Intelligent Design

The much-disputed neutral theory of evolution and the book that Professor Moran refuses to review: Larry Moran responds to my questions

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Professor Larry Moran has graciously responded to my five questions on the neutral theory of evolution in a recent blog post at Sandwalk, titled, Answering creationist questions about Neutral Theory (6 May 2014). I’ve highlighted Professor Moran’s responses below.

1. Do you agree or disagree with the view expressed by Motoo Kimura that natural selection is necessary to explain evolution occurring at the morphological level?

Professor Moran:
Some evolution at the morphological level can be attributed to natural selection and some is due to random genetic drift. The latter category includes neutral morphological changes and a small percentage of detrimental morphological changes.

I was influenced in this view by Masatoshi Nei’s book Molecular Evolutionary Genetics (1987). [Professor Moran then proceeds to quote a passage from Nei’s book, in which he acknowledges that “there is no question about the importance of natural selection in the formation of intricate morphological characters,” but then goes on to add that “in some morphological characters a substantial part of genetic variation is nonadaptive.”]

So, the answer to your question is “yes;” natural selection and random genetic drift are both necessary to explain evolution at the morphological level.

2. How do you respond to Dr. Gert Kothof’s Korthof’s claim that the neutral theory “is not a theory of evolution,” because it “is not sufficient to explain complex life and adaptations”? If not, why not?

Professor Moran:
I respond by saying that Gert Korthof – whoever that is — doesn’t understand the definition of evolution [What Is Evolution?]. Neutral Theory and random genetic drift are integral parts of evolutionary theory. They are not very good at explaining most adaptations but there’s a lot more to evolution than adaptations.

In a footnote to his post, Professor Moran seems to have taken back his criticisms of Dr. Korthof, implying instead that I had “quote mined” Korthof. I’ll say more about that below.

3. Can you point to any complex structures, functions or behaviors which you believe could not have arisen in the absence of natural selection? (You’ve already nominated the change occurring in the human brain over the past few million years as an event in which natural selection played an indispensable role; what else would you put on your list?)

Professor Moran:
The vast majority of complex structures seem to be adaptations of one sort of another. I suspect there are many “functions” and “behaviors” that are neutral, or even detrimental, but it’s difficult to rule out any adaptive component.

4. In which of the following events do you see natural selection as having played a decisive role: the origin of eukaryotes, the origin of multicellularity, the 20-million-year Cambrian explosion, the origin of land animals, the origin of the amniote egg, the origin of angiosperms, and the radiation of mammals immediately after the extinction of the dinosaurs?

Professor Moran:
I think that natural selection played an important role in all of those events.

5. Or is it simply your contention that natural selection, while not playing an important role in the origin of complex structures and novel morphological features, exerts a refining and purifying effect subsequent to their appearance, weeding out non-viable life-forms?

Professor Moran:
No. I have always contended that natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features. There are likely to many “novel morphological features” that are non-adaptive.

It’s also true that negative natural selection acts as a break on evolution by preventing detrimental changes and “weeding out non-vaible life forms.”

My verdict: An embarrassing climb-down for Professor Moran

Reading Professor Moran’s post, I was struck by its muted tone. Moran believes that “some evolution at the morphological level can be attributed to … random genetic drift,” including “neutral morphological changes and a small percentage of detrimental morphological changes.” He admits that “Neutral Theory and random genetic drift … are not very good at explaining most adaptations,” adding that “the vast majority of complex structures seem to be adaptations of one sort of another.” He then tentatively proposes that “there are many ‘functions’ and ‘behaviors’ that are neutral,” but concedes that “it’s difficult to rule out any adaptive component.” He finally acknowledges that “natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features,” but goes on to suggest that “there are likely to [be] many ‘novel morphological features’ that are non-adaptive.” However, since Professor Moran has already conceded that “the vast majority of complex structures seem to be adaptations of one sort of another,” it is difficult to know what to make of his last suggestion.

In short: Professor Moran’s endorsement of the neutral theory is hedged with so many qualifications that his post might as well have been written by Professor Jerry Coyne, who articulated his views with the utmost clarity, in a post dated December 5, 2012:

Regardless of the source of genetic variation, if new variants are to become “fixed” (i.e. ubiquitous) in natural populations after they arise, and to become part of complex adaptations, there is no credible alternative to natural selection for the process causing that fixation.

Too hot to handle: the book that Professor Moran refuses to review!

One of the commenters on Professor Moran’s blog post, Claudiu Bandea, posed a question about a book by the accalaimed molecular evolutionary biologist, Professor Masatoshi Nei (pictured above, courtesy of Wikipedia), which Professor Moran had previously praised to the skies, hinting that it was about time for him to honor his promise to review the book:

About a year or so ago, our host Lary (sic) Moran wrote a post entitled “Mutation-Driven Evolution” (http://sandwalk.blogspot.com/2013/06/mutation-driven-evolution.html). The post was a preview of a new book by Masatoshi Nei entitled “Mutation-Driven Evolution.” Larry ended his post saying: “I can’t wait to get my hands on a copy of this book. Look for a review in a few months.

