the protein sequence havent realy changed (in the dna level)during one bilion years, then we can conclude that most of the mutations in this gene arent neutral. even for synonimous codons. do you agree with this conclusion?

    2)do you have a reference that those exmaples are rare and not common?

    3)you said:

    “Mutations are usually either neutral or deleterious.”-

    i think that most of them are actually deleterious. i show how in the fly example. if most of them was neutral then the fly genome need to be a lot more different then it is compare with the mosquito.

    4)you said:

    “Ka/Ks is a measure that is done on existing protein coding genes, comparing their nucleotide sequence.”-

    can you explain how? thanks.

    as for 5) after another thinking i think its not a good example. so lets focus in the other point above.

  111. 111
    jerry says:

    From what I understand the difference between chimps and humans are not so much in the genome but in control sequences in the genome and in epigenetics and their effect of what proteins get expressed.

    http://bit.ly/1TfR5Ha

    Despite our close genetic match with the chimpanzee, the human genome is radically different in its expression and radically different in its outcome. Though we share 98.7% of the same protein-coding sequences, the difference between our species is not in the 1.5% of the genome that codes for proteins, but rather in the 98.5% that controls their production. No other lineage has evolved as fast as ours, at least within the last 1.5 million years. The changes which differentiate us are primarily due to rapid changes in genetic control sequences. These changes involve every known class of control element, with the most profound changes found in the noncoding control elements shaping our neural system, especially the frontal cortex of the cerebrum. Further, the speed of the change is in large part due to the unique action of retrotransposons acting as “genetic engineers,” providing the raw genetic material selected in support of our cultural explosion. Although these are “natural” forces which we in part can understand, as Christians we should remember that they reveal what God ordained in eternity and realized through providence.

    This is published in a Christian science venue hence his reference to what God has ordained. I assume Wilcox’s analysis is fairly accurate and if so what led to these differences between humans and chimps?

  112. 112
    Davem says:

    Try taking any kind of ape or monkey you want, and through selective breeding, create something similar to a human being.
    Most of us would agree that it’s impossible, yet we are to believe that somehow nature did it on it’s own?

  113. 113
    jerry says:

    This is published in a Christian science venue hence his reference to what God has ordained. I assume Wilcox’s analysis is fairly accurate and if so what led to these differences between humans and chimps?

    This was written poorly as I was between other projects. It should be a Christian venue on science. It is ASA. Definitely not Christian Science.

  114. 114
    vjtorley says:

    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 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.

    Cheers.

  115. 115
    vjtorley says:

    Hi gpuccio,

    You asked me about the ratio of neutral to beneficial mutations:

    “After all, those numbers are derived assuming that no design intervenes. If you consider design as a true factor, then everything changes.”

    I may be wrong, but as far as I can tell, the calculation for the number of neutral mutations in the human line makes no assumptions regarding design. The number is calculated using the postulates of the neutral theory.

    If you can show me where the calculations assume no design, then of course, I’m open to changing my mind.

  116. 116
    Eric Anderson says:

    VJT:

    There have been a lot of comments since you responded, so I apologize if I’m missing an answer already given, as I’m just responding in order. You said:

    The 340 beneficial mutations that are believed to have taken place in the human line during the same period represent only a tiny fraction (0.001%) of the mutations that were fixed in the human line, but it is these mutations that explain the important physical differences between humans and chimps.

    Color me skeptical, but I am extremely skeptical of the proposition that 340 mutations turned an ape-like creature into a human. It just doesn’t pass a basic credibility test. The simple fact is that we have almost no hard evidence about what changes would be required to turn organism A into organism B. We simply don’t understand the engineering involved. But we do have some sense of the scale of the problem to build even one molecular machine. We also know that lots of information is involved in building an organism in addition to the raw DNA sequence. What we do know is that it is a massive engineering undertaking.

    What we further know is that at nearly every step of the way in this journey of discovery over the past 60 years the biological community has seriously and grossly underestimated the integrated, functional, information-rich complexity that is required to build even those machines that initially appeared to be simple.

    Until there is some real evidence — I’m talking molecular-engineering-based evidence, not scratch-the-surface-database-comparisons of selected aspects of some portions of DNA — until there is some real engineering understanding, any claim about what turned an ape-like creature into a human is little more than unsubstantiated speculation.

    As I envisage it, many (but not all) of these mutations would have been intelligently directed.

    Fair enough and reasonable enough. As a corollary, does that also suggest that we would not have expected 340 beneficial mutations within that timeframe, based on normal mutation rates?

  117. 117
    Eric Anderson says:

    gpuccio @78:

    Thank you for the additional thoughts and for a view of where you are going.

    Just as an aside regarding whether the new discovers you point to regarding gene formation will have any impact on Darwinian claims, the answer, unfortunately, is no.

    You note that the options are:

    1) Design

    or

    2) RV + sheer luck (Remember, NS cannot be invoked here).

    Quite true. Yet that has always been the case with almost everything Darwinian evolution claims to have produced. Behe’s whole point with irreducible complexity, after all, was to highlight the folly of relying on natural selection for incomplete and inchoate phenotypic features.

    But the Darwinists muddle on, and, in those rare instances in which they are not shooting the messenger they invoke all manner of absurd explanations: co-option, HGT, neutral mutations that later inexplicably poof into beneficial mutations, and so on. Each of these proposed “mechanisms” is just another form of blind, dumb luck.

    There are myriad molecular machines in biology that don’t have a chance of working without all their parts in place — up front, coordinated, and controlled. And, by definition, everything has to be in place and built and functioning before natural selection can even waive its magic and mythical wand over the scene.

    Yet none of these engineering and logical constraints slow the Darwinist imagination one whit.

    Chance did it.

    Luck rules the day.

    Stuff Happens.

  118. 118
    Eric Anderson says:

    Mung @92:

    Perhaps we should cease to speak of common descent and speak of descent with modification. That might help distinguish the arguments, whether they are against shared descent or whether they are concerned with the means of modification.

    Indeed, this is much of the disconnect — at least among design proponents.

    Among traditional evolutionary theorists the two words “common descent” very clearly mean “purely natural, unguided, undirected, purposeless, common descent.”

    I take it gpuccio, and if I understand him correctly, VJT (and Behe, for that matter), are talking about “descent with designed modification”.

    Other than Biblical literalists, probably most design proponents could get behind that at some level — or at least would be willing to consider it as a reasonable possibility.

    —–

    Edit: I see that gpuccio @102 and bill cole @103 beat me to it.

    Keen minds running in the same vein and all that . . . 🙂

  119. 119
    Eric Anderson says:

    Dionosio @107:

    You touch on a very important point, and one that is very relevant to knock-out experiments and other claims of non-function. It is possible to have many, many things that are functional, but would not be observed as functional in particular circumstances or over particular timeframes. Redundancies, correction mechanisms, functions not required in a particular environment, built-in workarounds that mask the effect of the lost function, functions that are available but not activated (the front-loading idea), and so on. Then we have the whole suite of nice-to-have-but not necessary-for-immediate-survival functions, as you highlight.

    Until we know what is actually going on in organisms — at an engineering level — any claim that X is non-functional rests on shaky ground.

    The history of evolutionary claims about non-functional organs, vestigal features, and so on, enjoys the very dubious distinction of being nearly always wrong in the long term.

    We might do well to adopt a stance of caution about similar claims of non-function as we delve into the molecular realm.

  120. 120
    Eric Anderson says:

    Davem @112:

    Most of us would agree that it’s impossible, yet we are to believe that somehow nature did it on it’s own?

    Of course. You just have to believe real hard.

    And don’t ask too many hard questions. 🙂

  121. 121
    Dionisio says:

    Eric Anderson @119

    Yes, you explained it very clearly. Thank you.
    Many biology research experiments must be done in vivo within real conditions through long time periods in order to reproduce valid situations, though that still doesn’t guarantee recreating all possible scenarios.
    Since so much data obtained from wet labs is available in the cloud, dry labs can process it using valid algorithms.
    Work in progress… stay tuned. 🙂

  122. 122
    Origenes says:

    Gpuccio: For me CD means only that engineering happens in existing living beings, and that what is not re-engineered is transmitted from one species to another.

    Thank you for clarifying. Do you hold that — with the exception of the first organism — all species/information/sequences are introduced by CD? Are e.g. the Cambrian animals introduced by CD?

  123. 123
    gpuccio says:

    mk at #110:

    “about point 1)if the protein sequence havent realy changed (in the dna level)during one bilion years, then we can conclude that most of the mutations in this gene arent neutral. even for synonimous codons. do you agree with this conclusion?”

    But the sequences do change at DNS level, because synonymous mutations can be observed there. If you look at my computation of Ka/Ks for histone H3, you can see that the rate of synonymous mutations is about 100 times greater than the rate of non synonymous, in a protein coding gene which is extremely conserved at the level of AA sequence. That is exactly the important point.

    2)do you have a reference that those exmaples are rare and not common?

    First of all there is the simple fact that, as said, we can observe a lot of synonymous variation in perfectly functional proteins.

    Of course we know that some synonymous mutations can affect function, mainly through alterations of splicing, translation and folding. There is great interest in that, especially for human diseases.

    However, the fact remains that most known genetic diseases are associated to non synonymous mutations.

    You can find a recent review about that here:

    http://www.ncbi.nlm.nih.gov/pm.....MC4253807/

    I quote a pertinent part:

    Most tools focus on coding SNVs rather than other SNVs

    Decoding the relationship between genotype and phenotype is a major challenge in genetics. In humans there are more than four million DNA differences between two random individuals.22,23 Because additions and deletions typically have stronger impact,24–26 and are selected against more often, ?80% of these differences are single nucleotide variations (SNVs).27–29 Over the entire human population, an estimated 81%30 to 93%31 of human genes contain at least one SNV. Although only a small fraction of variants are non-synonymous single nucleotide variations (nsSNVs), about 10,000 are found between two random individuals,27–29 and over 85% of known disease associations are culled from this important class of mutations.1 For this reason, methods for predicting the impact of SNVs have historically focused on the high-yield category of non-synonymous coding SNVs. The existence of disease-associated synonymous mutations32,33 and nocoding variations with effects on lincRNA,34 miRNA,35,36 and promoters37,38 has produced interest in other types of mutations as well, but different tools will be needed to analyze these types of variations and such tools are comparatively still new and untested.39–41

    Some synonymous mutations could act as weak deleterious events, for example as predispositions to diseases. In that sense, they could be considered “quasi-neutral”.

    “3)you said:

    “Mutations are usually either neutral or deleterious.”-

    i think that most of them are actually deleterious. i show how in the fly example. if most of them was neutral then the fly genome need to be a lot more different then it is compare with the mosquito.”

    I agree. But there is a lot of difference in those genomes, anyway. Probably neutral, but certainly also functional and designed. Otherwise, why would a mosquito be different from a fly?

    For example, I have blasted p53, an important transcription factor 385 AAs long in the fly, fly vs mosquito: there is only 35% identities and 52% positives in the AA sequence. That means that half the AAs are radically different. And yet both proteins are perfectly functional. And this is only the non synonymous variation. If we look at the synonymous variation, it will certainly be even greater, as expected for a protein which, however, is rather conserved (I have not done it because the process is longer, but if you want I can do it).

    More in next post.

  124. 124
    gpuccio says:

    mk:

    Your final question:

    “4)you said:

    “Ka/Ks is a measure that is done on existing protein coding genes, comparing their nucleotide sequence.”-

    can you explain how? thanks.”

    Yes. You have to get the nucleotide sequence of the two genes in the two (or more) species). It must be strictly the coding sequence. Then you have to align the two sequences. I do that with Clustal, a specific software.

    Then you import the alignment into some software which can compute Ka/Ks. I use the R module seqinR.

    This kind of software uses a rather complex algorithm, which evaluates sites in the sequence which are potentially “synonymous” or “non synonymous”, according to the potential effects of variation in that site. Then the rate of variation between the two sequences in non synonymous (Ka) and synonymous (Ks) sites is counted, and finally the rate of the two rates is the Ka/Ks.

    For a simple summary, here is the Wikipedia page about the subject.

  125. 125
    gpuccio says:

    VJ at #115:

    “I may be wrong, but as far as I can tell, the calculation for the number of neutral mutations in the human line makes no assumptions regarding design. The number is calculated using the postulates of the neutral theory.

    If you can show me where the calculations assume no design, then of course, I’m open to changing my mind.”

    The calculation assume no design, exactly because they are made using the postulates of the neutral theory, which does no consider design as a possible source of variation.

    If we consider the possibility of design interventions, everything changes.

    Indeed, any designed variation which takes place in parts of the genome whose function we don’t understand (especially regulatory parts) would be conflated with neutral variation in the classical neutral theory.

    Neutral theory can be more or less correct in explaining how true neutral random mutations can accrue, but certainly it cannot tell us anything about how many designed variations are present in a genome.

    For protein coding genes, we can have an idea of the introduction of new functional information looking at the appearance of new genes, or at the modifications of existing genes. But, in the apes-to-humans transition, we already know that the role of protein coding genes is limited, and that most of the difference must be related to different epigenetic regulations. Therefore, the design interventions which implemented the transition will be conflated with neutral variation, if we just apply the neutral theory.

  126. 126
    gpuccio says:

    Eric Anderson:

    “Yet none of these engineering and logical constraints slow the Darwinist imagination one whit.

    Chance did it.

    Luck rules the day.”

    I know, I know… 🙂

  127. 127
    gpuccio says:

    Eric Anderson:

    “Keen minds running in the same vein and all that . . .”

    Indeed! 🙂

    So be it: Descent with designed modifications!

  128. 128
    gpuccio says:

    Origenes:

    “Do you hold that — with the exception of the first organism — all species/information/sequences are introduced by CD? Are e.g. the Cambrian animals introduced by CD?”

    Very good question! I really don’t know, and probably we have not enough data to decide, at present. That’s what I mean when I say that CD needs not be universal.

    As I see it, the available facts on which we can reason are:

    1) While each complex functional transition (for example one new functional protein) can in general justify a design inference, there are a few events in natural history which are true “avalanches” of new functional complexity.

    They are essentially:

    a) OOL

    b) Eukaryogenesis

    c) The appearance of metazoa

    d) The rather sudden appearance of practically all basic body plans (Cambrian Explosion)

    Where c and d could be almost contemporaries, or slightly distant in time, according to the different views.

    There are certainly other examples. The Ediacaran explosion is very interesting and highly controversial, for example. The flowering plants explosion could be another example.

    Now, a theory of universal CD would be that, while OOL could have been a special event of very massive design implementation “from scratch” (which is my hypothesis that LUCA was also FUCA), the rest of design implementation was realized through descent with designed modifications. That is certainly possible.

    But it is also possible that, at least in the massive events of eukaryogenesis and/or metazoa development and body plan generation, the process could have been different again, for example multicentric and with components “from scratch”.

