Intelligent Design

Professor Larry Moran poses five questions for the ID movement

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In a recent post over at his Sandwalk blog, Professor Larry Moran has been attempting to set the cat among the pigeons, with a list of five issues which, he anticipates, will lead to bitter recriminations within the “big tent” of the Intelligent Design movement.

Professor Moran is shocked, shocked, that Intelligent Design advocates sometimes publicly disagree on certain issues, as illustrated by a recent series of posts (by Sal Cordova, Dr. Branko Kozulic and myself) on the neutral theory of evolution. He writes:

The reason why this is so remarkable is that it almost never happens under the creationist big tent. Different Intelligent Design Creationists have widely conflicting views ranging from Young Earth Creationism to Theistic Evolution Creationism but they always manage to cover up those conflicts and present a united front in attacking evolution….

So, here’s the situation. If the IDiots actually start understanding modern evolution then there will be consequences. Some of them realize the implications and they are not happy. Here’s a brief list of issues that are now on the table under the big tent.

1. Darwinism: If the Idiots have been misinformed about evolution, which they have, then who is responsible and why were they misled by so many of their leaders?

2. Social Darwinism: If evolutionary biologists really believe in Neutral Theory and random genetic drift then how can they be supporters of the evil consequences of nineteenth century Darwinism? What about all those posts where evolutionary biologists were compared to eugenicists, racists, and Nazis?

3. Common Descent: This is a biggy. If Sal Cordova and the evolutionary biologists are right about the sequence differences between humans and chimpanzees, then it must mean that humans and chimps share a common ancestor. There will be no room under the big tent for Young Earth Creationists.

4. Junk DNA: If Cordova is right then most of the stochastic substitutions in the human genome are neutral. This must mean that most of our genome is junk. Oops! That won’t sit well with many creationists.

5. Theistic Evolution: There’s only one group that’s more evil than materialistic scientists and that’s theistic evolutionists. They are traitors. But if the IDiots actually were to accept the fundamental concepts of evolution, as Sal Cordova and Vincent Torley seem to be doing, then where does that leave Theistic Evolution Creationism? This cold be embarrassing when you look at all the posts on Uncommon Descent where theistic evolutionists have been mercilessly attacked.

Before I continue, I’d just like to point out something: the recent lively exchange of views between Intelligent Design advocates who have been blogging on Uncommon Descent on the subject of the neutral theory of evolution, has been carried out in a polite and cordial fashion, without even a trace of the name-calling, sarcasm and vulgarity that one so often finds at Websites run by outspoken atheists. That should tell you something.

I’d now like to address Professor Moran’s five questions, in turn.

1. Darwinism

1. Darwinism: If the Idiots have been misinformed about evolution, which they have, then who is responsible and why were they misled by so many of their leaders?

Professor Moran is assuming here that Intelligent Design advocates are more misinformed than most people, regarding what modern biologists believe about evolution. On this point, I think he is mistaken: nearly everyone who isn’t a biologist shares the same set of misconceptions.

A typical layperson’s view of evolution: E = NS acting on RV

In a recent post titled, Both wrong (13 February 2014), Professor PZ Myers referred to the view that “evolution is primarily a consequence of natural selection” as “a factually incorrect assertion.” Quite a few of his regular readers were sorely perplexed by this statement, and wrote in to say so:

Okay, so what am i missing? (Apart from a formal education in the biological sciences.)

I know (a little) about random mutations, the founder effect, & genetic drift. Aren’t they what natural selection acts upon? If so, it looks to me as though evolution is primarily a consequence of natural selection. (Dick the Damned)

How is evolution NOT a result of natural selection? Isn’t that exactly what Darwin taught? I am completely surprised and confused now. (dalehusband)

*Meekly raises hand*

I was under the (evidently mistaken) impression that, in nature, evolution is primarily driven by natural selection? (Sven)

I’m waiting for PZ to explain hisself here, but if he doesn’t do so soon I’m going to have to do it myself… and nobody wants that. (ChasCPeterson)

If certain lay Intelligent Design advocates such as myself, have (like most laypeople) been misinformed as to what modern biologists believe about evolution, it certainly isn’t because they were misled by leading figures in the Intelligent Design movement.

Natural selection dominates media and Internet coverage of evolution

One significant reason for the widespread confusion among laypeople is the fact that science bloggers write a lot more frequently about natural selection than about genetic drift – a point which was astutely made by commenter John Harshman, who wrote:

Well, I’m a bit surprised at the comments. Apparently Larry Moran was right, and most people have no idea about the prevalence of neutral evolution. But I can see why. Who writes popular books on the glories of drift? All the cool stuff — flight, big sharp teeth, fancy ornaments, tool use, etc. — is selection. All the science blogs are full of bizarre adaptations, but seldom a word about the boring, pointless bulk of fixations. Junk DNA just isn’t as much fun, even for many biologists, which is why so many are trying to kill it off.

The most vocal leading scientists who popularize evolution are neo-Darwinians

The other main reason why laypeople (including myself) have been misled regarding what evolutionary biologists currently believe about evolution, is that a small but vocal minority of biologists continue to espouse the neo-Darwinian view. The following quote by Richard Dawkins is typical of those scientists who fall into this camp:

There is one particular property of living things, however, that I want to single out as explicable only by Darwinian selection. This property is the one that has been the recurring topic of this book: adaptive complexity. (The Blind Watchmaker, New York: W. W. Norton & Company, Inc., 1986, Chapter 11, “Doomed Rivals,” p. 288.)

In the book’s preface, Dawkins states that he wrote the book “to persuade the reader, not just that the Darwinian world-view happens to be true, but that it is the only known theory that could, in principle, solve the mystery of our existence.”

Dawkins is not the only vocal defender of natural selection. Here’s a short passage, taken from a post titled James Shapiro goes after natural selection again (twice) on HuffPo (22 August 2012) by evolutionary biologist Jerry Coyne, in which he roundly declares that modern evolutionary biologists regard natural selection as “the only game in town” when it comes to explaining adaptations, and criticizes biologist James Shapiro for thinking otherwise:

How on earth do cytogenetics or molecular genetics alone explain the transformation of fish into tetrapods, deerlike animals into whales, or account for cryptic coloration, mimicry, and adaptive behaviors? They can’t, for there has to be some process that winnows out the variation that arises. That process is natural selection…

I wouldn’t go after Shapiro except that he spews this anti-evolutionary nonsense at HuffPo, and naive readers might get the impression that biologists are beginning to doubt that natural selection is important. Well, as far as evolutionary biologists regard adaptations, it is: natural selection is the only game in town.

Yes, we now know of a whole host of new mechanisms to generate genetic variation, including symbiosis and the ingestion of DNA from distantly related species. But to produce adaptation, something has to winnow out the wheat from the chaff: those variants that reduce reproduction from those that enhance it. And that’s natural selection. There is no alternative, and Shapiro, despite his endless series of “blogs,” has never suggested one.

How I gradually came to realize that evolutionary biologists aren’t neo-Darwinians anymore

Gradually, however, I came to realize that Coyne’s views were no longer typical of modern evolutionary biologists. I had previously written about the views of a few dissenting biologists back in 2012, in a post titled, Larry Morgan defends Paul Nelson! (December 11, 2012). But I still imagined them to be representing the views of a beleaguered minority of scientists in the field. It was only recently that I became aware that this “beleaguered minority” was actually a majority!

What prompted this startling realization was the publication of a couple of recent posts by prominent evolutionary biologists PZ Myers (The state of modern evolutionary theory may not be what you think it is, 14 February 2014) and Larry Moran (On the difference between Neutral Theory and random genetic drift, 15 February 2014). In his post, PZ Myers summed up the findings of science over the last few decades as follows:

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.

Professor Moran concurred:

What Neutral Theory tells us is that a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection. The conclusion is inescapable. Random genetic drift is, by far, the dominant mechanism of evolution.…

The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there’s more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don’t understand evolution.

There was more. Professors PZ Myers and Larry Moran also argued that a non-Darwinian mechanism could account for the origin of most complex structures in living things. In a post entitled, Complexity is not usually the product of selection (11 December 2012), PZ Myers forthrightly declared:

I think if selection were always the rule, then we’d never have evolved beyond prokaryotes — all that fancy stuff eukaryotes added just gets in the way of the one true business of evolution, reproduction…

The bottom line is that you cannot easily explain most increases in complexity with adaptationist rationales. You have to consider chance as far more important, and far more likely to produced elaborations…

Even in something as specific as the physiological function of a biochemical pathway, adaptation isn’t the complete answer, and evolution relies on neutral or nearly neutral precursor events to produce greater functional complexity.

Professor Larry Moran subsequently endorsed P.Z.Myers’ article, in a post of his own, entitled, On the Evolution of Complexity (11 December 2012), in which he wrote:

Can you go from some simple character to a more complex feature without invoking natural selection? Yes, you can. Complex features can evolve by nonadaptive means. Just think of our complex genome and read The Origins of Genome Architecture by Michael Lynch.

Want a more simple example? Read the latest post by PZ Myers: [αEP: Complexity is not usually the product of selection]1.

This is an important point. You can’t just assume, without question, that a complex trait must be an adaptation and must have arisen by natural selection. That applies to molecular complexes and also to complex behavior.

These posts, coupled with the two February 2014 posts by Professors Myers and Moran on the triumph of the neutral theory, made me decide that the time had come to stop going after neo-Darwinian evolution, as most biologists no longer accepted it anyway, and focus instead on the neutral theory of evolution. This is what I attempted to do in my first post on the neutral theory. My decision to focus on fixation rates turned out to be tactically unwise, and the factual errors that Professor Moran subsequently exposed in my post proved to be a valuable learning experience for me. But my intention – which was to shift the focus of attack away from neo-Darwinism and direct it at modern-day versions of evolution – was, I believe, quite right.

2. Social Darwinism

2. Social Darwinism: If evolutionary biologists really believe in Neutral Theory and random genetic drift then how can they be supporters of the evil consequences of nineteenth century Darwinism? What about all those posts where evolutionary biologists were compared to eugenicists, racists, and Nazis?

The Uncommon Descent posts on Social Darwinism highlighted the enormous harm wrought by three central ideas that were actively promulgated by nineteenth-century evolutionists: first, the denial of the human soul; second, the assertion that our every act (leaving aside random quantum fluctuations which cannot truly be called actions) is determined by circumstances beyond our control, which takes away our freedom of choice; and finally, the progressivist accounts of evolution that were widely propagated not only by Haeckel but also by Darwin himself, as I’ve documented in my post, Rewriting history: Can a Darwinist believe in the scala naturae? (Darwin did.) and Darwin, Kingsley, evolution and racism. (Good arguments for the existence of an immaterial human soul can be found here and here; see also here, here and here. For a refutation of arguments that the scientific evidence for determinism is so strong as to preclude the possibility of free will, see here and here; see also here, here and here.) The first two ideas debased people’s view of what it means to be human, causing many people to think of themselves as mere “meat machines” instead of individuals made in the image and likeness of God, their Creator; while the third idea lent a new legitimacy to scientific racism (which had first appeared back in the eighteenth century), as some races were thought to occupy a much higher place on the evolutionary ladder than others.

The first two ideas continue to poison people’s minds, and the neutral theory of evolution is just as imbued with them as neo-Darwinism is.

Professor Moran might point out that progressivist models of evolution are badly flawed, and that contemporary biologists unanimously reject racism. But he might do well to ponder Stephen Jay Gould’s dictum that human equality is a contingent fact of history. From a materialist standpoint, this is surely correct: were the Neandertals or Denisovans alive today, I doubt whether most evolutionary biologists would regard them as their moral equals, with the same rights to life, liberty and the pursuit of happiness as we currently enjoy.

3. Common Descent

3. Common Descent: This is a biggy. If Sal Cordova and the evolutionary biologists are right about the sequence differences between humans and chimpanzees, then it must mean that humans and chimps share a common ancestor. There will be no room under the big tent for Young Earth Creationists.

Hold on a second, Professor Moran! First of all, lumping Sal Cordova in with “evolutionary biologists” is a bit of a joke, as Sal is a committed young-earth creationist. Second, Sal Cordova is well aware of the genetic similarities and differences between humans and chimpanzees, and some time ago, he wrote a carefully worded post (which Moran reviewed), in which he drew a distinction between physical ancestors and what he called “conceptual ancestors,” and went on to argue that extensive physical similarities between two species of organisms did not mean that they were related. Third, Sal has recently written a post titled, Larry almost got it right, but he just can’t turn the corner (17 April 2014), in which he elucidates his views on the genetic differences between humans and chimpanzees, and on the neutral theory of evolution.

For my part, I have made no secret of my belief in the common descent of organisms. But if someone in the Intelligent Design movement thinks they can explain the genetic similarities and differences between humans and chimps without postulating a common ancestor for these two primates, then all I can say is: good luck to them. Why is that? Because in the ultimate scheme of things, I don’t see the question of whether we’re related to chimps as a very important one. Nothing really hangs on it, in terms of the way we live our lives. At the very most, the discovery might bring limited medical benefits, which Professor Jerry Coyne summarizes in a post titled, Of what value is evolutionary biology in medicine? (3 April 2009).

Far more important, however, than the historical question of whether we share a common ancestor with the chimp is the more fundamental philosophical question: are the genetic differences between humans and chimps at least partly the result of an act of intelligent design, or are they entirely caused by unguided processes? In a future post, I hope to outline my reasons for believing that intelligent design is the best explanation for some of the major differences between humans and other primates.

In short: the Intelligent Design “big tent” remains standing. In order to see why it’s still standing, Professor Moran just needs to get his philosophical priorities straight.

4. Junk DNA

4. Junk DNA: If Cordova is right then most of the stochastic substitutions in the human genome are neutral. This must mean that most of our genome is junk. Oops! That won’t sit well with many creationists.

Sal Cordova has already responded to Professor Moran’s argument in the post I mentioned above. I’d like to make a few comments of my own.

It appears to me that Professor Moran’s reasoning is faulty on two counts. First, the fact that “most of the stochastic substitutions in the human genome are neutral” doesn’t imply that the sections of the human genome in which they occur serve no function. It simply means that the (mostly neutral) changes taking place in that section of the genome will neither help nor harm the organism. By itself, that tells us nothing about what percentage of the genome is junk.

Second, Professor Moran is committing a verbal sleight-of-hand here: he is equating “neutral” with “junk.” As Professor Moran himself writes: “The correct definition of ‘junk’ is DNA that has no known function.” Note the wording here: “no known function.” A neutral mutation, on the other hand, is simply one that does not affect an organism’s ability to survive and reproduce. That doesn’t mean the mutation has no function; it simply means that it has no present function. A neutral mutation that might not affect an organism’s ability to reproduce, but it could still conceivably have an impact (positive or negative) on the fertility of the organism’s distant descendants. Or again, the mutation might (for all we know) incorporate information that is of no use to the particular species of organism in which it occurs, but which eventually turns out to be useful to that species’ evolutionary descendants. Of course, one would want to see some experimental evidence for these scenarios. The reason why I’m mentioning them is simply to show that Professor Moran’s equation of “neutral” with “junk” is conceptually careless.

Junk DNA – how much is there?

I’d like to preface my remarks by saying that I have no expertise whatsoever in genetics, and my knowledge of junk DNA is very limited. However, I’ve watched Professor PZ Myers’ video on junk DNA, and I’ve also skimmed Professor Moran’s lengthy review of Dr. Jonathan Wells’ book, The Myth of Junk DNA (see here for some more positive reviews and here for a list of news updates on junk DNA, over at Evolution News and Views). Suffice it to say that when a Professor of Medical Genetics writes, “I strongly recommend The Myth of Junk DNA, a lucid account of the evidence that junk DNA has many diverse biological functions,” and when a Professor of Microbial Genetics and Cell Biology adds that “Jonathan Wells has clearly done his homework,” you know the book can’t be as awful as Professor Moran claims it is. A short summary of Dr. Wells’ views on junk DNA can be found in his online article, Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information.

I would also recommend reading Dr. Richard Sternberg’s article, Matheson’s Intron Fairy Tale, Professor Moran’s reply, Sternberg’s counter-reply, Moran’s second response to Sternberg, and the follow-up article by Dr. Jonathan Wells, titled, The Fact-Free “Science” of Matheson, Hunt and Moran: Ridicule Instead of Reason, Authority Instead of Evidence. The upshot of this discussion is that of the number of human introns (non-protein coding parts of genes) that undergo alternative splicing (which suggests that they have a biological function) is at least 45,000, out of 190,000 introns in the human genome – which is far more than the figure of up to 1,000 that was originally estimated by Matheson, but which may still represent less than 30% of all introns. In short: the question of junk DNA remains open.

Of more recent interest is the September 2012 announcement by the leader of the ENCODE team that 80 percent of the genome has a “biochemical function,” meaning that “It’s not junk.” (Birney has blogged about his announcement here and here. In a review article for Nature, titled, Fighting abut ENCODE and junk (Nature News blog, 6 September 2012), science correspondent Brendan Maher offers a cooler assessment:

…[P]erhaps the main conclusion should have been that 20% of the genome in some situation can directly influence gene expression and phenotype of at least one human cell type. It’s a far cry from 80%, but a substantial increase from 1%.