I don’t know if Lary (sic) kept his promise or not, but in the outline of his book Masatoshi Nei writes that, unlike Motoo Kimura and Jack King, who believed that phenotypic evolution (in contrast to molecular evolution) is caused primarily by natural selection, he believes that both molecular and phenotypic evolution are primarily caused by mutation.

John Harshman’s reaction was: “Larry, this seems to conflict seriously with your (and my) preferred definition of evolution”.

For whatever reason, Larry chose to be silent on this difficult and inconvenient issue about the Neutral Theory because, I presume, he wanted to read the book first. It would be enlightening, if Larry and John would be willing to discuss the significance of Neutral Theory and the Mutation Theory in explaining evolution. (Emphases mine – VJT.)

Professor Moran replied:

@Claudiu Bandea,

Sorry to disappoint you but I’m not going to write a review of Nei’s latest book.

You’re going to have to read it yourself.

Claudiu Bandea persisted with his question, asking Professor Moran:

The relevant issue here is science, not the book: do you agree with Nei’s proposition that Kimura and King’s perspective was wrong and that the molecular and phenotypic evolution are primarily caused by mutation?

To date, there has been no reply from Professor Moran.

Masatoshi Nei: A new kind of mutation is required to account for functional complexity!

I found out why Professor Moran hadn’t reviewed Professor Masatoshi Nei’s latest book when I had a look at what Professor Nei had to say on the origin of functional complexity. (Parts of his new book are accessible via Google books.) I was tipped off by a hint provided by biologist Kenneth M. Weiss in his Amazon review of Professor Nei’s book:

… Nei challenges the often automatic assumption that such traits are due to ‘selection’ rather than mutation. The prevailing idea has been that there’s always enough standing variation for selection to screen to enable new adaptations to occur. But Nei explains his challenge to that idea, that new adaptations for complex traits must await ‘constraint breaking’ mutations that enable new pathways out of entrenched developmental systems.

“Hmm,” I thought. “Sounds interesting.” And I wasn’t wrong. Professor Nei is no friend of Intelligent Design; he explicitly states in the last sentence of his book (p. 199) that in his view of evolution, “there is no need of considering teleological elements.” But what he has to say about constraint breaking mutations in the General Summary and Conclusion of his book (pp. 196-199) makes for fascinating reading:

The conclusions we have reached may be summarized as follows. (1) Mutation is the source of all genetic variation upon which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transpositions of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of a mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors. However, selective advantage of a mutation is also dependent on the set of other genes and the environmental conditions, the latter varying from generation to generation. (3) Evolution is a process of increase or decrease of organismal complexity and enhancement of phenotypic diversity among different species. It may or may not be associated with the increase of fitnesses (number of offspring per individual), and therefore evolution can occur by neutral genetic processes such as gene duplication and gene co-option as well as by natural selection. (4) A gene is not a random collection of nucleotides but a very specific arrangement of nucleotides that encodes a biochemically functional protein or RNA molecule. Because of this functional constraint, most mutations occurring in a gene are deleterious and eliminated by purifying selection. (5) For a gene to have a new function, constraint-breaking mutations caused by new combinations of harmonious genes and gene sequences are necessary. These mutations occur with a low frequency at functionally important sites. A gene cannot have any function without having interaction with other genes. Therefore, constraint-breaking mutation may be controlled by many gene loci. (6) A genome is an integrated and conserved set of genes that is capable of producing healthy organisms. The innovational change of phenotypic characters is generated when constraint-breaking mutations occur at the genomic level. There is a considerable degree of flexibility in genomic constraint so that diploid individuals with two different genomes can survive without trouble within a species. However, if two different populations are isolated for a long evolutionary time, interpopulational hybrids become inviable of sterile because of genomic incompatibility. This hybrid weakness occurs because the genomes of two populations evolve independently and therefore the compatibility of genes between different populations gradually declines. No positive selection is necessary for the establishment of hybrid sterility. (7) Although any organism lives under ecological constraints, such constraints are usually not very strong. Therefore, most organisms can live in a range of ecological niches, which can be called the ecological survival range. For this reason, a species may flourish easily in a new territory to which it was transferred. (8) Evolution occurs primarily as a result of constraint-breaking mutations rather than as a result of the struggle for existence. If a species moves to a new habitat (e.g. marine habitat to land), a radiational speciation may occur because of relaxation of purifying selection and some advantageous mutations for different new territories…

Neomutationism or the theory of mutation-driven evolution is also different from the classical mutationism, because it covers not only genic mutations but all kinds of genomic change including genome duplication. In neomutationism, the molecular study of mutational change as well as the selective advantage of new mutations are emphasized. Therefore the cause of mutation is no longer treated as a black box. For these reasons, neomutationism or the theory of mutation-driven evolution is applicable for much wider biological situations than classical mutationism and at the same time demands a more sophisticated molecular approach…

At the present time we have little idea about the evolution of the human brain or even less complicated characters such as parental care in some mammals. However, the evolution of these characters will eventually be clarified at the molecular level…

In the study of phenotypic evolution it is important to realize that there are two evolutionary forces operating at the genomic level. One is the genome conservation force that maintains the developmental integrity of genes within individuals and the reproductive unity of individuals within species or populations…

The other evolutionary force is the genomic diversification of different species. This occurs because many constraint-breaking mutations are species-specific and these mutations contribute to the diversification of different species.