    The only important point which is more in favor of universal descent with designed modifications is that the greatest part of basic protein information (IOWs protein superfamilies) is already present in LUCA or appears during the further differentiation of prokaryotes, and a lot of that existing information is re-used in eukaryotes, and therefore in metazoa.

    The explosion of multicellular beings, too, is vastly based on molecular tools which are already present in single celled eukaryotes.

    At each stage, however, a lot of new original information appears.

    That’s what I can say.

    Future data will certainly help to reason better about these issues, as a true biological science based on the acceptance of design principles emerges.

  129. 129
    jerry says:

    I have a question.

    Are there any other organisms/species besides humans that developed primarily by control mechanisms and not by differences in coding regions?

    I am sure there are some with minor differences due to control regions but none as massive as humans are from any other primates.

    It is apparent that the main difference between humans and chimps in not due to protein coding regions but to differences in control of which proteins get expressed. These differences are massive while the differences in coding regions are small. How did these control regions arise? I don’t see how mutations etc could have done it without creating numerous sub populations with and without the various changes in control mechanisms.

    So are humans the only species (and thus unique), that arose due to the differences between it and other species due to developments in the coding regions. The question is why are humans unique and this is the real question that all of evolutionary biology is missing.

    We are so focused on variation in coding regions as the source of species differences while for humans this is minimal while the differences in control regions are massive.

  130. 130
    bill cole says:

    gpuccio VJ eric all

    The only important point which is more in favor of universal descent with designed modifications is that the greatest part of basic protein information (IOWs protein superfamilies) is already present in LUCA or appears during the further differentiation of prokaryotes, and a lot of that existing information is re-used in eukaryotes, and therefore in metazoa.

    The explosion of multicellular beings, too, is vastly based on molecular tools which are already present in single celled eukaryotes.

    At each stage, however, a lot of new original information appears.

    That’s what I can say.

    Future data will certainly help to reason better about these issues, as a true biological science based on the acceptance of design principles emerges.

    I completely agree with this:-) I look forward to working with everyone to help put this fascinating puzzle together.

  131. 131
    Eric Anderson says:

    VJT:

    I’m sorry to come back to this, but I really have to ask:

    Do you seriously think 340 beneficial mutations in DNA could turn an ape-like creature into a human, and 3000 beneficial mutations in DNA could turn a land animal into a whale?

  132. 132
    jerry says:

    Eric,

    Do you seriously think 340 beneficial mutations in DNA could turn an ape-like creature into a human

    From what I understand it is tens of thousands of differences. I suggest you read the Wilcox paper I reference to above. The differences are not in the protein coding regions but in control mechanisms. We should stop talking about the human and chimp genomes in terms of similarity and differences in the coding regions and start talking about the real differences between the two species. The coding region comparison is a red herring.

    http://bit.ly/1TfR5Ha

  133. 133
    mk says:

    thanks for your answers gpuccio. i will focus now in my main a rgument (also because of my english limitation i try to make it short).

    you said:

    “However, the fact remains that most known genetic diseases are associated to non synonymous mutations.”-

    true. but again- we cant know if most of the synonymous codons have some function or not. we know for sure that there is some meaning for some of them. maybe even for all of them. it will change the whole picture. even if synonymous mutation doesnt make a diseases it dioesnt mean that it doesnt have a function.

    you said:

    “Yes. You have to get the nucleotide sequence of the two genes in the two (or more) species). It must be strictly the coding sequence. Then you have to align the two sequences. “-

    the problem is that you need to assume that those species evolved from a commondescent (and therefore you c an know how the originial sequence look like). so we need to assume first that evolution is true. or you talking about species from the same kind?(family)

    by the way gpuccio, what do you think about ic systems? i think that its a very s trong argument against a commondescent. it will be interesting to discuss about it. i have some interesting points.

  134. 134
    bill cole says:

    Jerry gpuccio VJT

    http://bit.ly/1TfR5Ha
    Although I have had time to only skim, this paper is very interesting. An important read for everyone.

    VJT: it would be great to get Joshua’s detailed thoughts.

    gpuccio: your thoughts would greatly appreciated.

  135. 135
    bill cole says:

    Jerry gpuccio VJT

    This article by Richard Sternberg is also very interesting and relevant.

    https://shar.es/1dWBZA

  136. 136
    vjtorley says:

    Hi Eric Anderson,

    You ask: “Do you seriously think 340 beneficial mutations in DNA could turn an ape-like creature into a human, and 3000 beneficial mutations in DNA could turn a land animal into a whale?”

    I have to say (reluctantly) that I haven’t seen any rigorous quantitative argument yet as to why this could not be the case. I attempted to provide one in an earlier post at http://www.uncommondescent.com.....o-a-whale/ and I was forced to concede that “the Darwinian scenario for whale evolution won’t be overturned simply by calculating the number of morphological and physiological changes that would have been required.” I also wrote that if 100 organs (or systems) in the whale underwent transformation, and if “only” 30 mutations per organ were required during the evolution of the whale, then we would obtain a total of 3,000 (= 30 x 100), which more or less agrees with Professor Larry Moran’s estimate of a few thousand mutations.

    For human evolution, I’m guessing that 30 to 50 separate organs (or systems) underwent transformation, and that there were 10 mutations per organ, with these mutations occurring more or less in sync (due to intelligent guidance), making 300 to 500 mutations. But I could be wrong, of course.

  137. 137

    I’d be happy to join the conversation, but apparently I my comments are still being moderated on a lengthy delay. Can someone turn that off. I”m pretty sure I’ve demonstrated at this point that I will remain respectful of this with whom I disagree.

  138. 138
    jerry says:

    This article by Richard Sternberg is also very interesting and relevant

    Thanks for the link. Interesting coincidence.

  139. 139
    Eric Anderson says:

    VJT @136:

    Thanks for your reply.

    You talk about whole organs requiring transformation, which is definitely true.

    Let’s just step back for a moment and have a reality check.

    How many nucleotide mutations would be required to bring a single molecular machine — something like a flagellum or the Calcium pump — into existence?

    We have it on good evidence that evolution is unlikely to build even a single functional protein from scratch during the timeframe of the whole universe. So you must be proposing something much more modest than from scratch. Indeed, you must be proposing that essentially everything was already in the genome and in the extra-genomic domain beforehand, with the mutations just tweaking a toggle here or a switch there. Everything else must have been there beforehand, in nascent or dormant form: the required detailed nucleotide sequence, the signalling and control mechanisms to determine when and how much of the gene product to produce, the folding algorithms, the chaperoning information to get the gene product to the right place, all the other gene products, and molecules and machines to seamlessly incorporate the new gene product into a new function. All of that was ready and in place up front, just waiting for a handful of lucky mutations and — Ta Da! — we have a newly transformed organ.

    Could this take place? Do we have any examples from our own experience where a complex, integrated, functioning system can experience a significant state change from just a tiny initiator? Yes. It is called a switch. And the only way it works is if everything else required for the new state is already in place, up front, ready to go.

    This would be an extreme example of front-loading. Might it be possible? Yes, in theory it might. But we need to exercise extreme intellectual caution before jumping to such a conclusion.

    First, in addition to the lack of evidence for such near-complete front-loading in the alleged ape-human transition, evolution would — by very force of definition and how the random mutational aspects of Neo-Darwinian theory work — be anathema to such front-loading. There is simply no way evolution is going to produce a front-loaded complex functional system that is invisible to the hand of natural selection until, one happy day, it flashes into existence with the flip of a couple of switches.

    Second, we have no evidence for such a radical state change in an organ through a small number of mutations. At least none that I’m aware of. If you can point me to at least a few confirmed examples of an organ undergoing functional transformation via a handful of mutations, that would be helpful.

    Third, we need to clearly understand that the people you are relying on for these claims have absolutely no inclination toward invoking design in the process. They are under the completely unsupportable impression that a few tweaks here, a mutation or two there and, presto!, we have a new organism. This is the whole mentality of traditional evolutionary theory. And it is completely devoid of hard evidence. Actually, it is much worse than that. It is contrary to everything we know about what is required to build complex, functional, integrated, information-rich systems.

    Now we could whitewash the laughable chance-did-it story by proposing that the 340 mutations were “designed” and that the other aspects of the system were previously “designed” and placed in the ape-like ancestor through aggressive front-loading. That at least is a rational and coherent approach from an engineering standpoint. But we then need to be very clear that we are talking about extensive and pervasive design intervention, both before and during the ape-to-human transition, not the “common descent” by random chance changes that everyone else in the Darwinian community is talking about.

    —–

    Furthermore, I have a great deal of respect for your thinking on evolution and design generally, so it pains me to note the incredible cognitive dissonance on display with respect to what you think we should accept as proof.

    You say:

    I have to say (reluctantly) that I haven’t seen any rigorous quantitative argument yet as to why this could not be the case.

    Maybe not a rigorous quantitative argument as to what is required to transform a specific organ. That is because, as I keep pointing out, no-one has any idea how to build an organ. But we do know through careful analysis and long experience that building even a simple molecular machine (much less a whole organ) is a tremendously complex and detailed and information-driven process.

    Yet, at the same time, you are willing to accept:

    . . .if 100 organs (or systems) in the whale underwent transformation, and if “only” 30 mutations per organ were required during the evolution of the whale, then we would obtain a total of 3,000 (= 30 x 100), which more or less agrees with Professor Larry Moran’s estimate of a few thousand mutations.

    and

    I’m guessing that 30 to 50 separate organs (or systems) underwent transformation, and that there were 10 mutations per organ, with these mutations occurring more or less in sync (due to intelligent guidance), making 300 to 500 mutations. But I could be wrong, of course.

    Good grief! While you are demanding a “rigorous quantitative argument” from the skeptics, that is the level of the Darwinian analysis?!

    —-

    The proposal on the table from the Darwinists you are for some reason relying on in this instance is that I can take a land-dwelling organism and turn it into a completely different land-dwelling organism with 340 beneficial mutations. That is a remarkable claim. It is an amazing claim. Might it be true? Yes, as a matter of sheer logic, almost anything might be true. But it is an astounding claim, and the ones putting forth the claim are responsible for providing evidence and proof for their claim.

    Unfortunately, in this case you have turned logic on its head, going so far as to demand (on the other thread) that it is up to the skeptics to “prove it” that all this wondrous creative transformation could not be performed by 340 mutations.

    Why require 340 mutations? Let’s assume I think evolution is even more magical and can do it with 170 mutations. Do I then get to demand that people take my outrageous claim seriously unless they can provide a rigorous proof that my claim is false? Of course not. I would deserve to be laughed at and dismissed unless and until I can provide a rigorous quantitative argument for my claim.

    Well, if I am being too obstinate in my skepticism I am happy to be accused of being incredulous. So be it. That is far preferable to being so credulous that I’m willing to believe anything, no matter how preposterous.

    https://billdembski.com/documents/2002.12.Unfettered_Resp_to_Orr.htm

    —–

    Lastly, and I truly hope I have misunderstood your position here, the claim of 340 mutations seems to ultimately tie back to the idea that calculations suggest there could have been approximately 340 beneficial mutations fixed in the human line since the most-recent common ancestor. Sure. Let’s assume that is true. What does that tell us?

    Well, one approach — the most rational approach, based on everything we understand about biological systems — is to conclude: “That isn’t enough time. That won’t cut it. Something else fundamentally different must be going on.”

    The other approach — the approach taken by materialist evolutionists and the one you seem to have adopted, at least numerically, if not in spirit — is to conclude: “Well, then that must be what happened: 340 mutations from ape to human. Remarkable! It all happened with only 340 mutations!”

    It would be difficult to find a more blatant example of circular reasoning.

  140. 140

    I am a Christian and a theistic evolutionist.

    Just to be clear, I am happy to invoke design. I do it all the time. I think God designed us. I think He created us. I’m 100% sure of this.

    My divergence from the ID community is over science’s ability to prove design. I do not think science is powerful enough to detect evidence of design. Science is just too limited and faulty of an effort.

    Maybe I am wrong. I’m happy to be convinced. But you have to actually show me. A priori, I have a great deal of doubt because of the profound limitations of science.

    As a Christian, also, I have an explanation for this in theology. God reveals himself to us in Jesus, through the Resurrection, so He has no need to reveal Himself again 2000 years later to western scientists through subtle signatures in DNA. In fact doing so would likely distract from his primary revelation to us in Jesus. This traces back to God’s character that we see clearly at play in the Babel Tower. God reaches out to us, to make Himself known. Our attempts to reach Him without His revelation might even be insulting to Him, with the naive presumption that created humans might build a tower tall enough to reach the heavens. God is so much greater than our ability to reach Him. He wants to rely on Jesus, His effort, not science, to reach Him.

    For me, Jesus is enough for confident belief. What about you? Todd Woods says something similar http://toddcwood.blogspot.com/.....latry.html.

    That being said. I am open to being convinced by reasonable arguments. However, I am devoted to Jesus, not to science. My skepticism isn’t rooted in devotion to evolution, it is rooted in my understanding of science’s profound limits and my understanding of the Gospel.

    http://www.new-wineskins.org/b.....-swamidass

  141. 141

    Also, regarding the sternberg article. This is a great example of an “argument from ignorance” that is entirely unconvincing in science.

    http://www.evolutionnews.org/2.....32961.html

    He sees a pattern in DNA he can’t explain and imagines God at work. It is the imagined ignorance of the biological community that provokes this reasoning, but this is a weak argument. First, he does not have a good handle on what biologists know and do not know. Second, even we when we cannot explain patterns, in time we usually do.

    As scientists, we look at that his pattern and look for biochemical mechanism. With some knowledge of the biology to focus queries (with plausible hypothesis), it is actually quite easy to turn up verified hypothesis to explain this pattern. I’m not including them here, because my point is more about the style of argument then the science.

    Is it possible that there is pattern in DNA that clearly points to design? Yes. But how would we tell if it was a signature for design, and not just something that will be explained eventually? Science has no way of telling us this. This is a big reason why I doubt science could ever detect evidence for design.

    Now, of course, we in our non-scientific thinking can make some inferences. However, we are always on shaky scientific ground.

    As an actual biologist and Christian, it is quite frustrating to me when people stake their faith on obvious ignorance of biology, as if their personal ignorance was proof God exists. This seems like such a shaky ground. Why not focus on the Resurrection?

  142. 142
    gpuccio says:

    mk:

    “the problem is that you need to assume that those species evolved from a commondescent (and therefore you c an know how the originial sequence look like). so we need to assume first that evolution is true. or you talking about species from the same kind?(family)”

    No, I don’t think we have to “assume first that evolution is true”.

    It goes this way. We measure an objective property of two or more nucleotide sequences: we align them, and we look at differences, and we analyze those differences categorizing them as symonymous or non synonymous. As you can see, there are no assumptions up to now.

    Then we hypothesize that those differences could be the result of neutral variation + negative selection (especially in the case of homolog sequences which have more or less the same function in the different species examined).

    Then we analyze the rate of non synonymous to synonymous differences in the light of that hypothesis, and we observe that the hypothesis explains well the pattern we observe. Remember, the pattern of differences is objective, while the hypothesis is a possible explanation.