Science writer Ed Yong (who originally broke news of ENCODE’s discovery), summarizes the ongoing controversy in an addendum to his report in Discover magazine (5 September 2012; update 7 September 2012):

Birney was right about the scepticism. [T. Ryan] Gregory [from Guelph University] says, “80 percent is the figure only if your definition is so loose as to be all but meaningless.” Larry Moran from the University of Toronto adds, “Functional” simply means a little bit of DNA that’s been identified in an assay of some sort or another. That’s a remarkably silly definition of function and if you’re using it to discount junk DNA it’s downright disingenuous.”…

Gregory asks why, if ENCODE is right and our genome is full of functional elements, does an onion have around five times as much non-coding DNA as we do? Or why pufferfishes can get by with just a tenth as much? Birney says the onion test is silly. While many genomes have a tight grip upon their repetitive jumping DNA, many plants seem to have relaxed that control. Consequently, their genomes have bloated in size (bolstered by the occasional mass doubling)… Conversely, the pufferfish has maintained an incredibly tight rein upon its jumping sequences. “Its genome management is pretty much perfect,” says Birney. Hence: the smaller genome.

But Gregory thinks that these answers are a dodge. “I would still like Birney to answer the question. How is it that humans “need” 100% of their non-coding DNA, but a pufferfish does fine with 1/10 as much [and] a salamander has at least 4 times as much?”

Regarding the onion test, readers might be interested in having a look at Professor Larry Moran’s post in response to a post by Jonathan M., and Jonathan M.’s subsequent reply to Moran, titled, Why the “Onion Test” Fails as an Argument for “Junk DNA” (2 November 2011). Professor Moran’s brief response is here.

Professor Moran, who still thinks that 90% of our DNA is junk, also makes the telling point that “almost 50% of our genome is littered with dead transposons and bits of transposons,” which one would not expect to have a function. Yet even he acknowledges that “there are some other scientists who think that all of the human genome is functional.”

In light of the above-mentioned uncertainties, I think a prudent estimate of the percentage of junk DNA in the human genome would be: somewhere around 50%. It could be quite a bit more … or it could be a lot less.

Junk DNA – how much could the Intelligent Design movement live with?

Suppose that the “50% junk” figure is true. Could the Intelligent Design movement live with that? Personally, I don’t see why not. Let’s try a little thought experiment. Would it bother you if 1% of our genome turned out to be junk? I don’t imagine so. All right. What about 10%? That still leaves 90% that is functional, so I can’t see why it would matter either. Well, what about 50%? Even if 50% of our DNA were junk, you could still say that half of the human genome is there for a reason, and that the remaining half, while non-functional, isn’t harming us. That doesn’t sound so bad to me. What’s the problem?

Professor PZ Myers, in a talk given to Skepticon IV on November 19-20, 2011, quotes [at 4:56] a well-known passage from the writings of Professor William Dembski on junk DNA:

[Intelligent] design is not a science stopper. Indeed, design can foster enquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.
(“Science and Religion” in First Things, 17 March 2009.)

As far as I can tell, all that follows from the hypothesis of Intelligent Design is that any organisms that were designed de novo, or from scratch, should be free of junk DNA. But even if the Intelligent Designer subsequently manipulated the DNA of these organisms’ descendants, to make other kinds of organisms, I see no reason to suppose that He would have also “wiped the slate clean” at the same time, and erased all traces of the junk DNA that had accumulated in that organism over the course of time. Of course, a Designer might do that, as an act of courtesy; but who is to say that He must? Why not simply let the junk stay there, if it’s not harming the organism and if it’s not likely to harm its descendants? What do readers think?

Dr. Richard Sternberg on letting God be God

In a 2008 article titled, How My Views on Evolution Evolved, Dr. Richard Sternberg writes:

I cannot overemphasize the number of times I have listened to evolutionary biologists theologize on the basis of some gnosis they have concerning divine actions. One case stands out in particular. Francis Collins, director of the National Human Genome Research Institute at the NIH, showed a small group that included me a presumably “dead gene,” a pseudogene. Now his line of argumentation went something like this:

A. We know this pseudogene has no function, and therefore no purpose.

B. We know also that God would not make functionless, purposeless objects.

Therefore God had no role in the creation of the pseudogene – it was a random event.

Based on my conversations with Collins, it became apparent to me that his god is a strict nineteenth-century utilitarian who would, if he deigned to create, manufacture only highly efficient and minimalist entities. His deity would only provide evidence of his handiwork by means of Bauhaus-like architectures, as Baroque or Rococo designs would be, well, excessive and wasteful. A purposefully, intelligently designed cell would, judging from his points, resemble ever so much Fritz Lang’s Metropolis. And since what we so often observe are over-the-top excrescences and strings of DNA that just don’t seem to have a purpose – bad, sloppy design according to Collins’ way of thinking – we know, we know – as a scientific fact, no less – that the genome is randomly cobbled together in length and breadth and all the way up and down.

It seems to me that Dr. Sternberg has a valid point here. It is presumptuous for us to assume that God would not allow any junk in the human genome. That being the case, we should be wary of predicting the occurrence of little or no junk DNA in the genome.

I’d now like to address Professor Larry Moran’s final point.

5. Theistic Evolution

5. Theistic Evolution: There’s only one group that’s more evil than materialistic scientists and that’s theistic evolutionists. They are traitors. But if the IDiots actually were to accept the fundamental concepts of evolution, as Sal Cordova and Vincent Torley seem to be doing, then where does that leave Theistic Evolution Creationism? This cold be embarrassing when you look at all the posts on Uncommon Descent where theistic evolutionists have been mercilessly attacked.

The term “Intelligent Design proponent” could be understood in a very broad sense, as including anyone who believes that the cosmos (or at the very least, some feature of it) was designed by an Intelligent Being. On this broad definition (used by Professor Michael Behe below), theistic evolutionists already qualify as Intelligent Design advocates.

However there are two major differences separating the ID and theistic evolution camps. As regards science, the critical question that separates Intelligent Design proponents from theistic evolutionists is not whether evolution occurred, nor even whether evolution (if it occurred) was guided by God, but rather, whether the existence of an Intelligent Being guiding evolution is scientifically detectable. Modern-day theistic evolutionists say no; Intelligent Design advocates say yes.

In addition, theistic evolutionists and ID advocates are also divided on a theological level. In a 2007 post titled, Kenneth R. Miller and the Problem of Evil, Part 2 (25 October 2007), Intelligent Design advocate Professor Michael Behe gives a very clear exposition of the key issues that separate him from Catholic biochemist Kenneth Miller, who like Behe accepts common descent but rejects Intelligent Design. Although he dislikes the label, Miller could fairly be described as a theistic evolutionist. At the end of Part 1 (October 24, 2007) of his series of posts, Behe had written:

So let me emphasize: Kenneth Miller is an intelligent design proponent. He believes that the laws of the universe were purposely set up to permit life to develop. Miller thinks that, to accomplish the goal of life, the universe had to be designed to the depth of its fundamental physical constants. I agree with him as far as he goes, but, on the other hand, as I write in The Edge of Evolution, I think design extends further into the universe, past physical constants, past anthropic coincidences, and well into biology. Yet, with respect to design, he and I differ only on degree, not on principle.

In Part 2, Behe continues:

Let me emphasize the last point of my previous post: Miller and I are only quibbling over the extent of design in the universe. The fact of design, the principle of design, we agree on.

Now, let’s look a little closer at where Ken Miller draws the limits of design (the edge of evolution, one might say). Although they are clearly necessary, is there reason to suppose that the bare laws and constants of the universe — even if properly tuned — are sufficient to assure life occurs in our universe, as Miller supposes? The answer is no — many other features than just the bare laws of the universe have to be gotten right. I discuss this at considerable length in the last chapter of the book. But don’t just take my word for it. The prominent bioinformatician Eugene Koonin recently published a paper entitled “The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life”, (Biol Direct., 2007, 2:15). The gist of the paper is that — even given fine tuned laws and constants — the origin of life in our universe is so unlikely, that the non-theist Koonin invokes an infinite multiverse to assure that life happens somewhere.

…So suppose Koonin is right that fine tuning the laws of the universe is far from sufficient to assure life. In that case, switching to Miller’s scenario, God would have set up a generic universe whose laws and constants were necessary for life, but not sufficient. Since many other conditions are required for life, Miller’s God likely made a fine tuned universe for naught. It would likely be a finely tuned universe that’s nonetheless barren of life.

In The Edge of Evolution I agree with Miller (and other “theistic evolutionists”) that the laws and constants of our universe are fine tuned, but argue that “fine-tuning” extends much more deeply into nature than previously supposed, and actually extends into life itself, at least down to the level of vertebrate class. I cleverly call this view “extended fine-tuning.” In the book I argue that any person who accepts a theistic evolutionary view, such as Miller does, should have no trouble in principle with the extended fine tuning view. It is, after all, just a matter of degree. In either case the designer fine tuned enough details of our universe to get intelligent life to arise.

In Part 3 of his series, Professor Behe goes on to address the real reason that he thinks theistic evolutionists balk at Intelligent Design: since some organisms that harm human beings (e.g. the malaria parasite) appear to have been designed according to the criteria used by the ID movement, that would appear to imply that the Designer is malevolent. In other words, the issue dividing the two camps, as Behe sees it, is a theological one. Behe’s thoughtful reply is well worth reading. After adducing supporting quotations, Behe argues that Kenneth Miller and Francisco Ayala “embrace Darwinism, at least in large part, for theological reasons”: if God is not involved in the “nuts-and-bolts” of designing Nature, then He cannot be held responsible for its dangerous by-products (such as mosquitoes). Behe doesn’t buy this argument: “It seems to me that designing a poor Darwinian process that inevitably spins off natural evils leaves One as vulnerable to being sued for incompetence as directly designing them as finished products.” He goes on to say that “as a scientist, one is obliged to look at the evidence of nature dispassionately and nonjudgmentally.” Behe adds that for all we know, parasites and viruses may “actually play positive roles in the economy of biology, of which we are in large part unaware,” in which case the harm they cause to humans is an unintended side-effect. Finally, he points out that “[e]ven if God purposely designed the malarial parasite, He may not have decreed that a particular infected mosquito would bite a particular person on a particular day.”

Behe’s conclusion is worth quoting in full:

As I wrote in The Edge of Evolution, it seems to me that our world was designed to be a a dangerous living stage, one that’s set up for improvisational theater. It allows for real suffering, real pleasure, real pain, real joy. It allows for real freedom and real consequences. But if the world were not designed in sufficient detail, then no intelligent life would be around to act on the stage.

115 Replies to “Professor Larry Moran poses five questions for the ID movement

  1. 1
    Joe says:

    Larry’s first point is just his ignorance talking- we are not misinformed wrt evolution. And, if the pro-evo posters on his blog are any indication, we have a better grasp on evolution than most evos.

    Old age hasn’t been kind to Larry. He is bitter, angry and confused.

  2. 2
    scordova says:

    VJ,

    Thank you very much for your courage and persistence. I’ve admitted at least 4 mistakes in things I said at UD this week, even a mistake over the usage of the word “postdicive” for the last 10 years. It’s no big deal.

    Disagreements can be expressed. What we have here is nothing like Richard Dawkins and Rebecca Watson and practically the entire atheist internet involved in Elevator Gate

    Here was some advice from one of the ID founders:

    Perhaps most significantly, however, we can admit our mistakes and receive instruction. The evolutionists cannot. Indeed, the moment they admit that we might have a point, they let the genie out of the bottle. To open evolutionary theory to critical scrutiny would destroy their monopoly over the study of biological origins. It is simply not an option as far as they are concerned. All the same, their no-concession policy is a loser as well. The problem with this policy is its heavy-handedness in stifling inquiry. I quoted Edward Sisson earlier about the psychology he sees at play as a litigator in which “opposing lawyers are primed to reject every statement by the other side because there is no advantage to considering that the statements might be true.” Although Sisson sees this psychology at play among evolutionists, he does not find it in our ranks: “I do not see that psychology in the work of intelligent design proponents. The fact that this psychology is missing from their work is one reason why I have come to trust them more than their opponents in the debate.” Our ability to inspire such trust is the key to victory in this debate.

    Bill Dembski
    Dealing with the Backlash

    Showing a commitment to truth over saving face inspires trust. The fact that we don’t cover up mistakes and reasoned disagreement is a sign of integrity in the process.

    I quoted Edward Sisson earlier about the psychology he sees at play as a litigator in which “opposing lawyers are primed to reject every statement by the other side because there is no advantage to considering that the statements might be true.”

    The anti-IDists will reject every statement made by our side even over trivial stuff:

    Vernal Equinox sees outbreak of DDS

    Do Dead Dogs Stay dead dogs

    A Statistics Question for Nick Matzke

    Yes Lizzie, Chance is Often an Explanation

    The Law of Large Numbers vs Keiths

  3. 3
    drc466 says:

    Here’s what I don’t understand. If evolutionary biologists are so sure that most DNA is junk because it doesn’t code for proteins, it would seem that there is a very simple way to test this (well, conceptually simple – I have no idea how difficult it would be to physically carry out).
    Strip all the “junk” out of a plant/animal’s DNA. Fertilize the egg with the “clean” DNA (following a procedure like the cloning procedure, as I understand it). See what happens.

    If creationists are correct, you’ll end up with either nothing or an extremely defective organism. If evolutionists are correct, it’ll be fine. I know where I’d put my money.

  4. 4
    scordova says:

    If creationists are correct, you’ll end up with either nothing or an extremely defective organism.

    Not necessarily, see:

    Fault Tolerance, a greater foe to Darwinism than IC

    and

    Airplane magnetos, contingency designs and reasons ID will prevail

  5. 5
    wd400 says:

    We aren’t sure most of the DNA is hjunk “because it doesn’t code for proteins,”, but for other good reasons. It’s not possible to strip all the junk DNA out of a cell.

  6. 6
    Joe says:

    I would say that we need to know more than we do before calling any DNA sequence junk. The apparent junk could be the physical storage space for information used to control transcription and other processes that DNA is involved in.

  7. 7
    Mung says:

    1. Darwinism: If the Idiots have been misinformed about evolution, which they have, then who is responsible and why were they misled by so many of their leaders?

    If Larry Moran is reading this thread and cares to answer in kind I’d certainly welcome his response.

    I will first answer this question and then respond with a few questions of my own.

    If I have been misinformed, then I am responsible and no one else. It is my responsibility and mine alone to make sure I am not misinformed, and to be always seeking the truth. There is a plethora of information out there against which to judge any claim by any so-called leaders.

    That said:

    Q1: Why isn’t Larry pointing out how IDiots have been misinformed by their so-called leaders? Wouldn’t that be more informative?

    Q2: What is the truth about evolution, and how does that “truth” obtain it’s status as truth? To be misinformed surely implies there must be a truth about which one might be misinformed. Can science demonstrate that evolution is true? How?

    Q3: Which is more valuable, to know “the truth about evolution” or to know how to tell truth from falsehood, information from misinformation and, by extension, to understand the limits of science and have the wisdom to refrain from making false claims about what the methods of science are capable of demonstrating?

  8. 8
    Mung says:

    VJT:

    Before I continue, I’d just like to point out something: the recent lively exchange of views between Intelligent Design advocates who have been blogging on Uncommon Descent on the subject of the neutral theory of evolution, has been carried out in a polite and cordial fashion, without even a trace of the name-calling, sarcasm and vulgarity that one so often finds at Websites run by outspoken atheists. That should tell you something.

    After having recently apologized for my own behaviour here at UD I am not sure I can agree with this statement! 🙂

  9. 9
    Mung says:

    Larry Moran:

    So, here’s the situation. If the IDiots actually start understanding modern evolution then there will be consequences.

    What is “non-modern evolution”? Darwinism? Neo-Darwinism? At heart you’re a Darwinist, admit it. Without Darwin there is no anti-Design argument.

    You’re going to try to explain “the appearance of design” by recourse to stochastic processes? Really?

    This is why many of us find it difficult to take the anti-ID camp seriously. The constant shell game.

  10. 10
    Mung says:

    VJT:

    In short: the Intelligent Design “big tent” remains standing. In order to see why it’s still standing, Professor Moran just needs to get his philosophical priorities straight.

    Speaking only for myself, I don’t see how this can be he case.

    Intelligent Design is an a-theological scientific enterprise. Young Earth Creationism is the exact opposite.

  11. 11
    doncarlo says:

    Professor Moran says:

    “What Neutral Theory tells us is that a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection. The conclusion is inescapable. Random genetic drift is, by far, the dominant mechanism of evolution.”

    “Junk DNA: If Cordova is right then most of the stochastic substitutions in the human genome are neutral. This must mean that most of our genome is junk. ”

    If this is correct is it correct to conclude that most of the evolution is due to junk DNA?

    Can you give solid arguments that evolution can be driven by random drift of random errors in a DNA full of junk? Isn’t that as saying we can build (whatever) by random destruction of garbage?

    How can 100000 generations of random drift of random errors in a DNA full of junk produce a human out of a monkey ancestor?

  12. 12
    gpuccio says:

    VJ:

    Here are my brief answers to Moran. But first, a general premise:

    If ID is a big tent, it’s just because whoever believe that design has a part in the configuration of natural reality is an IDist. I have said many times, here, that the beautiful thing in ID is that there is no party line. That is a good thing, not a bad thing.

    Obviously, exactly because there is no party line, I feel no obligation to believe everything that some other IDist, however important, believes. Not only I am not a YEC and not only I accept CD, which I have recently defended here, but I have also debated critically many aspects of what Dembski says, just as an example. I will go on agreeing with the things I agree with, and disagreeing with the things I disagree with. Basically, I believe in the big tent of science.

    That said, let’s go to the answers:

    1) Darwinism.

    So, according to Moran and Myers, neo darwinism is dead. That’s good news, because it means that the triumph of ID is complete. Indeed, there is not other game in place. ID is the only reasonable explanation left.

    Unfortunately, that is not so true as Moran and Myers, probably too eager to substitute a new party line for the old one, would like to believe. First of all, we should inform Dawkins and many others, including most of the debaters at TSZ, for example, that modern biology has understood, at last, that NS has no role in generating functional information in living beings, as we have always said. And that the inference to macroevolution from simple known examples of microevolution is a folly, as we have always said. They will not be happy, I presume, but who cares? At least, I will not have to spend days debating that functional selectable precursors to protein superfamilies don’t exist, and will never come into existence only because neo darwinists hope that will happen. Please, inform Petrushka, Mark Frank, Elizabeth, Zachriel, and all the intelligent people who have spent so many hours defending a wrong idea. They will not be happy, and I care for them, because they are sincere and smart persons.

    But, I don’t know why, I am not so sure that what Moran says is so final. I am not even completely sure that he really means it.

    After all, Myers states:

    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.

    Emphasis mine.

    And Moran states:

    We now know that random genetic drift is an important mechanism of evolution and there’s more to evolution than natural selection.

    Emphasis mine.

    So, what has changed under the not so big tent of neo darwinism?

    Nothing. NS is still the only useful actor. An actor who cannot act, but an actor just the same. Neutral variation and genetic drift are there, as we have always known, but are irrelevant to the problem we debate here. I have said that simple thing for years, here.

    After all, Dawkins has no reasons to be unhappy.

    2) Social Darwinism.

    I am simply not interested in the issue. However, it stands to reason that, if neo darwinism is not dead at all, as I tried to argue at point 1), then any criticism of its socail role, true or wrong that it is, is pertinent. And, if neo darwinism is dead, then those criticisms were certainly pertinent when it was still alive. So, where is the problem?

    3) Common Descent.

    My position is well known. I have been defending CD here many times, up to this same day.

    But, obviously, there is place under our “big tent” for anyone who sees design as the best explanation for biological information. Including YECs. I have the greatest respect and admiration for YECs like Sal and Paul Giem, for example. But I don’t agree with them on some important points. For clarity, I sum up here the most “conntroversial” points which I fully believe in:

    a) I believe that our earth is an old earth.

    b) I believe that Common Descent is real, that it is the best explanation for many of the facts we observe, and that it is a designed Common Descent.

    c) I am in no way a supporter of creation science. To be more clear, I don’t believe that scientific reasoning should in any way be motivated, guided or limited by what we believe religiously. What we believe religiously can certainly be an inspiration and will inevitably support us in our scientific activity, as it happens for whatever one strongly believes. But scientific activity must be kept free from undue influence of our religious beliefs.

    I hope that is clear enough.

    4) Junk DNA

    Here, the problem is very simple. Moran says:

    If Cordova is right then most of the stochastic substitutions in the human genome are neutral. This must mean that most of our genome is junk.

    Emphasis mine.

    That is simply not true. It “must not mean” anything like that.

    The simple truth is:

    a) Random Variation is mostly neutral.

    b) So called non coding DNA is mostly functional.

    c) The explanation for that is design.

    I am really disappointed Of Moran’s bad use of logic.

    The truth is that, without design, the whole genome would be junk, indeed it would not exists at all.

    5)Theistic Evolution

    That’s not a problem for me. I have never hidden what I think of TEs. They are not evil, they are not traitors. They are simply wrong. Their main idea is simply wrong and unsupported by facts.

    Now, there can certainly be variations of TE which I would even accept. So, just to be clear, I will state explicitly what I mean when I say that I don’t accept TE:

    a) I don’t believe that all the requisites for life to evolve algorithmically were set at the beginning of our physical universe. IOWs, while many of the properties of our physical universe are necessary for life to exist (see the fine tuning argument), in now way they are sufficient for life to evolve without any active design intervention after the big bang.

    But where is the problem? TEs, if they believe in that strict form of TE, are not IDists, for their own choice. They believe in design of the universe, but not in biological design, which is the main point of ID. Kenneth Miller is not an IDist, any more than Dawkins or Moran himself. They are out of the big tent, because they never entered it, and they will remain out of the big tent. And so?

    Again, I cannot see how neutral theory and genetic drift may have any relevance on the status of TEs. Again, Moran’s use of logic is really strange.

  13. 13
    StephenB says:

    VJ:

    The term “Intelligent Design proponent” could be understood in a very broad sense, as including anyone who believes that the cosmos (or at the very least, some feature of it) was designed by an Intelligent Being. On this broad definition (used by Professor Michael Behe below), theistic evolutionists already qualify as Intelligent Design advocates.

    But this broad definition can be very misleading as will become evident in these comments.

    However there are two major differences separating the ID and theistic evolution camps. As regards science, the critical question that separates Intelligent Design proponents from theistic evolutionists is not whether evolution occurred, nor even whether evolution (if it occurred) was guided by God, but rather, whether the existence of an Intelligent Being guiding evolution is scientifically detectable. Modern-day theistic evolutionists say no; Intelligent Design advocates say yes.

    Actually, I would say that the ID and theistic evolution camps are separated both in terms of [a] whether evolution was guided at all and [b] whether it is scientifically detectable. With respect to [a], no one I know in the TE camp admits that God guided evolution in such a way that it would produce a finished product that reflects His apriori intent, which would be the requirement for guided evolution. The problem here is that they (Collin’s, for example) use the rhetoric of guidedness and (sometimes) detectability (the “Languge of God”), but argue on behalf of non-guidedness and non-detectability as they embrace the the science of Darwinian (or Neutral) evolution, both of which are unguided.
    It is especially important to grasp the double-mindedness in Collins’ approach or much will be lost in the analysis. If God was really using “language,” it would be for the purpose of communicating through nature, but of course, neither Collins or any other TE believe that God communicates through nature, holding that His handiwork is undetectable. Thus, the word “language” has no meaning at all for Collins except to be used as misdirection.

    VJ quoting Behe:

    So let me emphasize: Kenneth Miller is an intelligent design proponent. He believes that the laws of the universe were purposely set up to permit life to develop.

    Well, with all due respect to Behe (and VJ), that isn’t exactly the point. Miller does not believe that God necessarily intended the result that evolution produced, which means that, for Miller, God did not design the laws of the universe to guide evolution toward a specific goal.

    Behe continued:

    He thinks that, to accomplish the goal of life, the universe had to be designed to the depth of its fundamental physical constants. I agree with him as far as he goes, but, on the other hand, as I write in The Edge of Evolution, I think design extends further into the universe, past physical constants, past anthropic coincidences, and well into biology. Yet, with respect to design, he and I differ only on degree, not on principle.

    I think the disagreement goes much deeper or at least it should. In order for evolution to be “guided,” which is a requirement for theism, it isn’t enough that the process should accomplish the “goal of life.” It must produce a specific kind of life that matches the precise intentions of the Creator. I know of no TE that believes that it does (with the possible exception of those who think like Behe).

    In The Edge of Evolution I agree with Miller (and other “theistic evolutionists”) that the laws and constants of our universe are fine tuned, but argue that “fine-tuning” extends much more deeply into nature than previously supposed, and actually extends into life itself, at least down to the level of vertebrate class. I cleverly call this view “extended fine-tuning.” In the book I argue that any person who accepts a theistic evolutionary view, such as Miller does, should have no trouble in principle with the extended fine tuning view. It is, after all, just a matter of degree. In either case the designer fine tuned enough details of our universe to get intelligent life to arise.

    Again, I am afraid that Behe misses the deeper point. If the laws and constants of our universe are sufficiently fine tuned, they will extend deeply into nature such that they guide evolution toward a specific goal. If evolution is not guided toward a specific goal, that is, if the result of the process is, as the TEs would have it, indeterminate, then either nature’s laws and fine tuning were not sufficient to produce what the Creator wanted, or else the Creator didn’t care or even know what would emerge from the process. This is not theism. I am not even sure that it rises to the level of Deism. In effect, Miller, Collins, BioLogos etc. are arguing that God designed the universe to degenerate into a hit and miss, evolutionary process that doesn’t know where it is going, which is exactly what the Godless proponents of Darwinistic (and Neutral?) evolution propose.

  14. 14
    StephenB says:

    I should have said, “If the laws and constants of our universe are sufficiently fine tuned, they will extend deeply into nature such that they guide evolution toward a specific goal” [or else the Creator will tweak them such that the desired result is attained]. Since the TEs will not allow for tweaking, and since they insist that secondary causes produce all biodiversity, they are saying that either [a] The Creator didn’t care about the final result or [b] The Creator did not sufficiently fine-tune the universe to produce a specific result. Neither argument can be reconciled with theism.

  15. 15
    gpuccio says:

    Stephen:

    I wholly agree with you. Miller is a true TE, and therefore everything I wrote in post #12 fully applies to him.

    For Behe, I am not sure. I have already criticized those passages of TEOE in the past, and I agree with you that they make no sense. But I am not sure that is really what Behe believes. I think that in that chapter he just tried to concede something to TEs, just as a possibility.

    I know, he shouldn’t have done that, but I believe he is really a very good person. Maybe too good. 🙂

    (By the way, this is not just my personal idea. When in the past I criticized those statement here at UD, someone answered me that they were probably not really Behe’s opinion, as far as he knew. Unfortunately, I cannot remember when and where exactly that discussion took place).

  16. 16
    wallstreeter43 says:

    Excellent post Stephen B, and I whole heartedly agree. It seems to me that Behe might sometimes be too gracious with theistic evolutionists like miller and Collins.

    I read Collins book language of God, and it was so disjointed in trying to describe how God fit into all of this that the Darwinists must have been having af field day with him.

  17. 17
    bornagain77 says:

    I have a few questions of my own:

    Since quantum teleportation/entanglement experiments have falsified reductive materialism as true, and have shown that we live in a universe that is information theoretic in its basis, as well as showing that the universe is dependent on a non-local, beyond space and time, cause for its continued existence, why do neo-Darwinists pretend that reductive materialism, which undergirds neo-Darwinian thought, is still true?

    2. Since non-local quantum entanglement/information, which is not reducible to a matter energy basis, is now found in molecular biology on a massive scale, why do neo-Darwinists pretend that information can ’emerge’ from a material basis?

    3. Since quantum mechanics shows us consciousness precedes material reality, instead of being emergent from it, why do neo-Darwinists pretend that consciousness is emergent from a material basis?

    4. Since the evidence for the veracity of Near Death Experiences is much, much, stronger than the evidence for neo-Darwinism is, why do neo-Darwinists so vehemently defend neo-Darwinism as true while so vehemently attacking Near Death Experiences as false?

    5. Since neo-Darwinism has no rigid mathematical basis so as to potentially falsify it, as other overarching theories of science do (including Intelligent Design), why do neo-Darwinists insist that only neo-Darwinsm is ‘scientific’ when in reality it is merely a non-falsifiable pseudo-science?

    (references upon request)

  18. 18
    kairosfocus says:

    Folks:

    I have a basic framing and tone problem with Dr Moran and ilk, as I have had occasion to say to him when he tried to target me.

    I have no reason to accept that “Creationism” is the big tent for design thought, which can be documented to have roots in the likes of that Bible-thumping fundy . . . NOT . . . Plato.

    In that context, the fallacy of the complex, insinuation-laced accusatory “question” lurks.

    So, instead of answering such questions, I think a few quick notes on underlying points and issues are appropriate:

    1 –> To become a reasonable interlocutor, Dr Moran needs to read and take to heart the UD Weak Argument Correctives. Failing which, his behaviour is willfully grounded on accusations and insinuations he knows or should know are false and toxic.

    2 –> To characterise intelligent, educated people, across the board as “IDiots” is bigotry, slander and invidious, smug stereotyping.

    3 –> To characterise us, similarly across the board, as misinformed on “evolution” is loaded and false. The theory itself is not hard to understand in essentials, whether at micro level [largely uncontroversial] or macro-level [hugely controversial, for good reason], or at a priori ideological level [even more controversial].

    4 –> FYI, the basic problem is that micro-level variations have been extrapolated beyond reason to a macro picture largely controlled by the Lewontinian a priori as aptly summarised by Lewontin in his well-known 1997 NYRB article:

    the problem is to get them to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations, and to accept a social and intellectual apparatus, Science, as the only begetter of truth [–> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]. . . .

    It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [[–> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [[–> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door. [And if you imagine that this summary is somehow “quote mined” or is justified, kindly see the wider citation and annotations in the just linked.]

    5 –> That is already enough to highlight a big problem on Science in Society, as evolutionary materialism is inherently, demonstrably, inescapably amoral; where moral is used in any sense worth having.

    6 –> In that context, the refusal to squarely face and address facts on the decades-long abuses tied to dominance of evolutionism and scientism, such as eugenics, so-called scientific racism, undermining of the sacred value of human life and the human being from conception to birth to natural death, and yes, the associated history, is a red warning flag.

    7 –> As one trained in physical sciences, with Hiroshima as the irremovable albatross around my neck as a direct result, I know that science can become a plank in an ideology that ends in awful things. When I see evolutionism advocates similarly owning the less happy facets of the past, I will have reason to be less concerned. Until that day, I will raise the biggest red warning flags I can find. Those who refuse to learn from sad history are doomed to relive it.

    8 –> Common descent is irrelevant to the focal question addressed by the design inference: whether or no, there are empirical signs that on vera causa basis, point to design as best current explanation of certain features of the natural world, including cell based life. On evidence, the best answer to this is, yes.

    9 –> As to various views on origins otherwise and their warrant, let every tub stand on its own bottom.

    10 –> That’s right, let the evidence decide.

    11 –> As in, a scientific, design perspective can live with universal common descent in an old earth and cosmos, indeed with a world in which purely natural means led to the origin and diversification of life to include us. Especially, as that implies fine tuning to an astonishing degree above and beyond what is already on the table.

    12 –> Which brings out, that the reason why it is argued that the world of life reflects signs of design is . . . because that is so blatantly so, as even Dawkins has long since had to concede in defining biology as the study of complicated things that have the [strong] appearance of design.

    ___________________

    I trust that we can now move to a more reasonable basis for discussion.

    KF

  19. 19
    kairosfocus says:

    BA77, in 17: I hereby request, show us the list — or maybe even better, link to an annotated bibliography page kept at Google Drive or the like. (Cf. the one I did for IOSE, meant as a 101, here.) KF

  20. 20
    Axel says:

    Thank you BA77 for your #17. It could well be that that, or an amplified version of it, will one day be a famously historical, because long overdue, setting forth of the basic truths of modern science, established as far back as the early 20th century.

    Moreover, since the progress of QM research has been uniquely successful, in terms of its relentless vindication by its practicable usage in industrial manufacturing, and yet is still marginalised by the materialist establishment in favour of idle, gratuitous conjecture, the shame attaching to the wilful stupidity of atheism’s brightest and best will know no bounds, in the eyes of everyone throughout all levels of society.

    Perhaps your conspectus will be the first text taught to science pupils in schools; together atheism’s mindless obstructionism. I hope so.

  21. 21
    Axel says:

    It is even written in a very simple and lucid style – which seems as uncommon for you as it is for me, when I hold forth.

    I think we normally demonstrate the Latins’ prolixity and verbosity: Balzacian, I would venture. The Italians, for that matter, will use six words where one would suffice. Isn’t that so, gp? However, the nature of the topics you address in any detail, by and large, evidently prohibit a simple treatment.

  22. 22
    gpuccio says:

    Axel:

    Even more than six, I would say! 🙂

  23. 23
    Axel says:

    I’ll happily concede on that, gp!

    I sometimes used to talk on the phone to a translator at the Court of Human Rights in Luxembourg, and he said he wouldn’t touch Italian for that reason.

    That would, of course, have been formal, legal language, but from what I’ve seen of the vernacular, it would be right off the dial!!!

  24. 24
    bornagain77 says:

    kf, seeing that I have gone over these basic points on several occasions, I’m a bit surprised you would request the references, as it would seem to be boring for you. But I guess you mean it, at the risk of boring people, to prove a point. So here is an overview of the references for each of the 5 questions that I asked at post 17:

    1.

    Since quantum teleportation/entanglement experiments have falsified reductive materialism as true, and have shown that we live in a universe that is information theoretic in its basis, as well as showing that the universe is dependent on a non-local, beyond space and time, cause for its continued existence, why do neo-Darwinists pretend that reductive materialism, which undergirds neo-Darwinian thought, is still true?