    We accept the hypothesis of descent and neutral variation in these cases because it explains well the objective pattern observed. Anyone is free to reject that explanation, but he has to provide some alternative explanation for the objective pattern observed, and that explanation must be convincing enough to at least compete with the “good” explanation we already have.

    The reasoning is the same, either we are discussion species of the same kind or more distant species.

    Of course this reasoning cannot be applied to molecules with new functions and new functional information. In that case, design is the only “good” explanation.

    “by the way gpuccio, what do you think about ic systems? i think that its a very s trong argument against a commondescent. it will be interesting to discuss about it. i have some interesting points.”

    I believe that most biological systems are IC. I think that that is a very strong argument for design. I don’t see why it is an argument against descent with designed modifications (which is how we will call CD from now on in an ID perspective). 🙂

    I am certainly eager to listen to your interesting points about that. Thank you in advance.

  143. 143
    gpuccio says:

    bill cole:

    Interesting article. In this moment I have not the time to comment about it in detail, so I will only discuss the abstract:

    Despite our close genetic match with the chimpanzee, the human genome is radically different in its expression and radically different in its outcome. Though we share 98.7% of the same protein-coding sequences, the difference between our species is not in the 1.5% of the genome that codes for proteins, but rather in the 98.5% that controls their production. No other lineage has evolved as fast as ours, at least within the last 1.5 million years. The changes which differentiate us are primarily due to rapid changes in genetic control sequences. These changes involve every known class of control element, with the most profound changes found in the noncoding control elements shaping our neural system, specially the frontal cortex of the cerebrum.

    Up to now, everything is fine. I absolutely agree.

    Further, the speed of the change is in large part due to the unique action of retrotransposons acting as “genetic engineers,” providing the raw genetic material selected in support of our cultural explosion. Although these are “natural” forces which we in part can understand, as Christians we should remember that they reveal what God ordained in eternity and realized through providence.

    Here I disagree:

    1) I believe that transposons are not “genetic engineers”. How could they? They are, instead, “genetic engineering tool”, used by some designer to implement new functional information.

    I have expressed this idea many times, and I express it again here. I believe that transposons are probably the most important tool used by the biological designer(s). There is already strong evidence for that. See for example the recent OP:

    http://www.uncommondescent.com.....evolution/

    2) They are not “natural forces”. They are designed tools.

    3) We can understand something of what they are, but certainly we cannot understand how they can generate functional information. If they were only the “natural forces” they are supposed to be, the result of their activity should be as random and destructive as for any other form of random variation. That is apparently not the case.

    4) I con’t know if they “they reveal what God ordained in eternity and realized through providence”. In a sense, everything that exists does that.

    But, from a scientific point of view, the only thing they reveal is the explicit intervention of one or more designers. In time and in space.

  144. 144

    One final point. Some of you have suggested using the term “descent with designed modifications” instead of “common descent.”

    From my point of view, in practice, these are nearly equivalent in science. Evidentially speaking, we expect DNA to be the same by both theories. So I am comfortable with you using that term. It essentially concedes that there is strong evidence for “common descent” while at the same asserting that, somehow, you believe God was involved.

    Now, I do not believe science can prove that involvement, and it is mystery to me exactly how God does His work in our history. But as a Christian, not a scientist, I would say it looks like creation-by-modification to me. Once again, this is just another common descent paradigm.

    I’m explaining this to tell you that I do agree with the approach you are taking with that terminology. Of course you want to make the case for design, but just telling scientists “I agree there is evidence for common descent, but design might also be needed,” is very helpful. It shows you have some intellectual honest and biological knowledge. Both these things, by the way, I think are you true of you.

  145. 145
    jerry says:

    Professor Swamidass,

    My divergence from the ID community is over science’s ability to prove design. I do not think science is powerful enough to detect evidence of design. Science is just too limited and faulty of an effort.

    My guess is that you do not fully understand the ID argument. It is never one of proof, but one of probable explanation. Also you will gets a very wide range of what people on this site hold, some of it based on science and reason and some of it on faith.

    You will be in high demand here since it is rare a knowledgeable commenter comes here and everyone will try to get a piece of you for their pet idea.

    This is a great example of an “argument from ignorance” that is entirely unconvincing in science.

    Is it? I would re read what Dr. Sternberg said. It sounds pretty reasonable to me. What he said was there was a remarkable coincidence. He has loads of qualification in evolutionary biology.

    The problem with universal common descent is that it reaches a real road block at the Cambrian Explosion. If the only evidence for UCD is DNA commonality, that is not a strong argument. What does UCD really mean then?

  146. 146
    jerry says:

    gpuccio,

    Here I disagree:

    I suggest you read the whole article. The changes are partially accomplished through transposons so it is a literary technique he is using when he calls them engineers. In the paper at the end Wilcox essentially does not know how it happened but as some point it was designed in. He implies that it could have been designed in at the creation of the universe though he does not say that specifically.

    I doubt you will disagree with anything he says. It is mostly a review article and one that completely undermines the conventional wisdom of chimp/human differences. From article

    And of all things, that ultimate genomic parasite, the transposon or jumping gene, looks like an agent of genomic engineering.

    That sounds like saying that many derived human characteristics are a matter of “untraceable” genetic “engineering” (mutations) for novel genetic combinations rather than due to the environmental selection of small variants.

  147. 147
    gpuccio says:

    Prof. S. Joshua Swamidass at #140:

    A brief answer.

    I will not comment on the religious ideas. I appreciate them, in part I disagree with them, but I am here only to discuss science,and that I will do.

    You say:

    “I do not think science is powerful enough to detect evidence of design. Science is just too limited and faulty of an effort.”

    Well, I disagree. Definitely. I share with you the concept of the limitations of science. Science is not a place for absolute truth. It has severe limitations. Agreed.

    But that is exactly its great power. Science must be humble, aware of its limits. But, if it is used correctly, and humbly, and with a sincere desire to understand what it is possible to understand, it is a great thing.

    And that is exactly the point: detecting design is exactly one thing that science can do, and do well!

    You say:

    “Maybe I am wrong. I’m happy to be convinced. But you have to actually show me.”

    I think you are wrong. I would be happy to try to convince you, and to actually show you why I believe what I believe.

    If you have the patience to listen.

    But where should I begin? From scratch? How familiar are you with ID theory?

    I have only one important warning: if it has to be, it will be a purely scientific discussion, about science and what science can say about this issue. No religious arguments allowed.

  148. 148
    gpuccio says:

    jerry:

    I will certainly read it as soon as I have a few minutes. As you can see, at present I am rather busy commenting here! 🙂

    However, if he admits that he does not know how that happened, that’s fine. I have my ideas, and I have expressed them.

  149. 149

    Jerry:

    I’m very familiar with ID arguments. I agreed with them for along time too. Working as a scientist changed my mind. Science is just very different, and much less intuitive, than I had been lead to believe.

    I say “proof” loosely, not as a taunt. Despite what you heard, science does not weigh evidence to find the most probable theory. Rather, as described by Owen Gingerich (christian and historian of science): science concerns itself with finding coherent explanations, and rather little with proof. The problem for ID, as I see it, is that it currently explains much less than common descent.

    I’m open to creation-by-modification, but this raises the theological question. I need a theological clear explanation of why God did not include disproving evolution in His design goals. Moroever, if this is not part of His design goals, why disproving evolution so important to the ID community? I cannot reconcile this theological puzzle. Maybe you can help.

    I am happy to communicate with thoughtful and polite people, even when I disagree. If you have an idea for an event, I would consider attending.

    About Sternberg…

    SINE distribution between species is a coincidence that is not random. Correct. That is the definition of a pattern. He makes a very week case that a mechanism to explain this does not exist. It turns out there are mechanism. It has a great deal of scientific info, but it is not a scientific type of thinking.

    With all due respect, of course. I’m sure he is a bright and knowledgeable guy. No animosity from me. His point is not even a little convincing. Especially after finding the articles that I did.

    You can see how this often plays out in, for example, Dr. Hunter’s argument. Though, Hunter is much more obviously and convinced in his ignorance…

    swami.wustl.edu/evidence-for-evolution#spatial

  150. 150

    Also, I would add that I have good relationships with many of the leaders of the ID movement. I imagine that is a surprise, but it is true.

    You are welcome to present anything you like. But if your main source of knowledge about this is the ID movement, you are not getting a good picture of what science is, let alone how to make a good science argument.

    Remember, with a few notable exceptions (e.g. Bradley and Behe), most of the ID movement is philosophers, lawyers, and lay people, making what they feel are intuitive arguments. Science, however, is anything but intuitive. It is one of the most non-intuitive activies I have ever encountered.

    But go ahead. Take your best shot.

  151. 151
    gpuccio says:

    Prof. S. Joshua Swamidass at #141:

    “Is it possible that there is pattern in DNA that clearly points to design? Yes. But how would we tell if it was a signature for design, and not just something that will be explained eventually? Science has no way of telling us this. This is a big reason why I doubt science could ever detect evidence for design.”

    I cannot speak for the Sternberg article, because I have not yet read it.

    However, the important point is that design detection by complex functional information is in no way an “argument from ignorance”.

    It is an argument based on positive and strong observations about what consciousness, understanding and purpose can generate, and the observable connection between those patterns and design.

    The inference of design is positive, and it is only supported by the negative demonstration that no alternative explanation has been proposed.

  152. 152
    bill cole says:

    Dr Swamidass

    From my point of view, in practice, these are nearly equivalent in science. Evidentially speaking, we expect DNA to be the same by both theories. So I am comfortable with you using that term. It essentially concedes that there is strong evidence for “common descent” while at the same asserting that, somehow, you believe God was involved.

    If you listen closely to my conversation with Mike Behe you will see when you mention god you are creating a straw man to the design argument. The argument is simply inferring design from the evidence. The “how” is not currently part of the argument. Using design in front of decent separates it from the neo darwinian theory to avoid confusion. Common decent implies RMNS as a mechanism to most people.

  153. 153
    gpuccio says:

    Prof. S. Joshua Swamidass at #144:

    “From my point of view, in practice, these are nearly equivalent in science. Evidentially speaking, we expect DNA to be the same by both theories. So I am comfortable with you using that term. It essentially concedes that there is strong evidence for “common descent” while at the same asserting that, somehow, you believe God was involved.”

    I am happy that you agree with that. The new “term” has essentially the purpose to overcome some resistance in the ID field from those who instinctively conflate CD with unguided evolution. For me, CD has always meant, in ID perspective, only descent with designed modifications, and nothing more.

    Just to remain scientific: my inference is simply that some conscious intelligent purposeful being (one or more designers) was involved. No inference about God. None at all.

    I agree with you that our ideas about God should come from other sources.

  154. 154

    And feel free to take your best shots at design arguments. I’m happy to read them. I’ll respond when it makes sense. Because of limited time, it will not be to everything.

  155. 155
    gpuccio says:

    Prof. S. Joshua Swamidass at #150:

    I am not sure if that is addressed to my comments. Could you please clarify to whom you are commenting?

    I am happy that you have good relationships with ID leaders. Why should that be a surprise? I don’t know you, and I have no idea of your personal relationships.

    I have been discussing ID from a purely scientific point of view here for years. I think many others have been doing that extremely well, for example Behe. I am a medical doctor, and I try to discuss almost exclusively biological issues here.

    I will certainly go ahead, but not immediately. For now, I have no more time available.

  156. 156

    #150 Was a composite response to everyone =).

    I’m glad you are not surprised that I am a friendly evolutionist. I get demonized pretty frequently…

  157. 157

    #152 to Bill

    I see the argument. That is just not how it works in science. That makes sense in philosophy, but that is not how mainstream science works. I think the design inference, at times, makes sense in philosophy. I support it, at times, there.

    In science it is another set of rules…we think about things differently. We care primarily about the how. You demonstrate the “what” by showing the “how.” This is the part that is missing from the ID argument. I understand it in philosophy, in science thought it makes no sense.

  158. 158
    mk says:

    hi gpuccio.

    you say:

    ” and we analyze those differences categorizing them as symonymous or non synonymous. As you can see, there are no assumptions up to now.”

    true.

    “Then we hypothesize that those differences could be the result of neutral variation + negative selection (especially in the case of homolog sequences which have more or less the same function in the different species examined).”

    here is the problem. we need to assume here 2 things: that those changes are neutral and that those sequences have been changed since the last ancestor of the 2. we can actually fit those evidence for a design model (for example: by claiming that those ” changes” are actually how the original sequence look like.

    but lets move on.

    “I think that that is a very strong argument for design. I don’t see why it is an argument against descent with designed modifications”-

    ok. its interesting. so you believe in a commondescent but also you believe that something like the flagellum evolved in one step?(theistic evolution). if so in this case we both agree besides i doesnt believe in a commondescent. why you accept a commondescen but reject creation de novo? i think that we have evidence that contradict this claim. it will be interesting to discuss it. for start: what kind of evidence will convince you that a commondescent isnt true? thanks…

  159. 159
    mk says:

    prof joshua, is the sine sequences are functional then its a design product and not evolution. i think that this is the original claim by creationists. its basic logic that if its functional then the designer put it in the same locus in different species.

    so id model explain those shared sine without any need for a commondescent.

    i also think that we can detect design very well. i know for example that if i will find a self replicating machine ( a ufo?)in other planet i can conclude that this machine was design.

  160. 160
    jerry says:

    Professor Swamidass,

    I still maintain that you do not understand ID. Your comments indicate this. For example, ID is not about disproving evolution whatever definition of evolution you use. ID is about finding the best explanation and if naturalistic evolution is improbable so be it. If it is feasible, so be it.

    The method of evolution is not an essential part of ID.

    As I said you will be inundated with comments from everybody. Good luck in trying to answer them.

  161. 161
    bill cole says:

    Dr Swamidass

    In science it is another set of rules…we think about things differently. We care primarily about the how. You demonstrate the “what” by showing the “how.” This is the part that is missing from the ID argument. I understand it in philosophy, in science thought it makes no sense.

    I think this a very reasonable comment. The issue is the “how” is not well understood in either case. Darwin used inference to the best explanation as his standard. Like you I prefer the scientific method but macro evolution has always used the inference standard. The “how” has never been validated experimentally. If we look at the origin of man, based on the inference standard, design is the best explanation for the novel DNA sequences, splicing sequences and timing sequences. There is no known natural mechanism (how) that can generate these sequences. The reality of the science here is way out sync with the public perception. I think this badly needs to be fixed. Unfortunately if this theory is held to the standard of the scientific method it becomes an untested hypothesis equivalent to the origin of life.

    You demonstrate the “what” by showing the “how.

    How do you think the theory of common decent does this without a mechanism?

  162. 162

    #160, great questions bill.

    Hunter makes an excellent foil here.

    He points out a pattern. I proposed a mechanism for that pattern. That mechanism is not only in the distant past, but also makes claims about how biological system function right now today. So we can go directly test this behavior to see for ourselves if the biological systems function this way. In fact they do. So now I’ve fleshed out part of the story, experimentally, not just with inference, of “how” common descent produced that pattern.

    Have we explained all the patterns this way? Absolutely not. We have, however, explained quite a bit. This are not “just so” stories. They are based on proven (as far as science proves things) understand of how biological systems behave.

    http://swami.wustl.edu/evidenc.....on#spatial

    This is a key point, and it shows how science progresses by testing and verifying the mechanistic explanations of patterns.

    The design argument does not follow this model. It does something different. It can’t really be placed in science, as I understand it. It could be correct, mind you. The resistance to interrogating specific mechanisms of design is a real challenge in science. Frankly, I’m not sure how we could even do the experiment.

    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.

    Design doesn’t work this way in science. It, all too often, becomes an argument to stop looking for a mechanistic explanation of the pattern. You see this play out with Hunter. He is so convinced the pattern is an unexplainable signature of design, that he does not even think of the obvious and testable mechanisms. Could one of the patterns we discovered and cannot yet explain be a signature for design, and entirely unexplainable by natural causes? Sure. But how do we know which one? This appears to be unknowable.

    Regardless, I don’t even agree with naturalistic macroevolution. No theistic evolutionist really does. That is why we are called “theistic.” I know, as a Christian, that God was involved. I just can’t prove it yet, and I’m not sure why that would be important to me any way. Remember, I already know God exists through Jesus.

  163. 163
    Dionisio says:

    Eric Anderson
    In addition to considering all the functional/structural changes required to change A into B, what about their developmental processes? Don’t they have to change too?
    Don’t the developmental mechanisms (regulatory networks, signaling pathways, etc) for A have to get transformed into the developmental mechanisms for B?

  164. 164

    Honest question here. I really am curious your answer. I’m not sure how you will respond, but I mean no disrespect.

    You all seem to care a great deal about science. You put a lot of time and thought into this. At the same time, it does not appear that you are science professionals. How did that happen?

    If you love science so much, why did you not seek out careers as scientists? (who knows, maybe you did?)

    You also seem fixated on evolution. Do you care about anything else in science? Why is evolution and intelligent design so important to you? Do you care about all the rest of science?

    Also, I assume most of you are Christians. But I never see you all talk about Jesus in science. How does He influence how you think about ID, evolution, and science as a whole? For me, He entirely reorders how I see everything, including science. Here on this website, however, He seems unmentioned and oddly irrelevant. I can’t get my head around that.

    I find this reality quite puzzling. I can’t really explain what I see here fully. Maybe you can pull the pieces together.

  165. 165
    jerry says:


    You also seem fixated on evolution. Do you care about anything else in science? Why is evolution and intelligent design so important to you?

    I find this reality quite puzzling. I can’t really explain it fully. Maybe you can pull the pieces together.

    Here is my 2 cents.

    I have a background in physics and mathematics in college, was in a Ph.D program in math, left in good standing to go into the US Navy. Am also ABD in another discipline which we studied the philosophy of science quite extensively and conducted experiments in the behavior of people in a consumer environment. Left to start a new business which required that I know certain areas of biology.

    Always believed in Darwinian evolution but then saw how some who questioned it were being censored. Went to an Intelligent Design presentation given by Dembski, Behe and Meyers 20 years ago and was blown away by the science. So I have been studying this for about 20 years.

    I found out that there is no support for naturalistic evolution. What Darwin discovered morphed into modern day genetics but no more. Would be very open to any plausible argument for any naturalistic form of evolution but have never seen any. The Achilles Heel of macro-evolution is the formation of new proteins.

    I am very rational and evidence driven and a science junkie. Name it and I probably have read something about it. Evolution is very interesting because of the behavioral pattern it elicits in people defending it and criticizing it.

    I really hope you stay here, or at least occasionally show up to have a conversation. You have very specific skills that are welcome here and would add to the level of understanding.

    Many of us try to keep religion out of our discussions because as soon as we mention it, the critics jump on our beliefs as religious driven and not science driven. My religious beliefs did not change one iota when I abandoned Darwinian evolution as an explanation for the appearance of new life forms on the planet.

    Also there are testable hypothesis that would solve the evolution problem once and for all. Not everything but it would put to bed whether there are naturalistic origins or not for the various species.

  166. 166
    Dionisio says:

    @143 there’s a link to another recent thread.

    In that thread there’s a question posted @3

    Would someone here answer it?

    Thank you.

  167. 167

    @165.

    * how is that location (of transposable elements in the genome) determined?

    Generally speaking, there are several ways of doing this. Nowdays, the most efficient is using a primer to build a sequencing library. Obviously, you could also do whole genome sequencing too. The easiest way, of course, is to use one of the many databases that are available on line that use computational algorithms to annotate all the TEs they find in genbank genomes.

  168. 168

    Well, I gotta go now, but consider putting together an online event. Or asking someone else to (e.g. the Apologetics Academy) organize one. I’m happy to interact directly with you guys, to help you understand where professional scientists like me are coming from in this debate. I liked the one Bill Cole asked Behe a question about common descent on. Something like that, I imagine, could be helpful as we all try and seek peace in this contentious area.

  169. 169
    Dionisio says:

    Please, feel free to address the question @165 if you will.
    The question is about how exactly the TEs end up where they are?
    What mechanisms put them where they are? how? why?

    BTW, do you know exactly how the cell fate intrinsic determinants get segregated in the asymmetric mitosis ?

    Also, do you know exactly how the morphogen gradients get spatiotemporally established and interpreted?

    Don’t those processes look designed?

    Thank you.

  170. 170
    Dionisio says:

    @166

    The question is about how exactly the TEs end up where they are?

    What mechanisms put them where they are? how? why?

    Thank you.

  171. 171
    bill cole says:

    Dr Swamidass

    Honest question here. I really am curious your answer. I’m not sure how you will respond, but I mean no disrespect.

    You all seem to care a great deal about science. You put a lot of time and thought into this. At the same time, it does not appear that you are science professionals. How did that happen?

    Many people on this blog are scientists. I am doing cancer research part time for the University of California. I am new to research but spent my life in technology using the scientific method to innovate and improve product.
    I became interested in evolution when I discovered the sequence dependence of DNA and mathematically how that created a problem for evolution. Prior to that I was a theistic evolutionist. Eventually I became convinced it was a show stopper. I am not an intelligent design advocate for many of the limitations you pointed out but I do think if the game is inference it is the best choice. I think the whole macroevolutionary paradigm is badly broken and we are deceiving the public. I think the word common decent needs to go away because it is attached to the old paradigm and misleads people. The real observation is common biochemical machines and information. If we would agree to strip evolution out of all its untested hypothesis I would be happy but if the standard is inference then my vote is for design.

    Do you have any issue with how we are describing evolution to our kids in the current biology text books?

    Of course, the inference to naturalistic macroevolution is leap from here.

    Until you have a reasonable explanation for how complex sequences are formed I think this statement is problematic because we don’t even have a valid inference at this point.

  172. 172
    Dionisio says:

    bill cole @170

    Many people on this blog are scientists.

    Perhaps I’m one of the few who are not scientists.

    That’s why my questions could be the dumbest of all.
    And the easiest for the rest of you to answer.

  173. 173
    Dionisio says:

    Have you studied the 2014 courses on Systems Biology by Uri Alon from Weizmann Institute for Science at Rehovot and by MIT? Would you answer some questions associated with the topic of those courses?

  174. 174
    bill cole says:

    Dr Swamidass

    It turns out common descent makes an experimentally testable prediction about how biological systems behave right now. Under the hypothesis of common descent, we expect that variations in divergence (i.e. human-chimp differences) to be partly explained by variations in mutation rate across the genome. We can directly measure human mutation rates across the genome, and test this hypothesis. Human chimp spatial variations divergence should correlate with spatial variations in mutation rate, but not perfectly because we know that mutation rates shift over time. This, of course, is directly testable by sequencing parent-child triads and characterizing the de novo mutation distribution across the genome. The first bits of data are starting to come in. Generally speaking, we see that de novo mutations spatially correlate quite well with human-chimpanzee divergence, and better models that take recombination into account even further improve on this correlation to explain virtually all of the spatial variation about which Dr. Hunter is so concerned (see Figure). This, again, is a very strong piece of evidence for common ancestry. This is a directly confirmed prediction of the common ancestry hypothesis, for which design has no explanation.

    This is an interesting exercise but until you can show how these genetic changes can form new DNA, Splicing, or Timing sequences you have not shown macroevolution to be valid and given the difficulty of creating these sequences your hypothesis is almost certainly wrong. IMHO the word common decent is smoke and mirrors.

  175. 175

    @170

    We have opposite stories =). I grew up slurping down the math in Dembski and Meyer’s work. I was, obviously, an intelligent design fanatic.

    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. It was an eye opener. I did a second read through them, and noticed that they often simplified biological systems and then started arguing simplified math based on those simplified models. It turns out that they over simplified the systems. Remarkably, this is actually a very common pitfall in modeling biology, that I am constantly working with new PhD students to change. Mathematically modeling biology is really hard. I love it, but it is very hard. Even, very smart people make very big mistakes here.

    Any ways, in terms of how evolution is taught in school. That is a good question. Twenty years ago, there was a lot of atheism strewn throughout textbook. That was a problem. It has since been cleaned up. Any remaining problems are easily addressed with authors and publishers. There is a real attempt among my colleagues to remove atheism from science. I appreciate that.

    If you have specific problems with statements made in current textbooks, you should consider talking to the authors and the publishers. If you are requests are reasonable, they will probably change the textbook. If you need help with that, show me the specific examples and I can show you language that might satisfy both you and them. This doesn’t have to be a fight.

    The larger issue, I think, is if we should care about how it is being taught in schools. I do not think it is very important. Just look at China. In the schools, they teach not only evolution but also atheism. The Church does just fine, and grows. What atheists teach in schools cannot hold what God wants to do in our world. I just do not see that it is worthwhile to fight over curriculums.

    The faith I know is very resilient to the state-sponsored atheism in China. Why would I be concerned about the silence of science curriclumns about God here in the US? I just tell students that science is just “part of the story,” it is “incomplete.” It doesn’t include God because science is limited and unable to comprehend even the most obvious evidence for God. Only foolish atheists disagree with me there.

    As for your last question. You seem to miss my point.

    I do not agree with naturalistic macroevolution. Remember, I am a theistic evolutionist. Naturlistic macroevolution is a metaphysical claim that goes well beyond science. Everyone agrees with that.

    However, within science, naturalistic macroevolution (even if it is false) is a powerful explanatory framework. It provides a coherent explanation of Biology (not invoking God, so not violating methodological naturalism). Moreover, has an amazing track record of guiding scientists to verifiable hypothesis about the behavior of biological systems and patterns.

    Outside of science, we think about things more broadly. Science isn’t a path to Truth. Just because it works in science doesn’t make evolution True.

    But your requirements are hard to meet. Reasonable, complex, and valid are all subjective poorly defined concepts outside of science. Regardless, I think naturalistic evolution fails here. Which is why I am a theistic evolutionist.

  176. 176
    vjtorley says:

    Hi Professor Swamidass,

    I’m very glad to see you commenting on my post. Welcome.

    I’d just like to comment on a remark you made above:

    You demonstrate the “what” by showing the “how.

    The reason why this worries me is that science has yet to explain human consciousness, and most likely never will. Any theory that could do that, would also have to explain itself, since our ability to form theories is part of what self-conscious human beings do. You can’t put the human mind in a box like that – or at least, we can’t. (Maybe God or some other higher intelligence can.)

    That being the case, someone who objects to human evolution can always point to human consciousness as something which the theory of evolution does not explain, no matter how good the fossil and genetic evidence for the theory may be. Hence it could never be convincingly shown that the scientific evidence favors human evolution overall, since the phenomenon of human consciousness could always be appealed to as a trump card that overwhelms the other evidence.

    If, on the other hand, we regard the hypothesis of common ancestry as a hypothesis about material origins rather than about mechanisms, then the scientific case for human evolution becomes a lot easier to argue. At least, that’s the way I see it. Also, scientists are then free to put aside the unanswerable question of how human consciousness arose, and focus on the more tractable question of how the human body arose. Even the latter question need not be explained purely in terms of blind, mechanical causes; rather, what scientists should attempt to do is retrace the steps followed by the process (whatever it may have been) that has generated the human body from an ape-like creature over the past six or seven million years. Having done that, scientists may then conclude that the overwhelming majority of these steps were the result of unguided natural processes, while at the same time conceding that at least for the time being, a few of the critical steps that led to us (e.g. the mutations that gave rise to the human brain) cannot, at the present time, be explained in such a fashion – leaving people free to draw an inference to intelligently guided evolution if they wish to do so.

    Thoughts?

  177. 177
    Dionisio says:

    @163

    I assume most of you are Christians.

    Mistaken assumption. This site seems to welcome commenters regardless of their philosophical/theological or professional association, or ethnic background or educational level or political affiliation.
    This is a huge “eintopf” 🙂
    Many don’t claim to be Christians, or openly claim they aren’t, But even among those who claim it, some are not.
    Some discussion threads are philosophical, others are about astronomy, physics, biology,
    However, when we discuss biology, we ask biology questions and want to get biology answers.

  178. 178

    @173

    “until you can show how these genetic changes can form new DNA, Splicing, or Timing sequences”

    Hey Bill, this is one of those things that is actually pretty easy to explain. It turns out that changing splicing and timing is very easy to modulate. Usually it has no effect on phenotype, so biological systems can tolerate a higher rate of mutation here than they can in, say, frameshift mutations.

    As you know, transposable elements have been jumping around the genome quite frequently. Frequently they carry binding elements that change how nearby genes are expressed (their timing). This provides a relatively safe way of rapidly (in evolutionary time scales) varying how genes are timed. Part of what contributed to the rapid evolution of humans is the increased activity of these elements.

    Moreover splicing is another way to much more safely than point mutations to vary the proteome. We only understand this system partially, but from what we can tell, single nucleotide changes can produce profound changes in splicing, both of a single protein and across several proteins at once. In other words, this is a type of plieotropy. Once again, most of the changes we see are probably not essential, but it does not take many genetic changes to produce dramatic changes in proteome.

    Of course, there is a lot being published about this. But it is much much easier to change splicing and timing sequences that evolve a protein from scratch.

    Which is probably what you mean by “new DNA.” As VJ points out though, de novo proteins in human are 98% similar to non-coding regions in chips. Its remarkable, and we can work out the math sometime if you like, but it turns out that even the de novo proteins for humans already exist (at exactly the expected genetic distance) in the chimp genome. It does not take much to turn some non-function pieces of DNA into a function protein. This is the cool and unexpected meaning of the ENCODE project.

    So the explanations are there. I would add that they are backed up by a lot of experimental work in the literature. Literally hundreds of papers. We do not know everything yet. But we are learning…

  179. 179
    Dionisio says:

    vjtorley and Prof. S. Joshua Swamidass and everybody else:

    My comments and questions posted @ 162, 165, 168, 169, 174, 172, 176 are for you too.