    Here are my references for the claim that “energy and mass both reduce to information”:

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    New Breakthrough in (Quantum) Teleportation – video
    http://www.youtube.com/watch?v=6xqZI31udJg
    Quote from preceding video:
    “There are 10^28 atoms in the human body.,, The amount of data contained in the whole human,, is 3.02 x 10^32 gigabytes of information. Using a high bandwidth transfer that data would take about 4.5 x 10^18 years to teleport 1 time. That is 350,000 times the age of the universe.”

    Physicists set new record for quantum teleportation with matter qubits – Apr 16, 2013
    Excerpt: “The greatest significance of our work is the dramatic increase in efficiency compared to previous realizations of matter-matter teleportation,” Nölleke said. “Besides, it is the first demonstration of matter-matter teleportation between truly independent systems and constitutes the current record in distance of 21 m. The previous record was 1 m.”
    http://phys.org/news/2013-04-p.....ubits.html

    How Teleportation Will Work –
    Excerpt: In 1993, the idea of teleportation moved out of the realm of science fiction and into the world of theoretical possibility. It was then that physicist Charles Bennett and a team of researchers at IBM confirmed that quantum teleportation was possible, but only if the original object being teleported was destroyed. — As predicted, the original photon no longer existed once the replica was made.
    http://science.howstuffworks.c.....ation1.htm

    Unconditional Quantum Teleportation – abstract
    Excerpt: This is the first realization of unconditional quantum teleportation where every state entering the device is actually teleported,,
    http://www.sciencemag.org/cont.....6.abstract

    As to the ‘information theoretic’ foundation of the universe:

    “it from bit” Every “it”— every particle, every field of force, even the space-time continuum itself derives its function, its meaning, its very existence entirely—even if in some contexts indirectly—from the apparatus-elicited answers to yes-or-no questions, binary choices, bits. “It from bit” symbolizes the idea that every item of the physical world has a bottom—a very deep bottom, in most instances, an immaterial source and explanation, that which we call reality arises in the last analysis from the posing of yes-no questions and the registering of equipment—evoked responses, in short all matter and all things physical are information-theoretic in origin and this is a participatory universe.”
    – Princeton University physicist John Wheeler (1911–2008) (Wheeler, John A. (1990), “Information, physics, quantum: The search for links”, in W. Zurek, Complexity, Entropy, and the Physics of Information (Redwood City, California: Addison-Wesley))

    Why the Quantum? It from Bit? A Participatory Universe?
    Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.”
    Anton Zeilinger – a leading expert in quantum teleportation:

    as to the dependence of the universe on a ‘non-local’ beyond space and time, cause to explain its continued existence:

    Bohemian Gravity – Rob Sheldon – September 19, 2013
    Excerpt: Quanta magazine carried an article about a hypergeometric object that is as much better than Feynman diagrams as Feynman was better than Heisenberg’s S-matrices. But the discoverers are candid about it,
    “The amplituhedron, or a similar geometric object, could help by removing two deeply rooted principles of physics: locality and unitarity. “Both are hard-wired in the usual way we think about things,” said Nima Arkani-Hamed, a professor of physics at the Institute for Advanced Study in Princeton, N.J., and the lead author of the new work, which he is presenting in talks and in a forthcoming paper. “Both are suspect.””
    What are these suspect principles? None other than two of the founding principles of materialism–that there do not exist “spooky-action-at-a-distance” forces, and that material causes are the only ones in the universe.,,,
    http://rbsp.info/PROCRUSTES/bohemian-gravity/

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect (Bohr vs. Einstein) – video
    http://www.metacafe.com/w/4744145

    Quantum Physics Debunks Materialism – video
    https://www.youtube.com/watch?v=4C5pq7W5yRM

  25. 25
    bornagain77 says:

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Zeilinger Group – Photons run out of loopholes – April 15, 2013
    Excerpt: A team led by the Austrian physicist Anton Zeilinger has now carried out an experiment with photons, in which they have closed an important loophole. The researchers have thus provided the most complete experimental proof that the quantum world is in conflict with our everyday experience.,,,
    In a nutshell: “Our photons can no longer duck out of being measured,” says Zeilinger.
    http://vcq.quantum.at/research.....s/419.html

    Closing the last Bell-test loophole for photons – Jun 11, 2013
    Excerpt: In the years since, many “Bell tests” have been performed, but critics have identified several conditions (known as loopholes) in which the results could be considered inconclusive. For entangled photons, there have been three major loopholes; two were closed by previous experiments. The remaining problem, known as the “detection-efficiency/fair sampling loophole,” results from the fact that, until now, the detectors employed in experiments have captured an insufficiently large fraction of the photons, and the photon sources have been insufficiently efficient. The validity of such experiments is thus dependent on the assumption that the detected photons are a statistically fair sample of all the photons. That, in turn, leaves open the possibility that, if all the photon data were known, they could be described by local realism.
    The new research, conducted at the Institute for Quantum Optics and Quantum Communication in Austria, closes the fair-sampling loophole by using improved photon sources (spontaneous parametric down-conversion in a Sagnac configuration) and ultra-sensitive detectors provided by the Single Photonics and Quantum Information project in PML’s Quantum Electronics and Photonics Division. That combination, the researchers write, was “crucial for achieving a sufficiently high collection efficiency,” resulting in a high-accuracy data set – requiring no assumptions or correction of count rates – that confirmed quantum entanglement to nearly 70 standard deviations.,,,
    http://phys.org/news/2013-06-b.....otons.html

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: The new hidden influence inequality shows that the getout won’t work when it comes to quantum predictions. To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed.
    Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can’t stay hidden, or they must have infinite speed.,,, “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    Why Quantum Theory Does Not Support Materialism – By Bruce L Gordon:
    Excerpt: Because quantum theory is thought to provide the bedrock for our scientific understanding of physical reality, it is to this theory that the materialist inevitably appeals in support of his worldview. But having fled to science in search of a safe haven for his doctrines, the materialist instead finds that quantum theory in fact dissolves and defeats his materialist understanding of the world.
    http://www.4truth.net/fourtrut.....8589952939

    2.

    Since non-local quantum entanglement/information, which is not reducible to a matter energy basis, is now found in molecular biology on a massive scale, why do neo-Darwinists pretend that information can ‘emerge’ from a material basis?

    and here are my references in that regard:

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

    Quantum Information/Entanglement In DNA – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement between the electron clouds of nucleic acids in DNA – Elisabeth Rieper, Janet Anders and Vlatko Vedral – February 2011
    http://arxiv.org/PS_cache/arxi.....4053v2.pdf

    Quantum Entanglement Holds DNA Together, Say Physicists – June 28, 2010
    http://www.technologyreview.co.....hysicists/

  26. 26
    bornagain77 says:

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009
    Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
    http://www.dailygalaxy.com/my_.....ave-t.html

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini and Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73
    Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
    http://www.scimednet.org/quant.....d-protein/

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from.
    To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
    Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.
    http://www.technologyreview.co.....f-protein/

    Persistent dynamic entanglement from classical motion: How bio-molecular machines can generate non-trivial quantum states – November 2011
    Excerpt: We also show how conformational changes can be used by an elementary machine to generate entanglement even in unfavorable conditions. In biological systems, similar mechanisms could be exploited by more complex molecular machines or motors.
    http://arxiv.org/abs/1111.2126

    INFORMATION AND ENERGETICS OF QUANTUM FLAGELLA MOTOR
    Hiroyuki Matsuura, Nobuo Noda, Kazuharu Koide Tetsuya Nemoto and Yasumi Ito
    Excerpt from bottom page 7: Note that the physical principle of flagella motor does not belong to classical mechanics, but to quantum mechanics. When we can consider applying quantum physics to flagella motor, we can find out the shift of energetic state and coherent state.
    http://www2.ktokai-u.ac.jp/~shi/el08-046.pdf

    It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (John Bell, A. Aspect, A. Zeilinger) Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

    3.

    Since quantum mechanics shows us consciousness precedes material reality, instead of being emergent from it, why do neo-Darwinists pretend that consciousness is emergent from a material basis?

    Here are a few of my references in that regard:

    Quantum physics says goodbye to reality – Apr 20, 2007
    Excerpt: Many realizations of the thought experiment have indeed verified the violation of Bell’s inequality. These have ruled out all hidden-variables theories based on joint assumptions of realism, meaning that reality exists when we are not observing it; and locality, meaning that separated events cannot influence one another instantaneously. But a violation of Bell’s inequality does not tell specifically which assumption – realism, locality or both – is discordant with quantum mechanics.
    Markus Aspelmeyer, Anton Zeilinger and colleagues from the University of Vienna, however, have now shown that realism is more of a problem than locality in the quantum world. They devised an experiment that violates a different inequality proposed by physicist Anthony Leggett in 2003 that relies only on realism, and relaxes the reliance on locality. To do this, rather than taking measurements along just one plane of polarization, the Austrian team took measurements in additional, perpendicular planes to check for elliptical polarization.
    They found that, just as in the realizations of Bell’s thought experiment, Leggett’s inequality is violated – thus stressing the quantum-mechanical assertion that reality does not exist when we’re not observing it. “Our study shows that ‘just’ giving up the concept of locality would not be enough to obtain a more complete description of quantum mechanics,” Aspelmeyer told Physics Web. “You would also have to give up certain intuitive features of realism.”
    http://physicsworld.com/cws/article/news/27640

    “I’m going to talk about the Bell inequality, and more importantly a new inequality that you might not have heard of called the Leggett inequality, that was recently measured. It was actually formulated almost 30 years ago by Professor Leggett, who is a Nobel Prize winner, but it wasn’t tested until about a year and a half ago (in 2007), when an article appeared in Nature, that the measurement was made by this prominent quantum group in Vienna led by Anton Zeilinger, which they measured the Leggett inequality, which actually goes a step deeper than the Bell inequality and rules out any possible interpretation other than consciousness creates reality when the measurement is made.” – Bernard Haisch, Ph.D., Calphysics Institute, is an astrophysicist and author of over 130 scientific publications.

    Quantum Physics – (material reality does not exist until we look at it) – Dr. Quantum video
    http://www.youtube.com/watch?v=D1ezNvpFcJU

    A team of physicists in Vienna has devised experiments that may answer one of the enduring riddles of science: Do we create the world just by looking at it? – 2008
    Excerpt: In mid-2007 Fedrizzi found that the new realism model was violated by 80 orders of magnitude; the group was even more assured that quantum mechanics was correct.
    Leggett agrees with Zeilinger that realism is wrong in quantum mechanics, but when I asked him whether he now believes in the theory, he answered only “no” before demurring, “I’m in a small minority with that point of view and I wouldn’t stake my life on it.” For Leggett there are still enough loopholes to disbelieve. I asked him what could finally change his mind about quantum mechanics. Without hesitation, he said sending humans into space as detectors to test the theory.,,,

    (to which Anton Zeilinger responded)

    When I mentioned this to Prof. Zeilinger he said, “That will happen someday. There is no doubt in my mind. It is just a question of technology.” Alessandro Fedrizzi had already shown me a prototype of a realism experiment he is hoping to send up in a satellite. It’s a heavy, metallic slab the size of a dinner plate.
    http://seedmagazine.com/conten....._tests/P3/

  27. 27
    bornagain77 says:

    Nonlocal “realistic” Leggett models can be considered refuted by the before-before experiment – 2008 – Antoine Suarez Center for Quantum Philosophy,
    Excerpt: (page 3) The independence of quantum measurement from the presence of human consciousness has not been proved wrong by any experiment to date.,,,
    “nonlocal correlations happen from outside space-time, in the sense that there is no story in space-time that tells us how they happen.”
    http://www.quantumphil.org/SuarezFOOP201R2.pdf

    A simple approach to test Leggett’s model of nonlocal quantum correlations – 2009
    Excerpt of Abstract: Bell’s strong sentence “Correlations cry out for explanations” remains relevant,,,we go beyond Leggett’s model, and show that one cannot ascribe even partially defined individual properties to the components of a maximally entangled pair.
    http://www.mendeley.com/resear.....relations/

    Violation of Leggett inequalities in orbital angular momentum subspaces – 2010
    Main results. We extend the violation of Leggett inequalities to the orbital angular momentum (OAM) state space of photons, which is associated with their helical wavefronts. We define our measurements in a Bloch sphere for OAM and measure the Leggett parameter LN (where N is the number of settings for the signal photon) as we change the angle ? (see figure). We observe excellent agreement with quantum mechanical predictions (red line), and show a violation of five and six standard deviations for N = 3 and N = 4, respectively.
    http://iopscience.iop.org/1367-2630/12/12/123007

    due to advances in quantum mechanics, the argument for God from consciousness can now be framed like this:

    1. Consciousness either preceded all of material reality or is a ‘epi-phenomena’ of material reality.
    2. If consciousness is a ‘epi-phenomena’ of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.
    3. Consciousness is found to have a special, even central, position within material reality.
    4. Therefore, consciousness is found to precede material reality.

    Four intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material reality (Wigner’s Quantum Symmetries, Wheeler’s Delayed Choice, Leggett’s Inequalities, Quantum Zeno effect):
    https://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit

    4.

    Since the evidence for the veracity of Near Death Experiences is much, much, stronger than the evidence for neo-Darwinism is, why do neo-Darwinists so vehemently defend neo-Darwinism as true while so vehemently attacking Near Death Experiences as false?

    And here are a few of my references in that regard:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Where’s the substantiating evidence for neo-Darwinism?
    https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

    Dr. Jeffrey Long: Just how strong is the evidence for a afterlife? – video
    http://www.youtube.com/watch?v=mptGAc3XWPs

    Facts about NDEs – video clip on the site
    Excerpt: In 1982 a Gallup poll estimated that 8 million Americans have had a near-death experience and a more recent study, a US News & World Report in March of 1997, found that 15 million have had the experience.
    http://www.ndelight.org/index......;Itemid=63

  28. 28
    bornagain77 says:

    Near-Death Experiences: Putting a Darwinist’s Evidentiary Standards to the Test – Dr. Michael Egnor – October 15, 2012
    Excerpt: Indeed, about 20 percent of NDE’s are corroborated, which means that there are independent ways of checking about the veracity of the experience. The patients knew of things that they could not have known except by extraordinary perception — such as describing details of surgery that they watched while their heart was stopped, etc. Additionally, many NDE’s have a vividness and a sense of intense reality that one does not generally encounter in dreams or hallucinations.,,,
    The most “parsimonious” explanation — the simplest scientific explanation — is that the (Near Death) experience was real. Tens of millions of people have had such experiences. That is tens of millions of more times than we have observed the origin of species (or origin of life), which is never.,,,
    The materialist reaction, in short, is unscientific and close-minded. NDE’s show fellows like Coyne at their sneering unscientific irrational worst. Somebody finds a crushed fragment of a fossil and it’s earth-shaking evidence. Tens of million of people have life-changing spiritual experiences and it’s all a big yawn.
    Note: Dr. Egnor is professor and vice-chairman of neurosurgery at the State University of New York at Stony Brook.
    http://www.evolutionnews.org/2.....65301.html

    “A recent analysis of several hundred cases showed that 48% of near-death experiencers reported seeing their physical bodies from a different visual perspective. Many of them also reported witnessing events going on in the vicinity of their body, such as the attempts of medical personnel to resuscitate them (Kelly et al., 2007).”
    Kelly, E. W., Greyson, B., & Kelly, E. F. (2007). Unusual experiences near death and related phenomena. In E. F. Kelly, E. W. Kelly, A. Crabtree, A. Gauld, M. Grosso, & B. Greyson, Irreducible mind (pp. 367-421). Lanham, MD: Rowman & Littlefield.

    Michaela’s Amazing NEAR death experience – video
    http://www.youtube.com/watch?v=jTcHWz6UMZ8

    The extremely ‘monitored’ NDE of Pam Reynolds – video
    https://www.youtube.com/watch?v=WNbdUEqDB-k

    “I think death is an illusion. I think death is a really nasty, bad lie. I don’t see any truth in the word death at all” –
    Pam Reynolds Lowery (1956 – May 22, 2010)

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video (notes in description)
    http://vimeo.com/29895068

    Quantum Entangled Consciousness (Permanence of Quantum Information) – Life After Death – Stuart Hameroff – video
    https://vimeo.com/39982578

    Evidence that the Mind is not the Brain:
    https://docs.google.com/document/d/15oyK3PlUILewPmxGZreNHd1gZrTTlZ68Gf9LURNTquY/edit

    5.

    Since neo-Darwinism has no rigid mathematical basis so as to potentially falsify it, as other overarching theories of science do (including Intelligent Design), why do neo-Darwinists insist that only neo-Darwinsm is ‘scientific’ when in reality it is merely a non-falsifiable pseudo-science?

    For this question, I will merely reference this quote and site:

    “nobody to date has yet found a demarcation criterion according to which Darwin(ism) can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote was as stated in 1973 LSE Scientific Method Lecture

    Darwinian Evolution is a Pseudo-Science – Part II
    https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/edit

    Verse and Music:

    Job 38:2-7
    Who is this that darkeneth counsel by words without knowledge?
    Gird up now thy loins like a man; for I will demand of thee, and answer thou me.
    Where wast thou when I laid the foundations of the earth? declare, if thou hast understanding.
    Who hath laid the measures thereof, if thou knowest? or who hath stretched the line upon it?
    Whereupon are the foundations thereof fastened? or who laid the corner stone thereof;
    When the morning stars sang together, and all the sons of God shouted for joy?