    Thank you.

  180. 180
    Dionisio says:

    Prof. S. Joshua Swamidass @174

    If you are requests are reasonable, they will probably change the textbook.

    If you are requests are reasonable?

    Did you mean:
    If your requests are reasonable?

    Just kidding 🙂

    I know that’s just a typo. Not a big deal.

    🙂

  181. 181

    @175

    VJ you raise a good point, and have a reasonable solution. Your landing point is almost exactly the position of most theistic evolutionists I know. It is remarkable to see you write that.

    The way I see it, science is profoundly limited. It can only address certain types of questions, and even then it has major blind spots. I’m okay with that: it is only a human effort after all. It would be absurd (as Dawkins does) to see science and evolution as a comprehensive worldview.

    Your example of consciousness is great. We know it exists, but cannot quite interrogate it scientifically. We know it is a property of brains, and can trace it to specific regions, but this more descriptive than mechanistic. We are likely never going to get much farther than this scientifically. But there are other things like this too. Morality (e.g. racism is wrong), beauty, existence of God, the Resurrection, and so much more.

    Science can really only get a handle on things by understanding the “how.” This is a place from which to explain to our world the science is limited, not to try and tweak it to fix it. Some very important things are not understandable through the “how.”

    I think it is so much more productive to argue that “science (or evolution) is not complete,” rather than to bet the farm that “science (or evolution) is wrong.” When people realize that, most of the debate really goes away.

    For the record, this is exactly what I do with the Veritas Forum and BioLogos:

    https://www.youtube.com/watch?v=gooQsVJ6Xl8
    https://www.youtube.com/watch?v=-_YKH3tAIqw
    https://www.youtube.com/watch?v=Bz2j-TLu-fo

    So what are the wedge issues between (most) theistic evolutionists and ID?

    1. The use of the word “evolution.” We are comfortable with the word because we understand its limitations, and know that it is only an incomplete understanding of the world. For ID people, evolution is usually spelled with four-letters. Without good reason, it appears to always be translated into “evolutionism.”

    2. Science curriculums. We see no reason to fight over this. We are happy to let scientists control science curriculums, and look to “soft” power of diplomacy instead of the “hard” power of law and politics to improve problems in textbooks. As a Christian, I think of the verse, “Give to Caesar what is Caesar’s.”

    3. Provability of design. We believe God is involved somehow (there is debate about how), but usually we are extremely doubtful science, with all its limits, could clearly see this. To be clear, I believe God designed everything. I just am not sure science can prove it. As a Christian, I think of Bonhoefer, “A god who let us prove his existence would be an idol.” If God exists, maybe He makes Himself known another way (i.e. Jesus).

    4. Nature of God. So I can’t prove God as Designer, but I believe it. But I’m not even sure this is the most important way to think about God. It is more important for me to understand Him as my Redeemer. I just can’t fathom spending so much time arguing about scientific proof for a designer. I do not see how it make sense in the context of the priorities of my faith.

    That is what I perceive as the differences. But in some really important ways, we seem to be very close. I see a lot of common ground.

  182. 182
    bill cole says:

    Dr Swamidass

    However, within science, naturalistic macroevolution (even if it is false) is a powerful explanatory framework. It provides a coherent explanation of Biology (not invoking God, so not violating methodological naturalism). Moreover, has an amazing track record of guiding scientists to verifiable hypothesis about the behavior of biological systems and patterns.

    I think this is a mistake. I think the odds of misleading science is much greater then helping. We don’t have a unified theory in physics yet we can model the mechanisms. If you listen to my second conversation with Mike at 1:53 I ask him how much do we understand about a eukaryotic cell at this point he said optimistically 1%. Several scientists have come up with that number. Based on this do you really think we are ready to unify biology with this level of knowledge?

    Also after doing 6 months of cancer research and studying transcription paths I can use design as a guide to be able to hypothesize new molecular pathways. I see potential use in teaching the mechanisms of design inside the cell like the ribosome, spliceosome and atp synthase along with how the cell regulates transcription with common designs and how these replicate human designs. I don’t have any use at this point for current modern evolutionary theory.

    All that being said I understand your argument that taking the next step beyond the current design hypothesis is difficult so I am very grateful for the dialog you have started 🙂

  183. 183
    vjtorley says:

    Hi Professor Swamidass,

    I’d like to offer a quick response to your questions about Jesus and ID:

    For me, Jesus is enough for confident belief. What about you?

    Why not focus on the Resurrection?

    Remember, I already know God exists through Jesus.

    Also, I assume most of you are Christians. But I never see you all talk about Jesus in science.

    For what it’s worth, I have written quite a few posts in my time on the arguments for the existence of God, including the argument from miracles. I have brought up the Resurrection, as well as other more recent miracles, such as the levitations of St. Joseph of Cupertino, which were witnessed on 2,000 occasions during his lifetime, often by large crowds of people. (The Vatican has 13 volumes of sworn testimonials by people who saw them happen.) I use this one because it’s a pretty solid case, and because it relies on the kind of evidence that would impress an atheist.

    So why don’t I focus more on the Resurrection? And why don’t I use it as my central argument for God’s existence? Good questions.

    It’s pretty hard to use arguments like that, when you’re up against atheists who deny or question the very existence of Jesus Christ, let alone His Resurrection. And I’m not talking lightweights either: Professors Larry Moran, Jerry Coyne and P.Z. Myers are all either Jesus-denialists or Jesus-skeptics. Also, it doesn’t help when the earliest manuscript fragments of the Gospels date from 90 years after Jesus’ death, and the earliest complete copies of the Gospels date from over two centuries after His death. Any atheist would have a field day, mocking evidence like that.

    That’s why I’m interested in natural theology. Of course, biological Intelligent Design doesn’t take us to God, but it takes us to a Designer of life, and the Fine-Tuning argument takes us to a transcendent Designer of the cosmos. Beyond that point, philosophical arguments can be used to establish the characteristics of this transcendent Designer. Collectively, these arguments make a strong case for God, to people of all faiths.

    Finally, I’d like to ask you a question. How would you have responded to an atheist (and there were some, even back then) who lived before the time of Jesus?

  184. 184
    Origenes says:

    Swamidass: Provability of design. We believe God is involved somehow (there is debate about how), but usually we are extremely doubtful science, with all its limits, could clearly see this. To be clear, I believe God designed everything. I just am not sure science can prove it.

    Design is often an inference to the best explanation. For instance, here James Tour is saying:

    We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made and how they could have coupled in proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex system, and eventually to that first cell. Nobody has any idea on how this was done when using our commonly understood mechanisms of chemical science. Those who say that they understand are generally wholly uninformed regarding chemical synthesis.

    From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks, let alone assembly into a complex system.

    That’s how clueless we are. I’ve asked all of my colleagues: National Academy members, Nobel Prize winners. I sit with them in offices. Nobody understands this. So if your professor says, “It’s all worked out,” [or] your teachers say, “It’s all worked out,” they don’t know what they’re talking about. It is not worked out.

    IOW — according to what we know today — intelligent design is the best explanation for the origin of life.

  185. 185

    @182

    I think you wildly underestimate the evidence for the Resurrection. Most of these atheist you point out are profoundly ignorant of what they reject. The problem is that they are making a rhetorical case without actually seeking truth.

    This is what I tell them (see this dialogue to see it in action https://www.youtube.com/watch?v=-_YKH3tAIqw):

    You believe in evolution, and it frustrates you how many people reject it. They expect you to make a 2 or 20 minute case for vast body of non-intuitive technical work. They then proceed to make an intuitive and rhetorically strong case against evolution, that is demonstrably wrong in science. That is really annoying and unfair. They need to chill out and become seekers. If they care so much about evolution, and cannot trust the experts, they have to take the time to willingly study a lot of non-intuitive biology. It will take a long time.

    I know you want God to come to you in science, but He instead decides to come to you through history, where you are not an expert.

    The Ressurection is just like evolution. There are over 100,000 relevant texts in languages you do not read. You do not even know what they are. There is a whole academic field devoted to studying 1st Century Palestine. There are a few holdouts, but even those that reject the Ressurection agree that there is compelling evidence for it. It is without doubt the most substantiated ancient miracle. For example, look at this remarkable dialogue between NT Wright and Sean Kelly (chair of philosophy at harvard) https://www.youtube.com/watch?v=RsKv9uX8rwE. It is ignorant to so thoroughly reject what you do not understand. In the same way you wish ID folk would be seekers in science, would take the time to read, for example, NT Wright’s masterpiece “the Ressurection of the Son of God”?

    I tell them that the “way God makes himself known to the world is through the death and Ressurection of Jesus. Of course there is evidence of God in nature, but without Jesus it is hard to appreciate it.”

    In my experience, having this conversation dozens of times, the reaction is:

    1. Why has no one ever told me there is evidence for the Resurrection?

    2. Yes, I really want to read that (followed up with lots of emails).

    As for how to atheists before Jesus. Look how Jesus explains it.

    He answered, “A wicked and adulterous generation asks for a sign! But none will be given it except the sign of the prophet Jonah.

    40 For as Jonah was three days and three nights in the belly of a huge fish, so the Son of Man will be three days and three nights in the heart of the earth.

    41The men of Nineveh will stand up at the judgment with this generation and condemn it; for they repented at the preaching of Jonah, and now something greater than Jonah is here.

    42The Queen of the South will rise at the judgment with this generation and condemn it; for she came from the ends of the earth to listen to Solomon’s wisdom, and now something greater than Solomon is here.

    To answer. I think without Jesus, you might find God, but it would not be confident belief. It would not be anything like what we can come to through Jesus.

    I know might all be out of left field. But I am speaking from experience living as a Christian in science.

  186. 186
    Dionisio says:

    Prof. S. Joshua Swamidass @166

    Apparently you missed seeing my comment @169 so I repeat it here:

    The question is about how exactly the TEs end up where they are?
    What mechanisms put them where they are? how? why?

    Thank you.

  187. 187
    Dionisio says:

    Prof. S. Joshua Swamidass

    Have you studied the 2014 courses on Systems Biology by Uri Alon from Weizmann Institute for Science at Rehovot and by MIT? Would you answer some questions associated with the topic of those courses?

    Do you know exactly how the cell fate intrinsic determinants get segregated in the asymmetric mitosis ?

    Also, do you know exactly how the morphogen gradients get spatiotemporally established and interpreted?

  188. 188
    StephenB says:

    Professor Swamidass, I appreciate your participation. I will respond to your scientific/theological comments in context. Please do not be mislead by the brevity. The point is to provide a big picture perspective from 30,000 feet.

    [a] ID science is based on an inference to the best explanation, which is precisely the same methodology used by Darwin. If ID methodology is not science, then Neo-Darwinian methodology is not science.

    [b] The “ability of science” to produce reasonable conclusions is based, in large part, on the integrity of the methodology employed. 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.

    [c] According to the Scriptures, we can know that God exists by simply examining the clues He left behind in the form of empirical evidence (Romans 1:20). Because of His natural revelation, we know that the universe is based on a rational principle, and we can then be confident that His Divine Revelation is also grounded in reason and therefore worthy of belief.

    [d] Science is not so much our efforts to reach God as it is a way of letting nature reveal her secrets to us, the most important one of which is that that reason is indispensable even on matters of religion. Indeed, God’s revelation and natural revelation teach us that faith and reason work together. One without the other is folly. Accordingly, we are not supposed to just believe, without warrant, any message that is reported to come from God. Any world religion should first pass the test of reason before we allow it to inform our reason. Only Christianity passes that test.

    [e] God and Darwin cannot co-exist. A (Neo)Darwinian process, as described, is open-ended. By virtue of its randomness (by which its proponents mean purposelessness), it is free to produce many possible outcomes, most of which will not reflect the Creator’s intentions. To guarantee the desired outcome, the Creator must design the mechanism so that unwanted outcomes are closed off.

    But if the process is constrained or closed off from the outside, then it is no longer “acting alone,” and is no longer “free” to produce unwanted outcomes. In other words, it is no longer a Darwinian process as defined by the evolutionary scientists. Thus, God cannot use a Darwinian mechanism to achieve a specific goal. If God did use evolution to create man, he would have had to either design, front load, program, or supervise the process.

  189. 189
    Mung says:

    Eric Anderson @139:

    So you must be proposing something much more modest than from scratch. Indeed, you must be proposing that essentially everything was already in the genome and in the extra-genomic domain beforehand, with the mutations just tweaking a toggle here or a switch there. Everything else must have been there beforehand, in nascent or dormant form: the required detailed nucleotide sequence, the signalling and control mechanisms to determine when and how much of the gene product to produce, the folding algorithms, the chaperoning information to get the gene product to the right place, all the other gene products, and molecules and machines to seamlessly incorporate the new gene product into a new function. All of that was ready and in place up front, just waiting for a handful of lucky mutations and — Ta Da! — we have a newly transformed organ.

    I seriously doubt that is an accurate representation of VJT’s views.

  190. 190
    Mung says:

    Creation Pacifism is an effort to organize Christians (including those who reject evolution) to honor Jesus by laying down their political swords to choose peace in the great Creation War. We choose peace with confidence because Jesus is greater than anything we find in science, no human effort can hold Him, and He needs not our defense.

    http://creationpacifism.org/

    Perhaps Prof. Swamidass does not need our defense. 🙂

  191. 191
    Mung says:

    Prof. Swamidass:

    As scientists, we look at that his pattern and look for biochemical mechanism.

    But why treat living organisms as machines? Aren’t you treating organisms like artifacts?

  192. 192
    Mung says:

    Prof. Swamidass:

    I’m open to creation-by-modification, but this raises the theological question. I need a theological clear explanation of why God did not include disproving evolution in His design goals.

    But what would disprove evolution? As for your question,

    The Biotic Message

    Argues that the message is one that “disproves” evolution.

  193. 193
    bill cole says:

    Mung

    I’m open to creation-by-modification, but this raises the theological question. I need a theological clear explanation of why God did not include disproving evolution in His design goals.

    I think when we got our first view of DNA in the 1950’s and saw that it was at least 4^100000000 of sequential space, I think it was revealed to us that a solution from known natural causes in nature was almost certainly wrong.
    Bill

  194. 194

    DionisioMay: I’m gonna pass on the basic bio questions. You can find answers on wikipedia and from reading the literature. If you are really curious, maybe considering a class at a local university. There are a lot of people who can help you with that.

    @189 Jesus needs not my defense, but I appreciate yours =).

    @190 That is exactly what science does. That is how it works.

    @191 Not convinced. This is my area of expertise. It is a great example of well-intentioned by poor mathematical modeling in biology.