    Apocalypitca – Nothing Else Matters –
    http://www.youtube.com/watch?v=RSMXMv0noY4

  29. 29
    fossil says:

    Bornagain77 at #17, What I see as the real problem Darwinists have with ID and creationism is the whole concept of a designer which has implications they don’t even want to think about. Because of that they have a commitment to exclude anything that can be interpreted as involving an outside intelligence. So for them, of necessity, everything must be a matter of random events and/or controlled by the laws of science and nothing more.

    As for what gpuccio said at #12, “But scientific activity must be kept free from undue influence of our religious beliefs” I don’t see how that can be achieved in any practical way. As Dr. Hunter so often says, “Religion drives science and it matters.” The problem is that we all have to start somewhere and that is usually our world view which is philosophical and religion based. Since our world view is usually the starting point how can our religious beliefs not be a part of the science we do?

  30. 30
    Upright BiPed says:

    I’m just shocked that Larry asked ID proponents about Social Darwinism and Theistic Evolutionists, while passing up the prime opportunity to ask us how an irreducibly complex semiotic system was arranged to bridge (yet maintain) the physical discontinuity between the primordial genotype and phenotype in order to organize the first Darwinian-capable cell on Earth.

    There must be some really good reason for this obvious oversight. Surely he would want to hit us where we hurt, no?

  31. 31
    gpuccio says:

    fossil:

    Of course our beliefs, religious or not, are a part of what we do, including science. And they influence what we do, many times without any awareness of that on our part. That’s why cognitive bias is a part of any cognitive activity, and cannot be avoided.

    But there are different kinds of cognitive bias. Some forms, as said, are physiological and unavoidable. Other forms are pathological bias, that should be avoided, especially in science.

    I will be more clear. Let’s say that I try to make science in a certain field. My beliefs, religious or not, will influence me, will inspire me, will be connected to my motivations and to my understanding. That is good, and there is nothing wring in that.

    So, I make science as impartially and objectively as I can, because it is part of my beliefs that I have to be impartial and objective in making science, and therefore I try. I will not be really impartial and objective, but I try. Why? Because I believe that science is an impartial way of searching truth, and as I believe in my beliefs, I am confident that truth, however pursued, is a good thing. And if some of my beliefs were wrong, I would be happy to change them, as soon as I am really convinced that they are wrong.

    This is one attitude.

    Another attitude is: I believe that my beliefs, religious or not, are right. Therefore, I will intentionally organize all my scientific activities with the explicit purpose of demonstrating scientifically that they are right. I will make science honestly, but not impartially, because my starting point is that my beliefs are right, and that conviction will consciously and intentionally shape all my scientific activities.

    The second attitude is, IMO, common to many darwinists and to many who are in creation science. I am not judging them in any way. But it is not the attitude that I choose, and I don’t think it is a good attitude for science.

  32. 32
    Axel says:

    Nice to see the full treatise in one place, to, BA77. Thanks.

    Intellectual zombies, materialists have been ‘dead men talking’ for far too long.’

  33. 33
    fossil says:

    Gpuccio on #31 thank you for clarifying your point and I do agree with you. However, I do think that conscious bias can be present with anyone regardless of their stand and doesn’t reside exclusively with Darwinists or Creationists. I am a Creationist but will listen to other viewpoints and consider them because I think they may have something valuable to contribute but when in theology mode I can become very stubborn. Therefore, the problem I see in science is a general unwillingness to consider opposing viewpoints which seems to have plagued science for centuries.

    Both the Darwin camp and those in Creationism have had to change their understanding as knowledge increased. At one time Creationists were locked on fixity but have changed that view because it became quite obvious that biology can change. Likewise Professor Moran, of necessity, had to drop the idea of selection because it is becoming very clear that there are other things that are also involved in biological change.

    The one thing that I like about Dr. Torley and Dr. Cordova is that they remain flexible and open to other opinions rather than being closed minded and dogmatic. They are even willing to admit they were wrong. I think that speaks mountains for their integrity which is something I have trouble saying about the fanatics in the other camp.

  34. 34
    ppolish says:

    Re-reading “On the Origin of Species” reminds one how quaint the theory is. Spectacular, sure, but quaint.

    Design in Nature is so obvious now. Heck, obvious to anti-Darwin D’Arcy Thompson years ago. Smart guy, that D’Arcy. Dawkin’s nomination for “most learned Polymath” ever. A Design Guy no less. Richard is learning. Baby steps.

  35. 35
    gpuccio says:

    fossil:

    Thank you for your comments. I agree on much of what you say.

    You see, my position is that I am an IDist because I am really enthusiast of ID as a scientific theory, and I am completely disappointed by the current dogmas in darwinism, neo darwinism, neo neo darwinism, moranism, and you name it.

    The concept of specified information, and of functionally specified information, has been for me love at first sight. It is simple, beautiful and powerful. It connects the realm of consciousness with the realm of objective science in a rigorous way that has never been achieved before.

    Biology has reached such depths of information that it is becoming the leading field in science. And biology and consciousness are strictly related.

    So, I believe that we are near to a true revolution in scientific thought, and in human thought. Current reductionist ideology is a real obstacle to this growth in understanding, and it must be defeated.

    I am enthusiastic about ID for what ID is. My religion is in perfect harmony with that, but it is not the cause of that. I am scientifically enthusiastic about ID, and it gives me huge intellectual satisfaction to deepen its aspects and potentialities. And I really try to do that impartially, as much as it is humanly possible, because that is the way to obtain the best results from a search for truth, from any search for truth.

    That is how I feel about that. And I like to feel that way.

  36. 36
    Querius says:

    gpuccio noted

    But there are different kinds of cognitive bias. Some forms, as said, are physiological and unavoidable. Other forms are pathological bias, that should be avoided, especially in science.

    One prevalent form of pathological bias is ideological contamination. A good example from many years ago is the seemingly a priori rejection of the clay matrix origin of life. Similarly, other people are overly quick to accept conclusions with which they find ideological affinity. For example, I understand that Marxist biologists in the former Soviet Union were quick to accept punctuated equilibrium.

    Another bias stems from a desire to let no mystery stand, and to force fit the most acceptable speculation as fact. I once looked up “pituitary” in a dictionary from the late 1800s. In it they quoted a now-laughable speculation (it involved the voice) from an authoritative source in the Royal Society.

    Oversimplification is also a logical bias. For example, non-coding DNA, might have regions that act as a genetic scratch pad. An unknown function is exactly that. Unknown. Dr. Ohno made a mistake in labeling it “junk” (although he did propose a benefit from having junk DNA as a mutational buffer.

    Personal qualities such as integrity and critical thinking play such a key role in science. As one of my chemistry professors used to say (paraphrasing H.L. Mencken), “For every problem in Chemistry, there is a solution. Neat. Plausible. And wrong.”

    -Q

  37. 37
    Joe says:

    Larry Moron:

    3.Common Descent: This is a biggy. If Sal Cordova and the evolutionary biologists are right about the sequence differences between humans and chimpanzees, then it must mean that humans and chimps share a common ancestor.

    Nope, that doesn’t follow. Camaros and Firebirds show quite a bit of similarity, via a common design.

    If and ONLY if what makes an organism (what it is) = its genome is Larry correct. Yet there still isn’t any evidence to support that claim.

    What has yet to be explained, ie what needs to be explained, are the physiological and anatomical differences between chimps and humans.

    After all voles have been evolving faster than chimps and humans and a vole is still a vole:

    The study focuses on 60 species within the vole genus Microtus, which has evolved in the last 500,000 to 2 million years. This means voles are evolving 60-100 times faster than the average vertebrate in terms of creating different species. Within the genus (the level of taxonomic classification above species), the number of chromosomes in voles ranges from 17-64. DeWoody said that this is an unusual finding, since species within a single genus often have the same chromosome number.

    Among the vole’s other bizarre genetic traits:

    •In one species, the X chromosome, one of the two sex-determining chromosomes (the other being the Y), contains about 20 percent of the entire genome. Sex chromosomes normally contain much less genetic information.

    •In another species, females possess large portions of the Y (male) chromosome.

    •In yet another species, males and females have different chromosome numbers, which is uncommon in animals.

    A final “counterintuitive oddity” is that despite genetic variation, all voles look alike, said DeWoody’s former graduate student and study co-author Deb Triant.

    “All voles look very similar, and many species are completely indistinguishable,” DeWoody said.

    In one particular instance, DeWoody was unable to differentiate between two species even after close examination and analysis of their cranial structure; only genetic tests could reveal the difference.

    Nevertheless, voles are perfectly adept at recognizing those of their own species.

    “Oh Joe, obviously the RIGHT genes didn’t evolve, otherwise it would have evolved into something unvole-like. You see it is those RIGHT genes that need evolving or else nothing much happens in the way of universal common descent.”

  38. 38
    Joe says:

    I do not accept Universal Common Descent for the simple reason it is untestable. And it is untestable because no one knows what makes an organism what it is. Dr Giuseppe Sermonti put it this way in “Why is a Fly Not a Horse?”:

    ”The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter [same as the book]. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”

  39. 39
    wd400 says:

    Gpuccio,

    The simple truth is:

    a) Random Variation is mostly neutral.

    b) So called non coding DNA is mostly functional.

    How to you marry (a) and (b)? Most of the genome is functional but randomly changing it has effectively no effect?

  40. 40
    bornagain77 says:

    too funny, wd400 counseling someone on how to handle the cognitive dissonance of a incoherent position. 🙂

    Perhaps when you are done counseling him wd400 you can tell me how you managed the incoherency in this Darwinian paradox:

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.arn.org/blogs/index....._contradic

  41. 41
    Mung says:

    Upright BiPed:

    There must be some really good reason for this obvious oversight. Surely he would want to hit us where we hurt, no?

    No doubt he would, if he could actually find a place to hit us where it hurt, and provided he’s not a total intellectual weakling.

  42. 42
    Mung says:

    Why does Moran lead off with Darwinism? I thought he was not even himself a Darwinist. So if it’s not a problem for him, why is it a problem for ID?

  43. 43
    Mung says:

    Upright BiPed:

    I’m just shocked that Larry asked ID proponents about Social Darwinism and Theistic Evolutionists, while passing up the prime opportunity to ask us how an irreducibly complex semiotic system was arranged to bridge (yet maintain) the physical discontinuity between the primordial genotype and phenotype in order to organize the first Darwinian-capable cell on Earth.

    Truly shocked, are you?

    Life is a striking state of material that emerged 3.6 billion years ago on our earth. It has the ability of self-reproduction, by keeping information about itself in itself. The marriage of information and matter makes it possible to implement the evolutional mechanism. Thus, life has developed to achieve a variety of amazing structures and functions. In particular, we humans have appeared, with the characteristics of intelligence and consciousness, constructing societies and culture. Now the time is ripe to understand the mechanisms of living systems, where information is kept and processed efficiently and robustly. These mechanisms are highly complex and exquisite; their structures range from the molecular level to the higher level of the brain function. Advanced information science/technology is required to decipher the information mechanisms of life.

    here

  44. 44
    Upright BiPed says:

    Thanks Mung, too bad the content isn’t in the file. I’d like to read the fundamentals.

  45. 45
    Mung says:

    I sure hope you can get your hands on some of these papers.

    …the elucidation of the genetic code and the consequent formulation of the central dogma represented the first, and so far only, discovery of a form of symbolic encoding of information in a natural system. The realization that living matter had evolved a mechanism to permanently store information about its own structure and function in digital form (using an alphabet consisting of only four different symbols) surely represents one of the most revolutionary discoveries in the history of the natural sciences.

    ……the cell is a complex, highly integrated system, whose components are constantly exchanging information with each other using a multitude of different languages, which are embodied into physical entities in widely different ways. No part of the cell could exist and function separately from the surrounding environment produced by it’s other parts, and the system can only develop and evolve as a whole; you cannot build a cell by assembling separately produced parts.

    Alberto Riva

    Click on the Look Inside link at the top.

  46. 46
    Mung says:

    DNA provided evolution with both an alphabet for representing evolved protein sequences in a symbolic, simplified way, and with the long-term storage device for permanently recording them.

    Information Processing at the Cellular Level: Beyond the Dogma

  47. 47
    Upright BiPed says:

    Yes, I will put it on my list to get a copy. They refer to the nucleotide as a symbol, which is generally a good sign (pun intended). But I disagree at a certain material level. A nucleotide is not a symbol; a nucleotide is matter used to create a symbol – a dimensional pattern recognizable to the translation apparatus. The codon is the operative symbol, and results in the functional effect.

  48. 48
    Upright BiPed says:

    Note: my post at 47 was not clear enough to make a proper distinction. Please feel free to ignore me. 🙂

  49. 49
    Mung says:

    Consider yourself ignored 😉

    But good point. I did not suss that out myself upon first reading. I’ll try to keep an eye out to see what appears later in the paper that clarifies that statement.

    It appears he is thinking of nucleotides as “letters” that can form “words” in the alphabet. IOW, there are only four letters in the alphabet, and he refers to these letters as symbols.

    I understand the distinction you are making.

  50. 50
    Mung says:

    Where is all the junk RNA?

    4. Junk DNA: If Cordova is right then most of the stochastic substitutions in the human genome are neutral. This must mean that most of our genome is junk. Oops! That won’t sit well with many creationists.

    Am I the only one to wonder about Junk RNA?

    Why this fixation on “junk DNA” when there is so much “junk RNA” out there?

  51. 51
    Dionisio says:

    Upright Biped @ 47

    A nucleotide is not a symbol; a nucleotide is matter used to create a symbol

    Agree.

  52. 52
    Dionisio says:

    Upright Biped @ 48

    Please feel free to ignore me.

    Should I ignore # 48 ? 😉

  53. 53
    Dionisio says:

    Upright Biped @ 47

    A nucleotide is not a symbol; a nucleotide is matter used to create a symbol

    Agree.

    In an electronic computer, a voltage level is not a symbol; a voltage level is energy used to create a symbol.

  54. 54
    vjtorley says:

    Hi StephenB,

    Thank you for your posts. I was a little surprised by your statement:

    Actually, I would say that the ID and theistic evolution camps are separated both in terms of [a] whether evolution was guided at all and [b] whether it is scientifically detectable. With respect to [a], no one I know in the TE camp admits that God guided evolution in such a way that it would produce a finished product that reflects His a priori intent, which would be the requirement for guided evolution. (Emphasis mine – VJT.)

    You’re saying that nobody in the TE camp thinks like that any more? Wow. The meaning of “theistic evolution” has changed a lot since the early 1970s, when I first encountered it.

    It’s funny, actually. Looking back at people who described themselves as “theistic evolutionists” back then, it becomes apparent that most of them would be called Intelligent Design advocates today. I guess the “theistic evolution” camp has moved to the left.

  55. 55
    StephenB says:

    Hi VJ:

    You ask:

    You’re saying that nobody in the TE camp thinks like that any more? Wow. The meaning of “theistic evolution” has changed a lot since the early 1970s, when I first encountered it.

    Thanks for the chance to clarify. When I say I that know of “no one” in the TE camp who embraces targeted evolution, I am referring to those who try to reconcile Darwin with God.

    On the other hand, there seem to be many non-Darwinian TEs who do accept targeted or guided evolution. I am guessing that Ed Feser falls into that category. Indeed, many like yourself, GPuccio, and Behe would fall into that category.

    But yes, in general, I think that the meaning of theistic evolution, which once conveyed the idea of guided evolution, does seem to have changed in the last few years. Possibly this could be because Christian Darwininists have hijacked that term in order to create the illusion that their position is coherent, which of course, it is not. It is madness to suggest that God directed a non-directed process, but that is precisely what so many modern day TEs try to argue:

    John Haught: “A God whose very essence is to be the world’s open future is not a planner or a designer but an infinitely liberating source of new possibilities and new life. It seems to me that neo Darwinian biology can live and thrive quite comfortably within the horizon of such a vision of ultimate reality.”

    Ken Miller: “Mankind’s appearance on this planet was not preordained… we are here… as an afterthought, a minor detail, a happenstance in a history that might just as well have left us out.”

    John Polkinghorne: “An evolutionary universe is theologically understood as creation allowed to make itself.”

  56. 56
    gpuccio says:

    wd400 at #39:

    It’s simple.

    Neutral random variation does not affect function. That’s why it is called neutral. If it is deleterious, it is mainly removed by negative selection. In that way, function is mostly conserved.

    That is obvious in protein coding genes: proteins change at sequence level throughout natural history, and still retain their structure and function. That certainly applies to functional non coding sequences too.

    Non coding DNA, when functional, is the product of design, not of neutral variation, as neo-darwinists (or however you want to call them, without offending Larry Moran’s susceptibility) seem to believe.

    So, there is no contradiction in my two statements:

    “The simple truth is:

    a) Random Variation is mostly neutral.

    b) So called non coding DNA is mostly functional.”

    Indeed, the two things are logically connected, and perfectly consistent.

  57. 57
    Joe says:

    Larry Moran is a liar and coward who is forced to delete posts that expose him as such. He can dish it but he cannot take it.