    @187
    [a] I’ve already explained the difference. Evolution gives a framework for producing testable hypothesis, which very frequently end up being experimentally validated. ID does not. It does not function the same way in science.
    [b] Methodology is important. SETI works entirely different then ID. ID is a different methodology than science. That is why it struggles in science. For that matter, so does SETI.
    [c] Your Biblical interpretation is off. This is important. Go back and read the whole context. Romans teaches that studying nature, uniformly, leads to idolatry, not to correct knowledge of God. It is a reason we are left without excuse. It is not a path to God.
    [d] “Science is not so much our efforts to reach God as it is a way of letting nature reveal her secrets to us” I approximately agree with that. Have you read abou the Two Books analogy? You might find that helpful.
    [e] In terms of evolution (which is not Darwinism or evolutionism) look at BioLogos. Leading historians and theologians show you how it can work together.

  195. 195

    So you guys have been great and respectful dialogue partners. I’d love to keep you informed of future stuff I do. For example, in about a month I’m planning a pretty important post on how humans are much more than just apes. It is based on a remarkable dialogue I did with a leading expert in human evolution. I think this will be of high interest to you.

    I’m also pretty involved in faith-science dialogue.

    What is the right way to let you know?

  196. 196
    bill cole says:

    Dr Swamidass

    Hey Bill, this is one of those things that is actually pretty easy to explain. It turns out that changing splicing and timing is very easy to modulate. Usually it has no effect on phenotype, so biological systems can tolerate a higher rate of mutation here than they can in, say, frameshift mutations.

    I look forward to your explanation. Random Exon level insertion deletions,IMHO, would almost certainly be lethal to the animal. If you have experimental information to the contrary I would be very interested. Since the origin of the splicing codes are not known at this point the only real scientific answer is, we don’t know. A real theory of common decent is a long way from prime time at this point again IMHO. Enjoyed the dialog thanks again 🙂

  197. 197

    Welcome Prof Swamidass,

    [b] Methodology is important. SETI works entirely different then ID. ID is a different methodology than science.

    I’m not sure what ID arguments you intended this comment to encompass, but we can be sure it doesn’t encompass all of them.

    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.

  198. 198
    Andre says:

    Prof Swamidass

    The argument for design in my assessment of it, is clearly demonstrated in the controls, checks, balances, trade-off’s in the living cell.

    The question I always ask is this…..

    How did an unguided process (Darwinian evolution) create guided processes to prevent unguided processes (Darwinian evolution) from happening?

    Also I am a biblical literalist and I accept the following explanation Genesis 2:7: “Then the LORD God formed a man from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being”

    The Creator of the universe got His hands dirty, bent a knee, to pickup mud and form you from the materials. This physical creative act sets man apart from anything else in creation.

  199. 199

    @196

    Exon insertions are often bad, but that is rare compared to insertion into regulatory regions. This is why they are relatively safe. Exon insertion are not usually lethal. Just look at the mouse knockout data. Some are lethal, most are not, but are not beneficial. A large number are silent, with no discernable effect (usually because biological systems are robust).

    About splicing codes, we actually do know a fair amount. There even reasonable predictors. We even known how they vary with SNPs. We know many of the cis and trans actors. It is still early though, give us about 20 years. It will make much more sense then. Remember, just now we are starting to learn about de novo mutations. The technology is only just now catching up with our ability to ask questions here.

    The really remarkable thing about humans and chimps. To a first approximation, we are made of essentially the same parts, just shuffled (by splicing and expression timing) in a different way. That is totally amazing, and really unexpected. I don’t think anyone quite expected this.

    From an evolutionary point of view, though, it is much easier to imagine how this could happen. Clearly splicing and expression are a consequence (for the most part) of the genome. Moreover, small mutations can have dramatic consequences on expression and splicing, not just locally but across the genome. Moreover, there are multiple ways (in the genetic code) to achieve the same splicing and expression phenotype. Moreover, it is usually safe to introduce variation in splicing and expression. Moreover, a random transposon into the genome is more likely to affect expression than anything else. (All these claims stuff have strong evidence; I’m not just spit balling).

    Taken together, and this is really remarkable, these biological facts seem to dramatically reduce the difficulty in evolving a human from a chimp-human common ancestor.

    How much easier? Well that is the million dollar question. We can’t really tell exactly if this is a low or high probability path yet. Though (I’lll post about this later) one prominent expert in human evolution (Ajit Varki) argues that human evolution is actually a very low probability path. He argues that something very exceptional happened in us. I’m inclined to agree, but it will probably take another 20 years (minimum) of scientific work to really resolve some of the most important and central questions. Honestly, this is so hard to resolve we may not have a definitive answer in our lifetimes.

    ==========

    Respectfully, on another point, I’ve read several of your pots. I see an important possible misunderstanding you have about biology.

    I notice you keep pointing to splicing and timing differences as the key to resolve all this, as if this has the code that explains why we are so different. And it seems like you assume that most of the changes you see there are relevant. There a couple problems with this notion.

    First, for the most part (epigenetics aside for a moment) genetic expression timing and splicing is correctly understood as a “phenotype,” a product of the genetic code. It is just a precise way of measuring the final differences between chimps and humans. All the information for these changes, though, are encoded in the DNA.

    Second, most of these changes are probably irrelevant. This is the very non-intuitive part of biology. Whenever we measure differences, in biology, usually the vast majority of observed differences are irrelevant. How do we know what is relevant? Usually we have to do very careful genetic experiments to figure this out. With humans we can’t do this. So instead we look for how alterations correlate with disease and other phenotypes. This is a slow hard slog, and we barely know the answer here because the field is so new.

    We do think, however, that this does not appear to be a dominant effect. Copy number variation is very common (and it is very similar to the effect of transposons, and even more common). We do see effect in disease, but is not as strong as some expected. Splicing variation only vary rarely causes disease (but that might be because we only recently have tools to look for it). Of course, as we study this more, many of these differences will be important. But the usual pattern in biology is that the vast majority will not be important. It is non-intuitive, I know, but that is the usual pattern.

    Any way, I hope that is helpful.

  200. 200
    StephenB says:

    Professor Swamidass, thank you for responding. You write,

    [a] I’ve already explained the difference. Evolution gives a framework for producing testable hypothesis, which very frequently end up being experimentally validated. ID does not. It does not function the same way in science.

    * ID does, indeed, test hypotheses:

    (1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

    (2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

    (3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

    (4) Much so-called “junk DNA” will turn out to perform valuable functions.

    Methodology is important. SETI works entirely different then ID. ID is a different methodology than science. That is why it struggles in science. For that matter, so does SETI.

    *ID, does, indeed, use the scientific method:
    Observation>>Hypothesis>>Experiment>>Conclusion. If that isn’t the scientific method, then what is? Please be specific.

    Your Biblical interpretation is off. This is important. Go back and read the whole context. Romans teaches that studying nature, uniformly, leads to idolatry, not to correct knowledge of God. It is a reason we are left without excuse. It is not a path to God

    *According to Romans 1: 20 God’s handiwork is “made evident,” by the “things that are seen,” therefore non-believers are “without excuse.” It means that we don’t have to rely on faith to testify to God’s existence. We can know it through the use of reason unaided by religious faith. That is the point of the passage. You are not reading out of the text (exegesis), you are reading into the text (eisegesis.) There is no way to extract your interpretation from the passages.

    In terms of evolution (which is not Darwinism or evolutionism) look at BioLogos. Leading historians and theologians show you how it can work together.

    *I have already explained why God and Darwin cannot work together. Meaning no disrespect, but Ignoring my reasons will not suffice as a substitute for addressing them. Please reread the points carefully and try to refute them. No one has yet been able to do so. Though invitations have been extended to them, BioLogos historians and theologians will not respond to the point.

    Here is another approach, though it is not meant to supersede the first argument.

    In the case of Teleological Theism, the design precedes and shapes the evolutionary process. In the case of Darwinian Evolution–the evolutionary process precedes and shapes the design (appearance of). Notice that there can be no reconciliation. To affirm one perspective is to negate the other. Either God’s real design precedes and shapes the evolutionary process (Teleological Theism) or, the evolutionary process precedes and shapes the appearance of design (Neo-Darwinism). It must be one or the other. It cannot be both.

  201. 201
    Eric Anderson says:

    Professor Swamidass:

    Thank you for posting here and joining the conversation. It is always wonderful to have someone join in the discussion.

    You said @140:

    I do not think science is powerful enough to detect evidence of design.

    I see others have responded, but I wanted to focus on that statement as well.

    Design detection is a well-established scientific and investigative principle in many fields of study, including archaeology, forensics, intellectual property infringement, illegal insider trading investigation, insurance fraud detection, reverse engineering, and many others.

    Do you object to design detection in all these fields, or do you only object to design detection in biology?

  202. 202
    Andre says:

    Prof Swamidass

    Your Biblical interpretation is off. This is important. Go back and read the whole context. Romans teaches that studying nature, uniformly, leads to idolatry, not to correct knowledge of God. It is a reason we are left without excuse. It is not a path to God

    Paslm 19:1-2 “1.) For the choir director. A Psalm of David. The heavens are telling of the glory of God; And their expanse is declaring the work of His hands. 2.) Day to day pours forth speech, And night to night reveals knowledge.”

  203. 203
    Eric Anderson says:

    Professor Swamidass @195:

    I’d love to keep you informed of future stuff I do. For example, in about a month I’m planning a pretty important post on how humans are much more than just apes. It is based on a remarkable dialogue I did with a leading expert in human evolution. I think this will be of high interest to you.

    . . .

    What is the right way to let you know?

    We would love to hear about your work on this topic. You can comment sometime on a post to let us know and I’m sure one of us authors will pick it up. I’m sure we’d be happy to link to your work or even have you do a guest post if you have time for that.

    —–

    Incidentally, just so you have a sense as to how broad the audience is, yes, it is true that many authors and commenters at UD are primarily interested in faith, God, and related matters, and these topics are often discussed at length in these pages. However, some of us are interested in intelligent design, and the evolution debate, primarily as a scientific issue, so we are much more interested in debating the issues from that standpoint, rather than from any particular faith-based position.

  204. 204
    StephenB says:

    Eric @203, for my part, I am interested in both. Theistic evolution, for example, is often informed by a fideist perspective on religion, which produces a built-in bias against ID even before the evidence is allowed to speak.

  205. 205
    bornagain77 says:

    As to this false claim:

    [a] I’ve already explained the difference. Evolution gives a framework for producing testable hypothesis, which very frequently end up being experimentally validated. ID does not. It does not function the same way in science.

    Contrary to that claim, Darwinian evolution is a unfalsifiable pseudo-science that is completely vacant on experimental verification and is also impervious to observational challenge,

    “The argument that random variation and Darwinian gradualism may not be adequate to explain complex biological systems is hardly new […} in fact, there are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation for such a vast subject — evolution — with so little rigorous examination of how well its basic theses works in illuminating specific instances of biological adaptation or diversity.”
    Prof. James Shapiro – “In the Details…What?” National Review, 19 September 1996, pp. 64.

    ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
    Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
    *Professor Emeritus of Biochemistry, Colorado State University, USA

    Michael Behe – Observed (1 in 10^20) Edge of Evolution – video – Lecture delivered in April 2015 at Colorado School of Mines
    25:56 minute quote – “This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not.”
    https://www.youtube.com/watch?v=9svV8wNUqvA

    Genetic Entropy – references to several numerical simulations analyzing the feasibility of natural selection and random mutations and finding them severely wanting ,,, (via John Sanford and company)
    http://www.geneticentropy.org/#!properties/ctzx

    “Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought.”
    ~ Cornelius Hunter

    In fact, since it has no rigid mathematical basis as other overarching theories of science have, Darwinian evolution does not even qualify as a real science in the first place but is in fact a unfalsifiable pseudo-science that is no better than tea-leaf reading

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    Darwinian Evolution is a Unfalsifiable Pseudo-Science (i.e. no demarcation/falsification criteria)– Mathematics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater

    Whereas, on the other hand, unlike Darwinism, ID does qualify as a rigorous science since it does indeed have a rigid falsification criteria (as well as having a rigid mathematical basis)

    “The National Academy of Sciences has objected that intelligent design is not falsifiable, and I think that’s just the opposite of the truth. Intelligent design is very open to falsification. I claim, for example, that the bacterial flagellum could not be produced by natural selection; it needed to be deliberately intelligently designed. Well, all a scientist has to do to prove me wrong is to take a bacterium without a flagellum, or knock out the genes for the flagellum in a bacterium, go into his lab and grow that bug for a long time and see if it produces anything resembling a flagellum. If that happened, intelligent design, as I understand it, would be knocked out of the water. I certainly don’t expect it to happen, but it’s easily falsified by a series of such experiments.
    Now let’s turn that around and ask, How do we falsify the contention that natural selection produced the bacterial flagellum? If that same scientist went into the lab and knocked out the bacterial flagellum genes, grew the bacterium for a long time, and nothing much happened, well, he’d say maybe we didn’t start with the right bacterium, maybe we didn’t wait long enough, maybe we need a bigger population, and it would be very much more difficult to falsify the Darwinian hypothesis.
    I think the very opposite is true. I think intelligent design is easily testable, easily falsifiable, although it has not been falsified, and Darwinism is very resistant to being falsified. They can always claim something was not right.”
    – Dr Michael Behe

    It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    The Law of Physicodynamic Incompleteness – David L. Abel
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”
    If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided.
    The time has come to extend this null hypothesis into a formal scientific prediction:
    “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    https://www.academia.edu/Documents/in/The_Law_of_Physicodynamic_Incompleteness

    Evolutionary Computing: The Invisible Hand of Intelligence – June 17, 2015
    Excerpt: William Dembski and Robert Marks have shown that no evolutionary algorithm is superior to blind search — unless information is added from an intelligent cause, which means it is not, in the Darwinian sense, an evolutionary algorithm after all. This mathematically proven law, based on the accepted No Free Lunch Theorems, seems to be lost on the champions of evolutionary computing. Researchers keep confusing an evolutionary algorithm (a form of artificial selection) with “natural evolution.” ,,,
    Marks and Dembski account for the invisible hand required in evolutionary computing. The Lab’s website states, “The principal theme of the lab’s research is teasing apart the respective roles of internally generated and externally applied information in the performance of evolutionary systems.” So yes, systems can evolve, but when they appear to solve a problem (such as generating complex specified information or reaching a sufficiently narrow predefined target), intelligence can be shown to be active. Any internally generated information is conserved or degraded by the law of Conservation of Information.,,,
    What Marks and Dembski prove is as scientifically valid and relevant as Gödel’s Incompleteness Theorem in mathematics. You can’t prove a system of mathematics from within the system, and you can’t derive an information-rich pattern from within the pattern.,,,
    http://www.evolutionnews.org/2.....96931.html

    As far as the ‘predictive power’ of Darwinian evolution goes, Darwinism fails big time on that score as well,,

    Darwin’s (failed) Predictions – Cornelius G. Hunter – 2015
    This paper evaluates 23 fundamental (false) predictions of evolutionary theory from a wide range of different categories. The paper begins with a brief introduction to the nature of scientific predictions, and typical concerns evolutionists raise against investigating predictions of evolution. The paper next presents the individual predictions in seven categories: early evolution, evolutionary causes, molecular evolution, common descent, evolutionary phylogenies, evolutionary pathways, and behavior. Finally the conclusion summarizes these various predictions, their implications for evolution’s capacity to explain phenomena, and how they bear on evolutionist’s claims about their theory.

    *Introduction
    Why investigate evolution’s false predictions?
    Responses to common objections

    *Early evolution predictions
    The DNA code is not unique
    The cell’s fundamental molecules are universal

    *Evolutionary causes predictions
    Mutations are not adaptive
    Embryology and common descent
    Competition is greatest between neighbors

    *Molecular evolution predictions
    Protein evolution
    Histone proteins cannot tolerate much change
    The molecular clock keeps evolutionary time

    *Common descent predictions
    The pentadactyl pattern and common descent
    Serological tests reveal evolutionary relationships
    Biology is not lineage specific
    Similar species share similar genes
    MicroRNA

    *Evolutionary phylogenies predictions
    Genomic features are not sporadically distributed
    Gene and host phylogenies are congruent
    Gene phylogenies are congruent
    The species should form an evolutionary tree

    *Evolutionary pathways predictions
    Complex structures evolved from simpler structures
    Structures do not evolve before there is a need for them
    Functionally unconstrained DNA is not conserved
    Nature does not make leaps

    *Behavior
    Altruism
    Cell death

    *Conclusions
    What false predictions tell us about evolution
    https://sites.google.com/site/darwinspredictions/home

    Why investigate evolution’s false predictions?
    Excerpt: The predictions examined in this paper were selected according to several criteria. They cover a wide spectrum of evolutionary theory and are fundamental to the theory, reflecting major tenets of evolutionary thought. They were widely held by the consensus rather than reflecting one viewpoint of several competing viewpoints. Each prediction was a natural and fundamental expectation of the theory of evolution, and constituted mainstream evolutionary science. Furthermore, the selected predictions are not vague but rather are specific and can be objectively evaluated. They have been tested and evaluated and the outcome is not controversial or in question. And finally the predictions have implications for evolution’s (in)capacity to explain phenomena, as discussed in the conclusions.
    https://sites.google.com/site/darwinspredictions/why-investigate-evolution-s-false-predictions

  206. 206
    Dionisio says:

    Prof. S. Joshua Swamidass @194

    DionisioMay: I’m gonna pass on the basic bio questions. You can find answers on wikipedia and from reading the literature. If you are really curious, maybe considering a class at a local university. There are a lot of people who can help you with that.

    Sir, your answer is wrong. You may want to read the questions carefully and you should realize that you could have answered them better.

    The precise answers to those questions are not in any literature nor their combination. Try again.
    Please, note that some of the questions are personal, hence require a personal honest response.

    BTW, please tell me what do you mean by “DionisioMay:”?

    Thank you.

  207. 207
    Origenes says:

    Swamidass: (…) science concerns itself with finding coherent explanations, (not invoking God, so not violating methodological naturalism).

    The ultimate ambition of naturalistic science is to explain all higher level coherencies from the level of fermions and bosons. IOW an ideal naturalistic science will be able to explain phenomena like life, consciousness and rationality bottom-up from the most basic material level.
    One problem with this ambition of naturalistic science is that, if all things are explainable from fermions and bosons, we have no control over our thoughts. Therefore naturalistic science is self-referentially incoherent. A coherent science must assume conscious free controlled rationality.

    The argument:

    (1). If naturalism is true, then determinism is true.
    (2). If determinism is true, then all our actions and thoughts are consequences of events and laws of nature in the remote past before we were born.
    (3). We have no control over circumstances that existed in the remote past before we were born, nor do we have any control over the laws of nature.
    (4). If A causes B, and we have no control over A, and A is sufficient for B, then we have no control over B.
    Therefore
    (5). If determinism is true, then we have no control over our own actions and thoughts.
    Therefore, assuming that rationality requires control,
    (6). If determinism is true, we are not rational.
    – –
    Van Inwagen explains that undetermined events (also) fail to ground rationality:

    “Let us look carefully at the consequences of supposing that human behavior is undetermined …
    Let us suppose that there is a certain current-pulse that is proceeding along one of the neural pathways in Jane’s brain and that it is about to come to a fork. And let us suppose that if it goes to the left, she will make her confession;, and that if it goes to the right, she will remain silent. And let us suppose that it is undetermined which way the pulse goes when it comes to the fork: even an omniscient being with a complete knowledge of the state of Jane’s brain and a complete knowledge of the laws of physics and unlimited powers of calculation could say no more than: ‘The laws and present state of her brain would allow the pulse to go either way; consequently, no prediction of what the pulse will do when it comes to the fork is possible; it might go to the left, and it might go to the right, and that’s all there is to be said.’
    Now let us ask: does Jane have any choice about whether the pulse goes to the left or to the right? If we think about this question for a moment, we shall see that it is very hard to see how she could have any choice about that.
    …There is no way for her to make it go one way rather than the other. Or, at least, there is no way for her to make it go one way rather than the other and leave the ‘choice’ it makes an undetermined event.”
    [Van Inwagen]

  208. 208
    Origenes says:

    Swamidass: The problem for ID, as I see it, is that it currently explains much less than common descent.

    It is as if you completely ignore the fact that multiple IDers (VJTorley, Gpuccio and others) in this thread have provided extensive argumentation for the compatibility of ID with common descent. This way ID encompasses any explanatory power common descent may have, and, on top of that, can throw in “intelligent modification” for additional explanatory power. This results in ID explaining much more instead of much less.

    Moreover, one problem for naturalistic science, WRT common descent, is that has no right to take an organism as the starting point of a “naturalistic explanation”, since it cannot explain it bottom-up. Before naturalistic science is allowed to incorporate an organism in naturalistic explanations such as ‘common descent’, it must show how (and why) fermions and bosons self-assemble into an organism. Note that “sheer dumb luck” is not an explanation; see also James Tour. Moreover it must explain why an organism, assuming that it is in fact nothing over and beyond fermions and bosons, does not fall apart — as it does, in fact, at the moment of death.
    IOWs before naturalistic science can rightfully claim common descent, as an explanation consistent with naturalism, it must explain coordination at the level of an organism as a whole from the level of fermions and bosons.

  209. 209
    jerry says:

    Prof Swamidass,

    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.

    We certainly understand the processes that lead to micro evolution and ID does not dispute any of this. These processes and the mathematics that go with are well accepted by the ID community. So I would not use them to discredit ID when in fact there is no issue with them and their implications. It is only certain types of evolution that ID has problems with. Namely, the paths that led to complex functional novelities.

    In regards to humans where the novelities are in cognitive processing, there seems to be something unusual going on. The changes are not necessarily in the coding regions but there are some there as well. Wilcox, who is a respected geneticist has written an extensive review on the changes in humans vs. chimps. Here is a paragraph from this review and linked to several times in this thread.

    http://bit.ly/1TfR5Ha

    In terms of the question of how this change was brought about, clearly transposons were a central factor. Alu’s in particular have been particularly active in altering the human genome. Does the use of such a uniquely high level of transposon activity in the production of the modern human genome militate against viewing human evolution as a providentially guided process? After all, transposon movement/insertion appears to be a matter of pure “chance,” unaffected by the “needs” of an organism. Does this make humanity a happenstance, the product of the biggest engine of chance in the animal kingdom? Or are we seeing the providential hand of God who is the Lord of “chance”? Or both? The evidence of “random” events does not exclude providence—in fact, the meaning can be viewed as quite the opposite. Our origin does not look like “business as usual” in the ecosystem, even if we can explain what happened. This judgment, I would suggest, can be viewed as a valid perception of “design” if one wishes to, but what can be seen is the design of the whole, not the designing of its parts. However, such perception requires the acceptance of the specifying assumption that God governs natural events (the doctrine of providence). Thus, it is rational to hold this view, but it is not necessarily statistically demonstrable to those who cannot perceive it. I do not know what new data will turn up in the next few years, but in my opinion, I do not think that we are irrational in holding that there was a highly directed process involved in the making of humanity.

    So we are led to believe that an almost impossible set of naturalistic occurrences led to humans with no other example in the history of evolutionary biology with similar patterns. Or there was design some how.

    ID does not discuss the “how” because these are one time events. We can see the “what” in the end result but because design by definition means a suspension of the laws of physics, there will not be a pattern that allows to know the “how.”

  210. 210
    Eric Anderson says:

    jerry @209:

    . . . design by definition means a suspension of the laws of physics . . .

    Respectfully, please don’t use that kind of terminology. It is exceedingly confusing to someone who is trying to understand ID and also contributes to all manner of red herring arguments by ID opponents that ID supporters think the laws of physics have been violated and such.

    There has been no suspension of the laws of physics and design certainly does not call for anything of the kind.

    Design simply means that there is a purposeful selection from among contingent possibilities.

  211. 211
    Eric Anderson says:

    StephenB @204:

    Good point and I agree. I think we are probably all interested in both aspects, to some greater or lesser extent.

    My interests in ID are primarily scientific. In particular because, as you point out, there is a tendency to force the evidence down a particular road if one adopts a specific faith-based narrative out of the gate before examining the evidence (a problem that perhaps plagues the pro-evolution side even more than the pro-ID side). I occasionally weigh in on these pages regarding faith/religious issues, but I typically find less value in the debates that hinge on someone’s personal interpretation of some vague passage of some book written ages ago for a different purpose and in an different context.

  212. 212
    Eric Anderson says:

    Origenes @208:

    IOWs before naturalistic science can rightfully claim common descent, as an explanation consistent with naturalism, it must explain coordination at the level of an organism as a whole from the level of fermions and bosons.

    Fermions and bosons? Oh, come on! I’d be willing to cut them a break and let them start from a complete suite of amino acids. 🙂

    http://www.uncommondescent.com.....challenge/

  213. 213
    jerry says:

    Eric,

    Respectfully, please don’t use that kind of terminology.

    ID supporters think the laws of physics have been violated and such.

    I see no reason not to use this explanation. We continually point to design in our environment and every instance resulted from a suspension of the four basic laws of physics. That is essentially what design is about. Unless you want to make the case that intelligence is the result of the four basic laws then everything is determined.

    That is why I say there is no real theory of design but design is a conclusion based on evidence that used the tools of science and analysis where the conclusion is that the four basic laws of physics can not explain the results. So some other force must have been present. That is the approach of Meyers in his books.

    I am willing to accept that something was designed without the four basic laws but then this design proceeds to produce something that is a result of these laws that is functional. The simplest example I can think of it the rerouting of a river to produce water for irrigation.

    I used an extremely complicated example a couple years ago how such a design might lead to OOL. This is essentially the point of view of the TE’s who say it is all in the original design of the universe and we are the result of cascading events due to the four laws of physics. Intelligent Design is a suspension of the four basic laws at some point.

    Design simply means that there is a purposeful selection from among contingent possibilities.

    This is an example of suspension of the four basic laws of physics

  214. 214
    Eric Anderson says:

    Professor Swamidass @164:

    Also, I assume most of you are Christians. But I never see you all talk about Jesus in science. How does He influence how you think about ID, evolution, and science as a whole? For me, He entirely reorders how I see everything, including science. Here on this website, however, He seems unmentioned and oddly irrelevant. I can’t get my head around that.

    You can’t get your head around it because you don’t understand ID, despite your claims to the contrary.

    Why would I need to invoke Jesus in the field of archaeology, or forensics, or intellectual property infringement, or numerous other areas? Why do you keep falling into the intellectual trap of thinking that design is unacceptable in biology?

    I’m trying to say this charitably, but it appears you have such a massive assumption — and therefore an intellectual blind spot — about design as it relates to biology that you can’t digest the basics of how the design inference works.

  215. 215

    Okay there seems to be a fair amount of confusion about my posts. I’m sorry about that. I just have to remind myself that you don’t really know me, and where I come from.

    I can honestly say I’ve heard the vast majority of these arguments from the horse’s mouth. I’ve read the books. I’ve talked to most of the authors. I was even an ID believer for a long time. When I give my 1 sentence dismissals, it is (obviously) unclear the reason why I find those arguments not compelling. From your point of view, has got to be frustrating. Please understand, I mean no disrespect. I just think it means I will be more judicious and selective from here about that to which I will respond.

    Sorry that I came off as rude the first time. It was unintentional.

  216. 216
    jerry says:

    Prof Swamidass,

    Here is a very long explanation I wrote about 10 years ago to explain ID to people who are not familiar with the issues. You do not seem to be familiar with what ID is concerned about.

    The following is an analysis of the changes in life forms and where ID has interests.

    Evolution is essentially a multi-tiered theory.

    The first tier is the origin of life or how did a cell and DNA, RNA and proteins arise. Quite a sticky issue with no sensible answer by science. Lots of speculation and wishful thinking but nothing that makes sense. The problem is enormous yet few admit its size. The solution is always just around the corner and things like the Miller Urey experiments are still used as illustrations of what works. Just imagine how you construct a ribosome by chance or ATP synthase. A high percentage of ID concerns are in this tier and zero concerns by neo Darwinism which essentially starts with the first cell. However, a discussion in a Robert Shapiro’s article in Scientific American over a year ago was about this and it is interesting that he invoked Darwinian processes to bolster his claims. I believe Dawkins has used natural selection as a factor in OOL. Usually, evolutionary biology stays away from origin of life issues but nearly every biology book deals with it. The complexity of the origin of life issues is one studied extensively by ID proponents and their conclusion is that only an intelligence could have produced such complex systems.

    The next tier I will call the evolution of single celled organisms. There is really quite a lot of development of significant capabilities here, including a commenter’s example of eukaryotes and such things as photosynthesis and of course the favorite, the origin of the flagellum. There are lots of changes in single celled organisms and these examples are new to us but should be examined. The question is whether the changes can be explained by naturalistic means or not. For most of this I don’t pretend to be very knowledgeable so I shy away from discussing it other than to ask questions about how much change took place and what could have caused this change and to discuss whether current answers are satisfactory or not. For example, Behe listed the flagellum as an irreducible complex system with extraordinary capabilities. Several people have said they have answered Behe’s arguments and it is not irreducibly complex but after reading them, I find them wanting and not convincing and this topic is frequently debated here.

    The third tier is how did a single cell organism form multi-cell organisms and this include how did such complex organisms as the eye arise as these multi-cell organisms arose. How, did brains, limbs, digestive systems, neurological systems arise and all the complex signaling systems between cells and organs. These are immensely complicated but get little discussion except it all happened over time. We have all seen the “it must have evolved” or “it was selected” comment in journal articles and books which is the “begging the question fallacy.” This is also an important area for ID but not as much so for Darwinists. Irreducible complexity operates extensively in this tier. Also most of these systems must have developed before the Cambrian Explosion so there is relatively little geological time for these complexities to have developed and no fossil record of such a predecessor.