    Go change your diaper Larry

  58. 58
    wd400 says:

    Neutral random variation does not affect function. That’s why it is called neutral. If it is deleterious, it is mainly removed by negative selection. In that way, function is mostly conserved.

    Right. But you said random variation is neutral. If you are looking at variatoin after the action of non-random selection then you aren’t looking at random variation.

    More importantly, I don’t think you’ve really understood what Moran is saying. If, as almost everyone here now accepts (?), the number of difference between humand and chimp genomes is very similar the neutral expectation then is stands to reason that most of the genome is not subject to purifying selection and is likely functionless junk.

    Your example on coding DNA illustrates the point perfectly. Protein coding sequences are conserved between species, display many fewer among-species differences than neutral theory would predict, and have have fewer common variants and lower herterozygosity that non-coding sequences. That’s because purifying selection is operating on coding sequences. For the most part, non-coding sequences don’t display these signatures of selection.

    Why do you think that is?

  59. 59
    Joe says:

    wd400- natural selection is only non-random in that not all organisms have the same probability of being eliminated. That means whatever is good enough survives to get a chance at reproducing.

    IOW saying NS is non-random isn’t saying vey much.

  60. 60
    tragic mishap says:

    In response to your question on junk DNA, there is another possibility. God could have created with no junk DNA and neutral evolution could have degraded the original design. This could be true on TEC or some version of frontloading.

  61. 61
    gpuccio says:

    wd400:

    Right. But you said random variation is neutral. If you are looking at variatoin after the action of non-random selection then you aren’t looking at random variation.

    And so? My point was simply that there is no reason at all for neutral random variation to generate junk sequences. Its only role is to change sequences inside the functional space. Why should neutral variation operating on functional sequences generate junk sequences? There is no logic in that idea. Neutral variation operating on functional sequences can have only one result: the function is conserved, even if the sequence can, to a certain point, change.

    More importantly, I don’t think you’ve really understood what Moran is saying. If, as almost everyone here now accepts (?), the number of difference between human and chimp genomes is very similar the neutral expectation then it stands to reason that most of the genome is not subject to purifying selection and is likely functionless junk.

    First of all, the accumulation of non coding DNA is not specific of humans. It is a common characteristic of evolution in all higher species. On the contrary, protein coding genes are more stable in higher species, even if a certain number of new genes appears even in mammals and humans.

    For example, consider that about half of protein superfamilies are already present in LUCA, and that the other half appears gradually, but with a slowing rate as evolution proceeds.

    On the contrary, non coding DNA increases throughout evolution.

    The simplest explanation for those data is that the evolution of function in higher species is mainly based on changes in the regulations, rather than on changes in the effectors (proteins). And regulations are mainly located in non coding DNA.

    Now, two important points must be considered:

    1) A significant fraction of non coding DNA is conserved. About 5% of the total of human genome is conserved. Only 1% of that is protein coding genes. The other 4% is non coding DNA. That means that 4/5 of conserved regions are in non coding DNA. Moreover, many non coding regions are much more conserved than coding regions. See, for example, here:

    http://www.garlandscience.com/.....9_ch09.pdf

    Page 2.

    2) Even more important, we have no idea of how much regulatory elements can vary form species to species, and therefore conservation is not a reliable indicator of function, in the sense that many non conserved sequences in non coding DNA can be functional, and still be different from those of other species. Regulation is probably much more species specific than protein sequence.

    This concept is very well expressed by Mattick, one of the main researchers in the filed of non coding DNA, in a very recent paper:

    “The extent of functionality in the human genome”

    http://www.thehugojournal.com/content/7/1/2

    I quote here the abstract:

    Recently articles have been published disputing the main finding of the ENCODE project that the majority of the human genome exhibits biochemical indices of function, based primarily on low sequence conservation and the existence of larger genomes in some ostensibly simpler organisms (the C-value enigma), indicating the likely presence of significant amounts of junk. Here we challenge these arguments, showing that conservation is a relative measure based on circular assumptions of the non-functionality of transposon-derived sequences and uncertain comparison sets, and that regulatory sequence evolution is subject to different and much more plastic structure-function constraints than protein-coding sequences, as well as positive selection for adaptive radiation. We also show that polyploidy accounts for the higher than expected genome sizes in some eukaryotes, compounded by variable levels of repetitive sequences of unknown significance. We argue that the extent of precise dynamic and differential cell- and tissue-specific transcription and splicing observed from the majority of the human genome is a more reliable indicator of genetic function than conservation, although the unexpectedly large amount of regulatory RNA presents a conceptual challenge to the traditional protein-centric view of human genetic programming. Finally, we suggest that resistance to these findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design.

    Finally, you say:

    Your example on coding DNA illustrates the point perfectly. Protein coding sequences are conserved between species, display many fewer among-species differences than neutral theory would predict, and have have fewer common variants and lower herterozygosity that non-coding sequences. That’s because purifying selection is operating on coding sequences. For the most part, non-coding sequences don’t display these signatures of selection.

    That’s not true (see previous point). But I will add some further considerations.

    There is no doubt that negative selection operates on coding sequences. And yet, in very distant species similar proteins often retain structure and function even with only 30-35% of sequence identity, and 45-50% of sequence similarity. Sometimes even less.

    Therefore, neutral selection can do a lot to change sequences while function remains the same.

    For non coding regions, we know very little about the sequence-function relationship. We cannot apply our genetic code, because it has no meaning in those sequences. We understand very little of how regulations are performed, especially in multicellular organisms, where the same genome has to generate the multiplicity of transcriptomes which characterizes different cell functions. That’s why evaluating conservation in regions whose function we don’t understand can be very tricky.

    So, to sum up:

    a) There are few doubts that a large part of non coding DNA is functional. That part is constantly increasing in our present understanding, practically every day.

    b) The main functions that we understand of non coding regions is regulatory. That is probably the type of function which is most important in higher species.

    c) About 4% of non coding DNA is conserved, some of it ultraconserved. That part is almost certainly highly functional.

    d) Much of the rest, although not conserved, is probably functional just the same.

    I would add that some regions of non coding DNA are conserved in vertebrates, and they change a lot in humans. They are the very interesting HARs, mostly non coding regions:

    From Wikipedia:

    “Human accelerated regions (HARs), first described in August 2006,[1][2] are a set of 49 segments of the human genome that are conserved throughout vertebrate evolution but are strikingly different in humans. They are named according to their degree of difference between humans and chimpanzees (HAR1 showing the largest degree of human-chimpanzee differences). Found by scanning through genomic databases of multiple species, some of these highly mutated areas may contribute to human-specific traits.”

  62. 62
    wd400 says:

    And so? My point was simply that there is no reason at all for neutral random variation to generate junk sequences. Its only role is to change sequences inside the functional space. Why should neutral variation operating on functional sequences generate junk sequences? There is no logic in that idea. Neutral variation operating on functional sequences can have only one result: the function is conserved, even if the sequence can, to a certain point, change.

    You have not understood the argument at all. It’s not that “neutral variation” would create junk, but that randomvariation (the term you used…) would not, for the most part, be neutral in functional sequences.

    I think everyone other than Kozulic now accepts the number of differences between the human and chimps genomes is pretty close to what you’d expect given the neutral theory and what we know about mutation rates.

    But if most of genome was under purifying selection this would not be the case – new variants entering the population would be selected against and the rate at which differences accrue would be lower than the individual mutation rate.

  63. 63
    gpuccio says:

    wd400:

    Have you at least read my post #61?

    Conserved sequences in human genome are about 5% of the total. 4% is non coding.

    That leaves 95% non coding DNA which is not specially conserved.

    The idea that the rate of variation here is “pretty close to what you’d expect given the neutral theory and what we know about mutation rates” can be more or less true, but in no way demonstrates that those variations are neutral, or that they are neutral because that 95% is not functional. That is a completely gratuitous conclusion.

    The simple fact is that we don’t know how regulatory sequences work, and what is the sequence – function relationship in them. When we pass from one species to another one, we have no idea of what changes in regulatory sequences. Indeed, we have no definite idea even of what regulations are, where they are written, least of all of how they change.

    I don’t understand what, in your opinion, should explain the differences between humans and chimps (or mice, or any other species). Do you believe that the difference is explained by neutral variation in protein coding genes, which leaves the function the same? Or by variations in non coding sequences which, according to you, are not functional?

    I really don’t understand what you and Moran really think. Please, explain.

    And by the way, Mattick and many others apparently do not agree with your conclusions.

  64. 64
    wd400 says:

    I read your post. It doesn’t really relate to mine, which I tried to explain.

    The less said about Mattick the better.

    The idea that the rate of variation here is “pretty close to what you’d expect given the neutral theory and what we know about mutation rates” can be more or less true, but in no way demonstrates that those variations are neutral, or that they are neutral because that 95% is not functional

    It pretty much demonstrates variants in most regoins of the genome are selectively neutral – how else could that result arise? If regions aren’t functionless and changing sequences in them at random have no ill-effects then these functional can’t be very sequence-specific.

    I don’t understand what, in your opinion, should explain the differences between humans and chimps (or mice, or any other species). Do you believe that the difference is explained by neutral variation in protein coding genes, which leaves the function the same? Or by variations in non coding sequences which, according to you, are not functional?

    Why is it sort for people to understand that when I say “most of the genome is junk” I don’t mean “all non-coding sequences are junk”?

    Most of genetic differences between humans and chimps are due to drift. It’s possible some of the phenotypic differences are too. Others are the result of positive selection on proteins in either lineage, still more are canges to regulatory sequences in either lineage.

    It’s quite possible accept that (a) some non-coding DNA is funcational (b) most of it is junk.

    The less said about Mattick and that paper the better.

  65. 65
    Optimus says:

    Gpuccio @ 61
    Nice link to the Mattick paper! I really enjoyed reading that one.

  66. 66
    gpuccio says:

    wd400:

    Just to be more clear, we have absolutely no reason to believe that the variation is really random, and neutral because it happens in non functional sequences.

    Th point is exactly the opposite: what appears as random variation is indeed designed variation. It happens in functional non coding genes, but it adds new and different functions. Therefore, conservation is no more a criterion for functionality, because we have new functions here, and the sequences that implement them are not conserved, because their function is new.

    For example, how would you explain HARs? They are non conserved regions in what was before a conserved region. Abd that’s exactly the reason why many consider them probably functional.

    As you can see, your reasoning about neutral variation is trivial and gross.

    The simple fact is that humans and chimps are different, and something must explain that fact.

    The simple fact is that non coding DNA shows every day new functions, either it is conserved or not.

    The simple fact is that you cannot apply to regulatory regions the same principles you apply to coding genes, which obey very different principles.

    The simple fact is that neutral variation, if it were really all that happens, can never explain functionality, least of all new functions in new species.

    The simple fact is that in the end you will probably recur again to NS, that powerless myth of traditional darwinism, because you have no way to explain anything, otherwise, given your a priori commitment to non design explanations.

    So, please be clear. You are stating that most or all the changes between the chimp genome and the human genome are random variations that occur in non functional regions, and therefore they are neutral. Is that your idea?

    So I ask again, what explains the functional differences between chimps and humans? (you know, the brain etc.) And if there are functional differences explained by differences in the genome, which are those differences, and by which mechanism did they happen? RV alone? RV + drift? RV + drift + NS? Or just sheer luck?

    Please, be clear.

  67. 67
    gpuccio says:

    wd400:

    It pretty much demonstrates variants in most regoins of the genome are selectively neutral – how else could that result arise? If regions aren’t functionless and changing sequences in them at random have no ill-effects then these functional can’t be very sequence-specific.

    How could that result arise? But obviously, through non random designed variation!

    Most of genetic differences between humans and chimps are due to drift. It’s possible some of the phenotypic differences are too. Others are the result of positive selection on proteins in either lineage, still more are canges to regulatory sequences in either lineage.

    So, most of those differences, due to drift, have no real probability of being functional!

    And phenotypic differences due to drift would not be functional too!

    And, as I expected, you are back to NS in the end to explain something!

    It’s quite possible accept that (a) some non-coding DNA is funcational (b) most of it is junk.

    It’s quite possible to accept that:

    a) A lot of non coding DNA is functional

    b) Some of it is junk

    In that case, you would have some neutral variations in the functional part (difficult to quantify, because as said you cannot apply by default the same rules that you apply to protein coding genes), and a lot of functional designed variation in the new functional part. And, obviously, neutral random variation in the non functional part.

    That scenario is perfectly compatible with what we observe.

    The less said about Mattick and that paper the better.

    I find that statement of yours very unfair and irritating. Perhaps it is better for you, but only for you.

    I have criticized many scientific papers here, but I have always given detailed and explicit reasons for that.

  68. 68
    gpuccio says:

    Optimus:

    Yes, it’s very interesting. Mattick has done a lot of good work in that field.

  69. 69
    Mung says:

    Joe, loved your post on the vole.

  70. 70
    gpuccio says:

    To all:

    When someone uses arguments like “The less said about something, the better”, I feel strangely tempted to immediately say something about that thing. How evil is human nature! 🙂

    So, I post here the conclusions of Mattick’s paper which wd400 so much dislikes:

    It is our position that these arguments are misguided. Indeed, we have refuted the specific claims that most of the observed transcription across the human genome is random (Clark et al. 2011; Mercer et al. 2012) and put forward the case over many years that the appearance of a vast layer of RNA-based epigenetic regulation was a necessary prerequisite to the emergence of developmentally and cognitively advanced organisms (Mattick 1994; Mattick and Gagen 2001; Mattick 2004; Amaral et al. 2008; Mattick 2009a, 2011). This case is, moreover, entirely consistent with the broad tenets of evolution by natural selection, although it may not be easily reconcilable with current population theory and current ideas of evolutionary neutrality. In any case, that our understanding of the remarkably complex processes underlying the molecular evolution of life, including the likely evolution of evolvability (Mattick 2009c), is incomplete should not be surprising. With the emergence of transformative technologies, such as massively parallel sequencing, which provide tools to view the inner molecular workings of the genome that were inconceivable less than a decade ago, it is as important as ever that we as scientists remain open to observations that challenge even the most fundamental paradigms that exist within biology today.

  71. 71
    Mung says:

    wd400 to gpuccio:

    I read your post. It doesn’t really relate to mine, which I tried to explain.

    🙂

    wd400 @ 5:

    We aren’t sure most of the DNA is junk “because it doesn’t code for proteins,”, but for other good reasons.

    What are these “other good reasons” that we know most of DNA is junk? Just a few bullet points. I’ll go back and rad your remaining posts in the thread and see if you covered them.

    It’s not possible to strip all the junk DNA out of a cell.

    I agree. We don’t know what’s junk and what isn’t. Therefore, it’s just not possible to strip all the junk DNA out of a cell. Not knowing what is junk and what isn’t, we may not be able to strip any junk DNA out of a cell.

  72. 72
    Mung says:

    In case anyone missed it:

    “This case is, moreover, entirely consistent with the broad tenets of evolution by natural selection, although it may not be easily reconcilable with current population theory and current ideas of evolutionary neutrality.

    thanks gpuccio!

  73. 73
    wd400 says:

    I’m sorry, I can’t find a logical thread in any of this? Are you really proposing some sort of directed mutation mechanism to explain the rate of molecular evolution? Which just happens to mimic the neutral-expectation almost perfectly?

    I welcome people to read the Mattick paper. If they can find, just to take one example the “broadly consistent rise in the amount of non-protein-coding intergenic and intronic DNA with developmental complexity” he claims exists, I’d love to see it.

  74. 74
    wd400 says:

    Mung,

    You bullet points would be something like

    +c-value ‘paradox’
    +mutational load
    +lack of conservation
    +lack of other signals of purifying selection
    +The negative correlatoin between strength of selection in a species and that species’ genome size
    +The preponderance of repeptive DNA in many genomes

    Together, these make a case that “pervasive transctiption” a la Mattick and others hardly dents.

  75. 75
    Mung says:

    I appreciate that list, thank you.

  76. 76
    gpuccio says:

    wd400:

    Are you really proposing some sort of directed mutation mechanism to explain the rate of molecular evolution?

    Yes, obviously. That’s what I have always proposed here.

    Which just happens to mimic the neutral-expectation almost perfectly?

    No, it does not mimic anything. It’s people like you and Moran who expect something from your theories. The simple facts is that observed facts are perfectly compatible with the design explanation, and do not require mythical algorithms like NS, which is supported by nothing observed, to explain functional complexity.

    “Almost perfectly” is really an exaggeration. Let’s say that your explanation could be compatible with neutral mutations, but then it cannot explain functional variation. Therefore, your explanation is completely inconsistent. You are back to depend on NS, after having tried in all possible ways to make it less important. NS is the only thing that remains to you, and it does not work.

    A previous paper by Mattick et al:

    “The relationship between non-protein-coding DNA and eukaryotic complexity.”