    This means that the organisms that appeared during the Cambrian Explosion and their relationship to each other is important. Nothing in the organisms of the Cambrian Explosion is consistent with a gradualist approach to species. It is definitely top down, not bottom up. There is little or no diversity within the various phyla, only isolated instances of various phyla. The diversity came later. A complete contradiction to Darwinian processes. James Valentine, the most knowledgeable of all paleontologists on the Cambrian Explosion, hypothesizes some unknown mechanism that accounted for the uniqueness of each of the phyla. Nothing but speculation but something had to happen because it had to happen without an intelligent input. He begs the question. It is the begging the question fallacy applied continually through out modern evolutionary reasoning.

    The next tier is the one that gets the most debate in the popular press and that is how did one species arise from another species when there are substantial functional differences between them. This is the majors of macro evolution even though the Cambrian Explosion represents the true epitome of the macro evolution problem. How did insects, birds and bats get wings to fly, how did land creatures develop oxygen breathing systems or how did man get such a big brain and why such a long time for children to develop and where did consciousness come from. How did 4 chamber hearts and warm vs. cold blooded arise. How did birds develop their unique oxygen transport system. How did giraffes develop their unique blood pressure system. There is lots of speculation but no evidence, only a series of “just so” stories. An occasional fossil is brought up to show the progression ignoring the fact that there had to be tens of thousands of other steps for these progressions of which only a handful have been found. I believe the forest animal to whale is now neo Darwinism’s best example here and one that commenters present and even this has millions of years between slightly similar fossils. Are these occasional fossil example of gradualism in action or do they just represent various examples of different organisms whose origin is at best a mystery. In this tier the ID and the Darwinist are sometimes on common turf fighting it out. But ID is relatively less interested in the issues here but still very interested and annoyingly point out the lack of evidence to back up any “just so stories”. There is another part of this tier which I call macro-evolution light or the minors. This is how did a lot of the orders and families develop? For example, within Carnivora how did all the families arise? ID seldom cares about this area but evolutionary biology does. I don’t think ID would care much if someone showed how all the family canidae or felidae arose by gradualistic approaches but yet the evolutionary biologists would claim that would be a major verification of their theory. ID would ask what truly novel functional complex capabilities arose during this process or could all just be explained by micro evolutionary processes working on an original gene pool. In other words is this process just a trivial outcome once an original gene pool was available and basic processes which ID does not dispute are the driving forces. This area is a bridge between the third tier and the final tier.

    The final tier is what Darwin observed on his trip on the Beagle and what most of evolutionist are talking about when they think evolution, namely micro-evolution and can be explained by basic genetics, occasional mutations, environmental pressures and of course, natural selection. Few disagree on this fifth tier including those who call themselves Intelligent Design proponents yet this is where all the evidence is that is used to persuade everyone that Darwinism is a valid theory. And even here the evidence is thin with a lot of the evidence coming from changes in single celled organisms. The evidence in this tier is used to justify the first four tiers because the materialist needs all five tiers to justify their philosophy of life but the relevance of the evidence in this last tier for the other tiers is scant at best. It should be understood that Intelligent Design assumes the basic neo Darwinism micro evolutionary process and does not dispute its power to perform minor changes to the genome which is so important in areas of medicine and genetic diseases. It would be interesting to see if anti-ID examples proposed end up in this final tier or are there more substantial changes to the genomes that would require more than normal micro evolutionary processes. What changes happened to the organisms in commenters examples.

    So to sum up, my experience is that ID concentrates on tier 1, 2 and 3, a fair bit on the novelties that show up in tier 4 and are not concerned at all with tier 5 which is what Darwin observed and supplies nearly all the evidence for neo Darwinism.

    This is a framework under which I look at the evolution problems and it has proved useful in understanding objections to ID and how they are usually misplaced.

    Maybe out of this we can come up with a working definition of macro evolution. One thing that has to be considered is that micro evolution is a process while macro evolution is a result. Macro evolution is not a process so they can not be defined similarly.

    Probably would re-write it a little but not much based on 10 years of additional information.

  217. 217

    Is ID the same as design detection in other fields?

    “Design detection is a well-established scientific and investigative principle in many fields of study, including archaeology, forensics, intellectual property infringement, illegal insider trading investigation, insurance fraud detection, reverse engineering, and many others.”

    So I’m most familiar with Dembski’s work advancing this case. I find it lacking. I’ve already given my one-sentence dismissal, which I’m sure seemed capricious and non-illuminating. So let me try again.

    The argument goes something like: (1) fraud detection is part of science. (2) ID is like fraud detection. (3) ID is part of science too!

    This is not a convincing argument to me because both claim (1) and (2) are tenuous enough to make the whole argument doubtful. Let’s focus on aim 2.

    I’m sure you can write posts and posts about how ID is like SETI, fraud detection, intrusion detection, etc. But let’s start with the other side. How many differences can you list out between ID (inference to a Designer in biology and cosmology) and these things?

    Of the top of my head, I can come up with about five material differences. 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.

  218. 218

    I am not ignorant. Please, stop arguing my ignorance is the problem.

    Reading Jerry’s tome (and a few other posts too), I realized another major misconception here.

    1. I believe God designed us. In that sense I believe in intelligent design (with lower case i and d).

    2. I think some of the design inferences are reasonable and probably correct (i.e. fine tuning and origin of life). As philosophical and theological exercises, the best ID arguments make sense to me.

    3. I think that some of the design inferences are genuinely bad. If you can’t attack the bad arguments that flatter your cause, who will trust you when you present a good argument?

    4. Even for the arguments I am convinced of, I do not see justification for including them as “science” or in science textbooks. Philosophy class “yes”, science class “no.”

    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.

  219. 219
    Andre says:

    Prof Swamidass

    ID has another branch that you seem to ignore. Engineering. How do we recognise design from an engineering point of view? This is of course my special interest in the debate and I am certain you can be convinced from an engineering point of view.

  220. 220
    jerry says:

    Why not just make a solid and sound philosophical argument based on scientific knowledge? This respectable, and would end like 90% of the conflict.

    This is what ID is about, using science to make a solid and sound argument. The Wilcox review of human evolution is certainly sound and solid and he is not an official ID supporter.

    I do not understand why #4 is necessary. Why is #2 not enough?

    And why should ID ignore evolution? It sounds like you want evolution off limits and that is not a sound and solid argument philosophically or scientifically. Or theologically!!! Sound and solid arguments are made about evolution too. But it is not the only area.

    It sounds like your theology determines what will be accepted as a science argument. This is one of our main concerns with theistic evolutionists. In a way this is part of what was driving objections to Galileo, theology not science.

  221. 221
    Eric Anderson says:

    Professor Swamidass @217:

    The argument goes something like: (1) fraud detection is part of science. (2) ID is like fraud detection. (3) ID is part of science too!

    Almost, but not quite. ID stands on its own ground as a legitimate, objective way to investigate. It examines the evidence, brings in our knowledge of what we know about causes currently operational in the world, and draws an inference to the best explanation.

    The reference to other fields is primarily to give examples to help those who have a mental block against using design detection in biology so that they can — hopefully — step back a moment and look in the mirror to closely examine the source of their objection in the field of biology.

    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.

    One other point:

    There are some, even ID proponents, who aren’t particularly interested in whether ID is “science.” I think it clearly is, by any reasonable definition. But others might rationally take the view that ID is not “science” under some narrow definition, but is still a worthwhile endeavor and worth pursuing as an avenue to help us understand the world around us.

    What is your definition of “science”, and if ID does not meet your specific definition, would you still be open to considering ID as a useful avenue of inquiry?

  222. 222
    bFast says:

    Re: Prof. S. Joshua Swamidass (218)

    In general, doc, I agree with you. I would debate with you about the “science” vs. “philosophy” however. What I see in “science” is a declaration that the modern synthesis is truly adequate to explain it all. I don’t find that to be correct.

    If the scientific position were much more humble, if the scientific community were much quicker to declare “I don’t know”, then I would agree with you. I hold that any challenge to the neo-darwinian explanation, such as the evidence from the cambrian explosion or the unusual changes in the HAR1F gene, belong within science.

    If these evidences are presented as challenges for the modern synthesis, ie, the modern synthesis does not seem to have a satisfactory explanation, then I am satisfied. However, the scientific community seems determined to deny all doubt.

  223. 223
    Origenes says:

    Eric Anderson:

    Origenes: Before naturalistic science can rightfully claim common descent, as an explanation consistent with naturalism, it must explain coordination at the level of an organism as a whole from the level of fermions and bosons.

    Fermions and bosons? Oh, come on! I’d be willing to cut them a break and let them start from a complete suite of amino acids. 🙂
    http://www.uncommondescent.com.....challenge/

    James Tour says the exact same thing in different words, only a few months later:

    All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated…

    So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal.

    You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.

    Interestingly Swamidass agrees with us on this point:

    Swamidass: I think some of the design inferences are reasonable and probably correct (i.e. fine tuning and origin of life).

    Okay, so does he also agree that naturalistic science cannot rightfully use ‘organisms’ and ‘common descent’ as starting points, since it cannot ground them? That is less clear, because he immediately adds:
    “As philosophical and theological exercises, the best ID arguments make sense to me.”
    So, according to Swamidass, design inferences are “philosophical and theological exercises” and not part of science?

  224. 224
    Dionisio says:

    Prof. S. Joshua Swamidass

    Apparently @194 you mistakenly referred to post #187 but commented on another post (maybe you meant # 188?).
    In any case, your comments don’t make sense within the context of the post number you referred to (i.e. 187):

    BTW, you have ignored all the questions I have asked you.
    They are very easy to answer.
    Why do you avoid them?

    Let me repeat my posts to save you the hassle of having to scroll up/down this thread:

    My comments and questions posted @ 162, 165, 168, 169, 174, 172, 176 were for you too.

    @186

    Prof. S. Joshua Swamidass @166
    Apparently you missed seeing my comment @169 so I repeat it here:
    The question is about how exactly the TEs end up where they are?
    What mechanisms put them where they are? how? why?
    Thank you.

    @187

    Prof. S. Joshua Swamidass
    Have you studied the 2014 courses on Systems Biology by Uri Alon from Weizmann Institute for Science at Rehovot and by MIT? Would you answer some questions associated with the topic of those courses?

    Do you know exactly how the cell fate intrinsic determinants get segregated in the asymmetric mitosis ?

    Also, do you know exactly how the morphogen gradients get spatiotemporally established and interpreted?

    @206

    Prof. S. Joshua Swamidass @194

    DionisioMay: I’m gonna pass on the basic bio questions. You can find answers on wikipedia and from reading the literature. If you are really curious, maybe considering a class at a local university. There are a lot of people who can help you with that.

    Sir, your answer is wrong. You may want to read the questions carefully and you should realize that you could have answered them better.
    The precise answers to those questions are not in any literature nor their combination. Try again.
    Please, note that some of the questions are personal, hence require a personal honest response.
    Thank you.

    Regarding @186, just state whether you know the exact answer to those questions or at least can point to the exact paper(s) where it is described precisely and explained satisfactorily.

    [162, 165, 168, 169, 174, 172, 176, 186, 187, 206]

  225. 225
    Eric Anderson says:

    Origenes @223:

    I saw this statement previously, but when you quoted it this time it jumped out at me:

    Swamidass: I think some of the design inferences are reasonable and probably correct (i.e. fine tuning and origin of life).

    It seems that part of what we may be dealing with is that Professor Swamidass may think there are different design inferences, or that the design inference operates in a different way for different biological questions. This would be an incorrect view of the design inference. While different facts may of course be under scrutiny in different situations, the design inference operates essentially the same across the board.

    My hunch, though, is that the objection is not that technical or nuanced. It seems to be a general objection to the idea of design in biology, while acknowledging the force of the OOL problem — both because:

    (a) OOL is completely intractable on any naturalistic grounds and lots of people, including ardent evolutionists have admitted as much (which, conveniently, means one can doubt OOL and still enjoy respectability within Darwinist-centric academia), and

    (b) OOL is prior to, and thus cannot rely on, the inscrutable magic of random mutations and natural selection.

    In any event, I agree with you and I am gratified that Professor Swamidass acknowledges the legitimacy of the design inference in the context of OOL.

    I hope if he gets some time he will clarify why the design inference is acceptable in the fine tuning of the universe and up to the point of OOL, but not thereafter.

  226. 226
    Mung says:

    Prof Swamidass:

    I’d love to keep you informed of future stuff I do. For example, in about a month I’m planning a pretty important post on how humans are much more than just apes. It is based on a remarkable dialogue I did with a leading expert in human evolution. I think this will be of high interest to you.

    I’m also pretty involved in faith-science dialogue.

    What is the right way to let you know?

    I’m hoping that someone will reach out to Prof Swamidass and offer to allow him to post an OP at any time.

  227. 227
    Mung says:

    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 Evolution

  228. 228
    Mung says:

    It seems clear to me that the good Professor thinks that “design inference” means “goddidit.”

  229. 229
    Mung says:

    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.

  230. 230
    Mung says:

    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.

  231. 231

    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.

  232. 232

    @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.

  233. 233
    Dionisio says:

    Prof. S. Joshua Swamidass

    Please, don’t forget to answer the questions @224:

    http://www.uncommondescent.com.....ent-607486

    Thank you.

  234. 234
    Andre says:

    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.or.....141030.jpg or this…. http://www.kidport.com/reflib/.....pJoint.jpg

    built itself……..

  235. 235
    Dionisio says:

    Andre @ 234

    Is that “generous” ?

    You definitely have a good sense of humor.

    🙂

  236. 236
    jerry says:

    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.

  237. 237

    @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/journ......3292.html
    http://www.ncbi.nlm.nih.gov/pm.....MC3329511/
    http://www.ncbi.nlm.nih.gov/pm.....MC3396900/

    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/pm.....MC2286568/

    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.

  238. 238
    Eric Anderson says:

    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.

  239. 239
    bill cole says:

    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?

  240. 240
    Eric Anderson says:

    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. 🙂

  241. 241
    jerry says:

    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.

  242. 242
    bill cole says:

    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.

  243. 243
    Origenes says:

    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: (…)

  244. 244

    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.

  245. 245

    @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.

  246. 246
    jerry says:

    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.

  247. 247
    jerry says:

    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.

  248. 248
    Origenes says:

    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.

  249. 249
    Dionisio says:

    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:

    http://www.uncommondescent.com.....ent-607486

  250. 250

    @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.

  251. 251
    Origenes says:

    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.

  252. 252
    Dionisio says:

    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:
    http://www.uncommondescent.com.....t-of-life/
    http://www.uncommondescent.com.....evolution/

  253. 253
    vjtorley says:

    Hi everyone,

    I would like to thank Professor Swamidass for his comments on this thread. Discussion is still continuing over here at

    http://www.uncommondescent.com.....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.

  254. 254
    Dionisio says:

    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.

  255. 255
    Mung says:

    Please forgive my blindness.

    It’s not the blindness, it’s the unbelief. 🙂

  256. 256
    Eric Anderson says:

    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.

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