    The abstract:

    “There are two intriguing paradoxes in molecular biology–the inconsistent relationship between organismal complexity and (1) cellular DNA content and (2) the number of protein-coding genes–referred to as the C-value and G-value paradoxes, respectively. The C-value paradox may be largely explained by varying ploidy. The G-value paradox is more problematic, as the extent of protein coding sequence remains relatively static over a wide range of developmental complexity. We show by analysis of sequenced genomes that the relative amount of non-protein-coding sequence increases consistently with complexity. We also show that the distribution of introns in complex organisms is non-random. Genes composed of large amounts of intronic sequence are significantly overrepresented amongst genes that are highly expressed in the nervous system, and amongst genes downregulated in embryonic stem cells and cancers. We suggest that the informational paradox in complex organisms may be explained by the expansion of cis-acting regulatory elements and genes specifying trans-acting non-protein-coding RNAs.”

  77. 77
    Mung says:

    Man. Those would make a great list of topics for a new op!

  78. 78
    jerry says:

    lack of conservation

    The preponderance of repeptive DNA in many genomes

    Could someone explain to me how a repetitive region is not a conserved region?

  79. 79
    wd400 says:

    conserved is a statement about how two sequences in different genomes (or with different evolutionary histories) compare.

    Repetitive is a statement about sequence classes within a single genome.

  80. 80
    wd400 says:

    No, it does not mimic anything. It’s people like you and Moran who expect something from your theories. The simple facts is that observed facts are perfectly compatible with the design explanation, and do not require mythical algorithms like NS, which is supported by nothing observed, to explain functional complexity.

    I’ve really lost track of what you think we’re talking about. Only ‘people like me’ think theories should produce expectations? natural selection is ‘mythical’?

  81. 81
    Mung says:

    Another question for Larry Moran:

    On paper, ribosomal RNA can fold in an almost infinite number of ways (over 10^80), yet only one catalytically active structure is adopted.

    p.22

    Q: Do you believe in miracles?

  82. 82
    jerry says:

    Could someone explain to me how a repetitive region is not a functional region?

    Or if it is not functional, why wouldn’t mutations ruin the repetitiveness over time?

    Most of the DNA is repetitive which implies that most of the genome is functional.

  83. 83
    wd400 says:

    repetitive sequences do ‘rot’ over time, but just at the neutral rate which takes a while so we can still see the repeat motif.

  84. 84
    Joe says:

    OK we get it. Blind and unguided processes cannot account for DNA but it can account for junk DNA. I believe tragic mishap covered that.

  85. 85
    gpuccio says:

    wd400:

    It’s very simple. One thing is when in physics you have a vert precise result which is expected bt a theory (see QM, and its great precision in computing results).

    Another thing completely is when in biology you observe things which are in a range which is grossly compatible with a possible explanation (your neutral theory) but also with many other possible explanations (my theory of guided functional variation plus some quantity of random neutral variation). In such a scenario, there is no sense in saying that one explanation “mimics” the expectations of the other. The simple truth is that both are quantitatively compatible with what is observed.

    Moreover, my explanation is hugely superior, because it is also compatible with another fundamental empirical observation: the constant association between design and complex functional information.

    On the other hand, your theory (neutral variation) is completely useless to explain what we observe (functional information in biological beings, and in particular the emergence of a lot of new functional information in a new species). So, it must recur to a completely different (and empirically unsupported) process, NS, to try to give some explanation. Therefore, your theory has no scientific credibility.

    Let’s go to NS. It is certainly a myth, not because NS does not exist (it certainly has a role in the few cases of microevolution we know of), but because it cannot generate complex functional information, as ID has argued for decade, and there is no single observed case of macroevolution which can be explained with NS.

    Indeed, all this discussion originated from the self-assured statements of Larry Moran about how we IDists understand nothing of biology, and how nobody believes any more in classical darwinism, no, in darwinism at all, and how neutral variation is the real thing, and so on, and so on.

    And now, in the end, we are again here debating NS as the only process that can generate new complex functional information in a natural system.

    Please, look at my post #12 here!

    So, what has changed under the not so big tent of neo darwinism?

    Nothing. NS is still the only useful actor. An actor who cannot act, but an actor just the same. Neutral variation and genetic drift are there, as we have always known, but are irrelevant to the problem we debate here. I have said that simple thing for years, here.

    After all, Dawkins has no reasons to be unhappy.

    Now, that is an expected result, if ever there was one! 🙂

  86. 86
    gpuccio says:

    Joe:

    OK we get it. Blind and unguided processes cannot account for DNA but it can account for junk DNA.

    Yes, you got it perfectly right!

    The simple point is that they are not interested in explaining functional information. They are only interested in self-justifying their artificial theories.

    “Who cares if humans have such a complex brain, and are the only biological beings which can develop abstract thinking and many other details? The important thing is that what is new in their genome could be the product of random neutral variation, if it were true that it is non functional. Well, that’s an amazing scientific achievement, after all! 🙂

    And let’s remind those IDiots, who still think that NS is the real (false) thing in biological naturalism, that we don’t believe any more in the importance of NS. After all, neutral variation and drift can explain all our supposed junk.

    Ah, yes, if they just insist in asking how functional novelty arises, please remind them that NS can always easily explain all that. But beware, it is no more the important thing!”

  87. 87
    gpuccio says:

    wd400 and all:

    I would like to discuss briefly a couple of concepts which, while implicit in much that I have said here, deserve probably better clarification.

    1) Neutral random variation is of two different kinds.
    Variation can be neutral (in the sense that it does not influence existing function, and therefore is not subject to any process of selection, neither negative nor positive) for two different reasons:

    a) It happens in a functional region, but it does not affect its function.

    b) It happens in a non functional region.

    The first case is well known in protein coding genes. Many mutations can occur in a protein coding gene without affecting the protein function. There are different reaosn for that too:

    a1) The mutation is synonimous, and therefore it does not change the protein sequence (although it can sometimes affect its transcription and translation, but we will will not consider that aspect for the moment). That is a direct consequence of the redundancy of the genetic code.

    a2) The mutation does affect protein sequence, but the new sequence retains the same structure and function. That is the case when an AA is changed into a similar AA, and the structure is not significantly altered, or when other compensatory modifications happen at the same time in the sequence, or simply when the AA which changes is not part of a functionally important part of the protein. IOWs, that is a direct consequence of the redundancy of the protein functional space.

    There is also another consideration. A mutation can affect the function of a protein, but only in part, or the protein could just not be really relevant for survival and reproduction. In both cases, although the mutation is not really neutral, still it would escape the effects of selection.

    In the second case (b) the mutation is neutral by definition, because it happens in a non functional sequence. Not only a non coding sequence, but a non coding sequence which has no other function, be it regulatory or else. IOWs, a mutation occurring in a truly “junk” sequence. In this case, the mutation is neutral not because it does not affect significantly the function of the sequence, but because the sequence has no function in the beginning.

    OK?

    2) We cannot apply the same quantitative principles to mutations and neutrality in coding genes, functional non coding genes, and non functional non coding genes.

    Let’s start with non functional non coding genes, which are a part (we don’t know how big) of the total non protein coding DNA (in humans, about 98% of the total genome).

    These sequences are non functional by our same definition, therefore any variation occurring in them is by definition neutral, and therefore neutral variation (of type b) will occur (and maybe fixed by drift) at the same rate as the general mutation rate.

    Unless they are designed variation, therefore building a new function. In that case, once the new function is complete and expressed (whatever it is) that variation will be subject to positive selection and fixation.

    In protein coding genes, the situation is different. Here, negative selection can fully act on variation, defending the existing function. IOWs, a relevant part of variation is no more neutral, and will be more or less efficiently eliminated by negative selection. IOWs, the sequence will show some (variable) degree of conservation. However, neutral mutations will still occur (of type a), and the sequence will change in time, to a certain degree, while retaining a minimum level of homology. The rate of variation, therefore, will be lower. It will vary from protein to protein, according to many variables, including the degree of functional information in the protein, as measure by the Durston method. But we can have a good idea of the mean rate of neutral variation in protein coding genes, because we know protein coding genes and proteins, we know the genetic code for protein synthesis, and we know much of the structure-function relationship in proteins.

    But what can we say of functional non coding DNA, IOWs, of non protein coding DNA with regulatory functions?

    First, we absolutely know that it exists, but we don’t know how big a part of the total non coding DNA it is. Indeed, the ratio between functional non coding DNA and non functional non coding DNA is exactly what is at stake here, and is at present the object of a true was among biologists, as clearly seen in this same thread.

    Second, we know almost nothing of what it is, how it works, and what its structure-function relationship is.

    That’s why we cannot absolutely apply to functional non coding DNA the same rules or expectations about variation neutrality that we apply to protein coding genes.

    Some things, however, we know:

    a) Whatever the regulatory function is, it is not based on the genetic code. IOWs, non coding functional genes are not written in codons intended to represent AAs. Therefore, the first cause of neutral variation in protein coding genes (synonimous mutations, due to the redundancy of the genetic code) does not apply here.

    b) We have no ideas about the functional redundancy of functional non coding sequences, because we know much less about them than about protein coding sequences. Indeed, in many cases we don’t even know what the regulatory sequences are. So, we cannot even start to estimate how much a functional non coding sequence can change, while its function is retained. The chance for neutral variation can be higher than in protein coding genes, or lower. We have no idea.

    c) Another fundamental difference with protein coding DNA is that functional non coding DNA is certainly more heterogeneous. We know that non coding DNA is made of different types, very different one from the other: introns, satellites of various kinds, SINEs, LINEs, transposons, pseudogenes, and so on. For each of them, different rules can be valid about neutral mutation rate, because their functions will probably be different. We already know of different kinds of regulatory function, with different mechanisms, and the bulk is still to be discovered. Moreover, even the same type of non coding DNA (for example, introns) could have different mechanisms of function in different contexts.

    The final conclusion is that we have no way to compute how much variation we would expect to find in the sum total of the genome, if we consider all these different aspects.

  88. 88
    wd400 says:

    Irrelevance piled upon irrelevance.

    Scientists know a lot more about the regulation of gene expression than you do, but that doesn’t actually matter. If most of the genome was functional then random variation (I remind you, your original claim, which you’ve apparently resiled from, was “Random Variation is mostly neutral”) wpuld mostly be non-neutral unless biological functional is not sequence-specific. When we see most of the genome evolving at the neutral rate through time, and meeting the neutral expectation in populations we can conclude variation in most of the genome is of no consequence. It’s very hard to imagine how that would be possible in a mostly functional genome.

    The counter, that variation is created by some outside force (?) at constant rate (how else would the branches on an evolutoinary tree relating Human, Neanderthal, Chimp, Gorilla have the same lengths) equal to the individual mutation rate is…. not really worth bothering with.

  89. 89
    Joe says:

    wd400:

    Irrelevance piled upon irrelevance

    That describes unguided evolution.

    Scientists know a lot more about the regulation of gene expression than you do, but that doesn’t actually matter.

    Knowing about something and being able to explain how unguided evolution produced it are two very different things.

    BTW design does NOT require outside force/intervention. And the branches on the evolutionary tree are imagined

  90. 90
    gpuccio says:

    wd400:

    Well, you are entitled to your own opinions. I have tried to explain my point of view, and I don’t think you have answered anything specific. You just stick yo your position. That’s OK.

    I must remind you that neutral RV happens in functional sequences, even in protein coding genes, and at rates which cannot be anticipated with precision, especially when the function and its molecular basis are not known.

    I wonder if you will be bothered when biological research will confirm and enlarge the functions of non coding DNA, or if you will still stick to your beloved theory with its expectations.

    We don’t see “most of the genome evolving at the neutral rate through time”. 4% of non coding DNA is conserved, and part of it ultraconserved. Understanding of the remaining part is still very incomplete. You just see genomes evolving, maybe, at a rate which is not completely different from what you expect. Don’t pretend that you have precise quantitative expectations, which are verified in detail.

    While neutral variation is certainly there, we have no evidence of how much of the variation is neutral, and how much is functional. Even you will admit that part of the variation must be functional, won’t you? Otherwise, why are humans capable of doing things that chips cannot do? Or do you deny even that?

    Because, you know, that is the big question. How does functional novelty arise? How much neutral variation is there can be interesting, but in the end it is not really important. It’s functional variation that we are interested in.

    You have said nothing about functional variation. Not where you think it takes place, not how much of it you think takes place, and especially nothing, nothing at all, about how it would take place, except for trying a tired and unconvinced revival of NS.

    Do you realize that functional variation is there, among the total variation? Do you realize that you should subtract it from the total variation, because it certainly is not neutral? Do you realize that what is neutral in a protein coding gene is different from what could be neutral in a regulatory gene, or in different types of regulatory genes? Do you realize that regulatory genes must be there? Have you subtracted a figure for them from your computations? Are you really being quantitative, or are you just trying to justify your theory with numbers ad hoc?

    The simple truth is that we should understand before how much of the genome is functional, and knowing that we could compute how much of variation is random, and how much of that random variation is neutral. Reasoning the other way round is pointless.

    You must ascertain function from functional studies, not from population genetics suppositions. That’s the right way, the only way. That’s what many biologists, including those at ENCODE and Mattick, whom you so much despise, are trying to do.

    But please, feel free not to be bothered by all those thing.

  91. 91
    jerry says:

    repetitive sequences do ‘rot’ over time, but just at the neutral rate which takes a while so we can still see the repeat motif.

    What are your references for this? It seems that these sequences have been around for millions of years and with mutations in every genome in the population and recombination during reproduction, that any sequence would have been turned into a mush. But yet the term repetitive is prevalent in all the literature. For example,

    Faulkner et al. The regulated retrotransposon transcriptome of mammalian cells Nature Genetics 41:5, 563-571 April 2009

    http://subviral.med.uottawa.ca/~rna/ng.368.pdf

    Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6–30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5′ of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3′ UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.

    This study indicates a large number of non-coding regions are functional. Here they use the number 250,000. And apparently they are under positive selection pressures

    http://www.osc.riken.jp/englis.....ievements/

    From this site:

    These are under positive evolution, and our data show that the evolution of humans was caused not only by changes of protein sequences, but rather changes of RNA expression level driven by these CpG promoters, that are under positive selection in recent human lineages. CpG broad promoters are prevalent in brain, highlighting the complexity of transcriptional regulation in this tissue and the role of epigenetic control in the control of expression in the brain.

    We should look into this phenomena more closely. Genomes from all over the world are now available and the number is increasing by large amounts each year. Apparently every research project using a new genome must submit their data for use by anyone else doing research. There are genomes dating back tens of thousands of years and there is a data set of the native populations of Australia, New Guinea and parts of the Philippines that separated from Africa about 70,000 years ago.

    So a lot of the ideas we speculate with could be answered by data available today or will shortly be available in the near future.

  92. 92
    gpuccio says:

    jerry:

    Thank you for the very interesting references. I don’t think, however, that wd400 will be bothered by them. 🙂

  93. 93
    wd400 says:

    What are your references for this? It seems that these sequences have been around for millions of years and with mutations in every genome in the population and recombination during reproduction, that any sequence would have been turned into a mush.

    Mutations will just fix at the neutral rate – human and chimp genomes are 98.whatever percent similar after 6 million years of evolution and any two repeats will be as similar. In fact, for a given alu element there is a ~25% chance any two alus in the human and chimp genome will be indentical after 6 million years.

    The paper you linked to shows that ~18% of transcription start sites come from the ~50% of the human gnome that is made of repetitive elements, and ~10% of those transcription start sites produce an mRNA that is known (at the time, I guess there’d be more npw). Even if we made the mistake of thinking mRNA production = function we’d end up with repetitive elements have being less functional than the rest of the genome (which, I shouldn’t need to stress, doesn’t mean all such elements are function-less).

  94. 94
    Mung says:

    wd400:

    Repetitive is a statement about sequence classes within a single genome…

    …repetitive sequences do ‘rot’ over time, but just at the neutral rate which takes a while so we can still see the repeat motif.

    Good point. But repetitive sequences are seen as evidence that supports the hypothesis of common descent of humans with other primate species, are they not?

    Now looking at JUST repetitive sequences in humans and other primate species, do they support the predictions of neutral theory? Do they exhibit the same or a different mutation rate?

  95. 95
    Mung says:

    gpuccio:

    On the other hand, your theory (neutral variation) is completely useless to explain what we observe (functional information in biological beings, and in particular the emergence of a lot of new functional information in a new species). So, it must recur to a completely different (and empirically unsupported) process, NS, to try to give some explanation. Therefore, your theory has no scientific credibility.

    Walter ReMine calls evolutionary theory a smorgasbord. It’s defenders pick and chose what they want or need at a particular moment in time to defend the particular argument they are making at the time. On the whole, “the theory” is incoherent.

    And yes, neutral theory does not and cannot explain “the appearance of design.” It does not explain adaptation.

    Which is why Larry Moran is a hypocrite, because at heart, he is a Darwinian.

  96. 96
    Mung says:

    gpuccio:

    OK?

    NOPE.

    You’ve turned neutral theory on its head!

    Neutral theory, similar to Punctuated Equilibrium, was devised to explain why certain observed facts did not align with Darwinian theory.

    It’s not a theory about why this or that mutation is neutral and doesn’t attempt to explain why this or that mutation is neutral.

    It’s simply a statement that most “evolution” cannot be under selection! Along with some nice maths to support it. 🙂

    I’m sure we’re saying the same thing, I just don’t want people to be sidetracked on to what’s a neutral mutation and lose sight of the bigger picture, that Darwinism is false.

    😀

  97. 97
    Mung says:

    gpuccio:

    2) We cannot apply the same quantitative principles to mutations and neutrality in coding genes, functional non coding genes, and non functional non coding genes.

    But if we are speaking of neutral theory, these are irrelevant, because neutral theory is not about those things and is not dependent upon those things.

    wd400:

    Irrelevance piled upon irrelevance.

    In one sense I clearly agree with you. Please comment on my post @ 96 and let me know if I am at least in the ballpark.

    Unless I am just mistaken, you’re talking about neutral theory.

    gpuccio is attempting to place neutral theory in a wider context. In the context of neutral theory some of what he is writing is indeed irrelevant.

    But in the larger context, those things are relevant.

    So for the most part I think you two gentlemen are just talking past each other. But it’s still entertaining!

    wd400, I certainly understand how this might be a “hostile” environment for you. You’ve no doubt been abused repeatedly for saying things that to you are just true on their face. But if you can find it within yourself, do what you can to make it clear when and where you and gpuccio are actually talking about the same thing and if not why not.

    I appeal to gpuccio to do the same. This is an interesting discussion! Let’s find the ground that you both need to be on so that you are both discussing the same thing and not seeing what the other says as irrelevant.

    Am I correct in my theory that the disconnect is over what neutral theory is actually about?

  98. 98
    Joe says:

    Mung, Voles will/ should be the “poster child” for neutral theory. 😎

  99. 99
    jerry says:

    Good point.

    I am not sure it is a good point. I can find no reference that repetitive sequences are not actually repetitive Saying they have rotted says they are not actually repetitive. They do not refer to them as formerly repetitive sequences. Or that the sequences can be seen to have been once repetitive. They are described as repetitive.

    repetitive sequences are seen as evidence that supports the hypothesis of common descent of humans with other primate species, are they not?

    Is this true? I assumed what is used for common descent is the conservation of coding regions, not the repetitive sequences. But I am certainly not sure of this and any references on this would be welcome.

    The term conserved means a lot of things. We all assume there is conservation within coding regions of a species. Isn’t this what the discussion of the neutral theory is about, saying that it changes the coding regions in some places and this is the source of speciation. But for within the same species there is conservation of the coding regions.

    For similar species many of the coding regions across species are also conserved. This later fact is what is used to support common descent as you said. This also implies across long periods of time. Are non-coding regions such as repetitive regions also used to infer common descent? I am curious about this.

    The term conserved can also mean conserved sequences within the same species in non-coding regions amongst the various individuals of a species. For example within humans are there similar non coding sequences amongst individuals from various regions of the world. If so then this would indicate function for these regions. The study I pointed to indicated there was selection going on for many non-cocing regions. These regions were also repetitive. This is interesting because some are very vocal about repetition as an indication of junk.

    Then there is the other issue that I and Allen MacNeill bring up Namely, the variation that is created by Allen’s list of engines of variation and how does this variation change over time. These are regions that really should rot or a better description is change randomly over time. This is claimed to be the source of new coding sequences for proteins or other functions as large parts of the genome which is truly junk mutates away.

  100. 100
    gpuccio says:

    Mung:

    I think we are saying the same thing, but I am arguing about the reasons why variation can be neutral. It’s not enough to observe that variation is often neutral, we have also to understand why it is neutral. And I have tried to detial that the reasons for neutrality can be different.

    When a mutation appears in an active protein coding gene, it is neutral only if it does not affect the protein function, or at least not enough to be “seen” by negative selection.

    When a mutation happens in a non functional sequence, it is neutral by definition: there is no function to be affected, therefore all variation in that sequence will be neutral.

    When a mutation happens in a functional non coding gene, it will be neutral if it does not affect significantly the function of that non coding sequence, whatever it is. And the probability of a mutation in that sequence being neutral will be different from the probability of a mutation in a protein coding gene being neutral, because the function is different and is differently related to the sequence. Moreover, as non coding DNA has functions which can be very different, even different types of functional non coding DNA can have completely different tolerance to variation.

    I don’t think these things are irrelevant. not at all. If we are discussing a theory about neutral variation, we must ask ourselves why variation is neutral in different contexts, especially if we are not just observing that some specific variation is neutral, but we are rather assuming that almost all the variation from one species to another is neutral, and from that assumption we are inferring that almost all the genome is non functional.

    I think that these considerations are very relevant. But if wd400 is not bothered by them, it’s OK. 🙂

  101. 101
    gpuccio says:

    wd400 and Mung:

    I will try another time, in name of a discussion which for me too has been interesting.

    Let’s start from the beginning. Larry Moran, in his original post at Sandwalk, which in some way is the origin of all this discussion, states that according to series of reasonable assumptions the number of fixed mutations in humans since they diverged about five million years ago from chimps is of about 22.4 million. I will accept that, but I want to clarify that it is only a gross estimate, which depend critically on assumptions which have a wide margin of error.

    OK, the second step is that, according to the neutralist theory, about 130 mutations per generation are expected in humans. Again, that is a wide approximation. The numbers on which that is bases can certainly be somewhat different than assumed.

    Finally, by other computations, again depending on reasonable, but not necessarily exact, assumptions, the number of mutations assumed in humans (22.4 million) “corresponds to a substitution rate (fixation) of 121 mutations per generation and that’s very close to the mutation rate as predicted by evolutionary theory”. (Larry Moran’s words)

    Well, this is the argument.

    I have already argue that, first of all, this is not an exact expectation. It is gross, and is based on many assumed numbers which can be tweaked as we like, and have wide margin of errors, which would strongly influence the “amazing coincidence” (again Larry Moran’s words). It is strange how non design theorists become suddenly sensible to “coincidences” sometimes, while utterly ignoring probabilistic arguments when they come from ID theorists. Oh, that’s probably human nature, after all. 🙂

    That said, I would like to ask wd400 a few simple questions starting from that model.

    1) Do you admit that there are important functional differences between humans and chimps?

    2) If that is the case (I would say it is), do you realize that, if we admit for the moment that those differences are related to modifications in the genome (let’s ignore for the moment the role of epigenetic transmission of information), then you are computing in those 22.4 million mutations, also the functional mutations.

    3) Now, I will assume (we can assume too!) that the functional mutations, whatever their number, are not the result of neutral mutations (that would really be an “amazing coincidence”). They can be designed, as I believe, or they can be the result of positive selection (the old neo darwinian explanation). But simple random variation cannot certainly explain them.

    4) Now I ask you: how many mutations, according to you, are responsible of the functional novelties in humans? I suppose you don’t know, and I don’t know either. But I care about that aspect, while you seem not to care. Beware, that number could be small, but it could be big. Let’s say, for the moment, let’s call that number X.

    5) Therefore, we must subtract the number X from our 22.4 million mutations. The result will be the real number of neutral mutations that have been fixed by drift.

    6) Then, we need to know how those 22.4 million mutations are distributed among the different components of the genome: how many in protein coding genes, how many in introns, how many in pseudogenes, how many in SINEs and LINEs, and so on.

    7) Now, we are really at a stop. because, to go on with our computations, and to verify how “amazing” is the coincidence which so much impresses Larry Moran (and, I suppose, you too), we should know:

    a) How big is X

    b) How the X mutations are distributed between the various components of the genome.

    8) then we would have something. But still we should try to understand more about the function of non coding segments, and how robust they are to variation.

    Only if we take into account all these aspects, our reasoning becomes serious and quantitative. Then, maybe we can find really some “amazing coincidences”. Maybe those coincidence would point strongly to a design explanation.

    I don’t think I can be more clear and detailed than so.

  102. 102
    Mung says:

    gpuccio:

    Larry Moran, in his original post at Sandwalk, which in some way is the origin of all this discussion, states that according to series of reasonable assumptions the number of fixed mutations in humans since they diverged about five million years ago from chimps is of about 22.4 million.

    So, are the mutations neutral or not, or does it even matter?

    I keep hoping kairosfocus will weigh in, as he seems to understand sampling.

    Wikipedia:

    Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population due to random sampling.

    Is that random sampling based upon the neutrality or non-neutrality of the allele? If it were, it would not be random. Am I wrong?

  103. 103
    gpuccio says:

    Mung:

    Those are the total mutations that happened (if the number is right).

    They could in principle be any kind of mutation: neutral, positively selected, or designed.

    Moran argues that they must be almost all neutral, because the number corresponds (more or less) to how many neutral mutations would be fixed by drift if the non coding DNS were really non functional, and therefore non affected by negative selection.

    I argue that he is ignoring that at least part of those mutations must be functional (we are different from chimps, and better at least for some tasks 🙂 ), and that the number of functional mutations, which I called X, could well be great. It must be subtracted from the number of true neutral mutations.

    Therefore:

    a) X mutations are functional, and can be explained only by design.

    b) 22.4 million – X mutations are neutral and fixed by drift.

    c) If X is great, the total number of neutral mutations no more corresponds to what would be (more or less) expected by the mutation rate.. It is definitely lower.

    d) Therefore, non coding DNA is functional, and is affected by negative selection.

    QED.

  104. 104
    gpuccio says:

    Mung:

    Errata corrige: it’s non coding DNA, not non coding DNS. Too much internet culture, I suppose. 🙂

  105. 105
    gpuccio says:

    Mung:

    Drift act randomly, therefore it should act mainly on neutral mutations.

    It is possible, obviously, that random drift act on potentially functional mutations, which are treated as though they were neutral (IOWs in that context their potential function cannot be “recognized” by the process going on). Sal has emphasized that possibility many times, and I think he is right.

    The simple fact is that “positive” NS is practically non existent. The few cases we know of are very special cases, with simple variation (usually with reduction of the existing function) and casual advantage in very stressing environmental contexts (see antibiotic resistance). It’s what we call “microevolution”.

    On the other hand, “negative” selection (also called “purifying” selection) is IMO an nimportant process, which takes place all the time.

    Mutations which happen in a functional sequence are either deleterious (and therefore eliminated, more or less, by negative selection), or neutral, and therefore potentially able to be fixed by drift.

    Instead, mutations happening in non functional sequences are by definition neutral, because there is no function to be lost.

    That’s why all mutations are neutral in non functional sequences, and the number of mutations that are fixed in that kind of sequences should be related to the total number of mutations.

    On the contrary, in functional sequences, some mutations are neutral and some are deleterious. Therefore, the total number of neutral mutations in that kind of sequence will be lower, and therefore not connected to the mutation rate.

    This is the basis of Moran’s argument.

    As you can see, the flaw of that argument is that it does not take into account the number of functional mutations.

    Now, they believe that those functional mutations are due to positive selection (yes, even neutralists in the end believe that). That is essentially impossible.

    We believe those functional mutations are designed.

    However, in both cases, the functional mutations will not behave like neutral mutations, and therefore Moran’s argument is wrong.

  106. 106
    Mung says:

    gpuccio:

    Drift act randomly, therefore it should act mainly on neutral mutations.

    But that is only because most mutations are neutral, correct?

    If most mutations were not neutral how would that impact or change genetic drift?

    My thinking is that it would not, because drift is about sampling and not about selection (or lack thereof).

    Am I making sense?

  107. 107
    gpuccio says:

    Mung:

    No, because if either NS or design are important driving forces, then functional sequences expand and are fixed for reasons that have nothing to do with drift. After one sequence expands because it is functional, and not because of drift, then that sequence is relatively “conserved” because of its function. IOWs, drift can still act on the sequence, but only on those mutations that conserve the function.

    So, if say half of the differences we observe between humans and chimps are functional, and have been fixed independently from drift (for example, because they were designed as functional and expanded by positive NS), then the number of mutations that expanded by random drift is half of what we would expect from the mutation rate.

    That’s exactly what we would expect if a large part of non coding DNA in the ancestor of humans and chimps was already functional.

  108. 108
    Mung says:

    gpuccio:

    Drift act randomly, therefore it should act mainly on neutral mutations.

    Are you asserting that genetic drift only acts randomly on neutral mutations, but it does not act randomly on non-neutral mutations?

    If so, I suggest, humbly, that you do not understand genetic drift.

  109. 109
    jean-claude perez says:

    Dear Pr Larry Moran
    here a step which coupld give progress in the comparaison human/chimp:
    “3. Common Descent: This is a biggy. If Sal Cordova and the evolutionary biologists are right about the sequence differences between humans and chimpanzees, then it must mean that humans and chimps share a common ancestor. There will be no room under the big tent for Young Earth Creationists.”
    Please read:
    http://fr.scribd.com/doc/18689.....mosomes4UK

  110. 110
    jean-claude perez says:

    then in the same time human and chimp whole genomes are >99% correlated at codon population: see:
    http://fr.scribd.com/doc/20016.....-close-pdf
    and book codex biogenesis:
    http://www.amazon.co.uk/Codex-.....2874340448

  111. 111
    gpuccio says:

    Mung #108:

    No. I did not say that.

    I paste again my statement:

    “No, because if either NS or design are important driving forces, then functional sequences expand and are fixed for reasons that have nothing to do with drift. After one sequence expands because it is functional, and not because of drift, then that sequence is relatively “conserved” because of its function. IOWs, drift can still act on the sequence, but only on those mutations that conserve the function.”

    The idea is simple. If a sequence expands, is fixed and conserved because of its function, let’s say by positive NS, (even if its origin is design), it is not fixed by genetic drift.

    IOWs, if we find some sequences which are fixed in a population, they could have been fixed:

    a) by drift

    b) by positive selection

    If a complex functional protein is generated by design, for example, it will expand and be fixed because it is functional, by positive selection, and not by drift.

    It is true that drift can act randomly both on neutral and on functional sequences, but most of random variation is neutral, s in practice drift act on neutral mutations, because functional random mutations are so rare that they are almost non existent.

    Designed functional variation certainly happens more often, but still it would be foolish to expect that it is fixed by drift, competing with the many neutral variations. Function originates by design and expands by positive selection.

  112. 112
    jean-claude perez says:

    But that is not close, to resume:
    1/ in my 2nd post, I show that distance between chimp and human is lower that generally considered: 99.99%
    2/ but in my first post, I show great differenciation between human and monkeys…
    3/ in https://plus.google.com/103572438711329205534/posts/26WczM9aQbS
    we show that Human chromosome4 has a typical property absent in all other species and particularly monkeys!

  113. 113
    jean-claude perez says:

    Dears Pietr, Joe or Gordon, I’m sorry for your unapropried comments on SANDWALK of the Sal Cordova entry entitled Vodka! Jean Claude Perez, the golden ratio, dragon curve fractals and musical design in “junk DNA”…

    The reason is that all (ALL) their comments were done without reading the basic original article:

    I suggest you reading the original basic peer review article of 2010 published in Interdisciplinary Science:
    http://fr.scribd.com/doc/95641.....atio-1-618

    and my 2013 peer review article: http://www.scirp.org/journal/P.....2Mwlfl_trA

  114. 114
    jean-claude perez says:

    Considering the point 3 of the pr Larry Moran question, I have to day sufficient consistent material, data and results to demonstrate – considering the chromosome4 – that this human chromosome is an exception and “out of continuity” comparing it with all other primates chromosomes4 and all 23 remaining human chromosomes:

    The 5 steps of my upcoming demonstration are:

    Phase 1 – Analysis of populations of codons:
    Correllations 99.99% of the genomes of humans and chimpanzees but emergence of two clusters of chromosomes highly differentiated (human chromosomes 16 17 19 20 and 22).

    Phase 2 – Evidence of a classification scale of the 24 human chromosomes (focusing particularly on the 2 extremal limit borders chromosome4 and chromosome 19).

    Phase 3 – The chromosome4: significant differentiations between primates (chimp, gorilla, oran utang).

    Phase 4 – The chromosome4: Meta-exclusive differentiation between humans and other primates (chimp, gorilla, oran utang).

    Phase 5 – chromosome4: Meta-exclusive differentiation vis-à-vis the other 23 human chromosomes.

  115. 115
    jean-claude perez says:

    Considering the point 3 of the pr Larry Moran question,

    “…/…3. Common Descent: This is a biggy. If Sal Cordova and the evolutionary biologists are right about the sequence differences between humans and chimpanzees, then it must mean that humans and chimps share a common ancestor. There will be no room under the big tent for Young Earth Creationists…./…”

    I have to day sufficient consistent material, data and results to demonstrate – considering the chromosome4 – that this human chromosome is an exception and “out of continuity” comparing it with all other primates chromosomes4 and all 23 remaining human chromosomes:

    The 5 steps of my upcoming demonstration are:

    Phase 1 – Analysis of populations of codons:
    Correllations 99.99% of the genomes of humans and chimpanzees but emergence of two clusters of chromosomes highly differentiated (human chromosomes 16 17 19 20 and 22).

    Phase 2 – Evidence of a classification scale of the 24 human chromosomes (focusing particularly on the 2 extremal limit borders chromosome4 and chromosome 19).

    Phase 3 – The chromosome4: significant differentiations between primates (human, chimp, gorilla, oran utang).

    Phase 4 – The chromosome4: Meta-exclusive differentiation between humans and other primates (chimp, gorilla, oran utang).

    Phase 5 – chromosome4: Meta-exclusive differentiation vis-à-vis the other 23 human chromosomes.

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