From the foregoing passage, it should be apparent that Professor Nei envisages his neomutational theory of evolution as a comprehensive theory of evolutionary change, which can ultimately explain even the evolution of the human brain at the molecular level. This is radically different from the more conservative position defended by Professor Moran in his replies to my five questions.

Why, then, is Professor Moran glossing over these differences between his theory and Professor Nei’s?

Professor Nei’s remarks on constraint-breaking mutations are also interesting. The critical question that needs to be asked is: can he demonstrate mathematically that the constraint-breaking mutations he envisages are capable of generating the kinds of structural, behavioral and molecular complexity that we observe in the world of living things?

Professor Masatoshi Nei’s explosive interview with Discover magazine

Still curious about why Professor Moran hadn’t reviewed Masatoshi Nei’s book, I did some research, and came across a very revealing interview which Professor Nei gave to Gemma Tarlach, in Discover magazine (“Mutation, Not Natural Selection, Drives Evolution,” March 16, 2014):

Charles Darwin said evolution occurs by natural selection in the presence of continuous variation, but he never proved the occurrence of natural selection in nature. He argued that, but he didn’t present strong evidence.

But among the people working on evolution, most of them still believe natural selection is the driving force.

If you say evolution occurs by natural selection, it looks scientific compared with saying God created everything. Now they say natural selection created everything, but they don’t explain how. If it’s science, you have to explain every step. That’s why I was unhappy. Just a replacement of God with natural selection doesn’t change very much. You have to explain how.

Mutation means a change in DNA through, for example, substitution or insertion [of nucleotides]. First you have to have change, and then natural selection may operate or may not operate. I say mutation is the most important, driving force of evolution. Natural selection occurs sometimes, of course, because some types of variations are better than others, but mutation created the different types. Natural selection is secondary…

Kimura believed morphology [appearance] evolves through natural selection. He applied neutral theory only on a molecular level. I say it can determine morphological characteristics as well because DNA determines everything, but to prove this has not been so easy. [Laughs.] Forty or 50 years later, I am still trying to prove it…

… Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant.

But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.

You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.

“Question dogma.” I have to say that I like Professor Nei’s iconoclastic attitude, and I hope we see more of it among evolutionary biologists, in the years to come.

Professor Moran suggests that I may have quote mined Dr. Gert Korthof

In my post, Will the real Neutral Theory please stand up?, in which I posed the above five questions, I quoted a passage from a review by Dr. Gert Korthof of Motoo Kimura’s book, The neutral theory of molecular evolution. Dr. Korthof seemed to be implying in his review that Kimura’s willingness to cede a dominant role to natural selection when accounting for the origin of morphological complexity was the decisive factor that rendered his theory acceptable to his Darwinist contemporaries. I then quoted the following remark by Dr. Korthof, in which he expressed his own opinion on the neutral theory of evolution:

Please note that ‘the neutral theory of evolution’ is not sufficient to explain complex life and adaptations. In that sense it is not a theory of evolution. (Emphasis mine – VJT.)

In a footnote to his recent blog post, Professor Moran, in response to a complaint by Dr. Korthof, proceeds to give what he calls “the full quote”:

‘Please note that ‘the neutral theory of evolution’ is not sufficient to explain complex life and adaptations. In that sense it is not a theory of evolution. However it is accepted that the neutral theory explains a lot of differences in DNA. Kimura:

‘Of course, Darwinian change is necessary to explain change at the phenotypic level – fish becoming man – but in terms of molecules, the vast majority of them are not like that. (7)’

Professor Moran then comments:

Looks like Vincent Torley might have quote mined a scientist. Isn’t that amazing?

A few of the commenters on Professor Moran’s blog post were more direct. One wrote: “Gert strongly opposes creationists on his blog, so it is funny to see Vincent Torley quote him in defense.” Another accused me of quote mining Korthof, while yet another commenter added that I have “the (sic) tendency to quote mine everybody in very interesting ways.”

Dr. Korthof himself claimed that the quote in my post “was wrong and out of context,” and in another comment, referred to it as a “misquote.”

What quote mining is – and isn’t

It seems that evolutionists need a basic lesson on what quote mining is. Here’s how RationalWiki defines quote mining:

Quote mining is the deceitful tactic of taking quotes out of context in order to make them seemingly agree with the quote miner’s viewpoint or to make the comments of an opponent seem more extreme or hold positions they don’t in order to make their positions easier to refute or demonize.

Let’s break this down into very simple steps.

1. In my post, I provided a direct link to Dr. Korthof’s review of Motoo Kimura’s book, enabling readers to check the accuracy of my quote at the touch of a button. Had my intention been to deceive, I obviously would not have done that. Since RationalWiki defines quote mining as a “deceitful tactic of taking quotes out of context” (italics mine), it follows that I cannot be guilty of quote mining.

2. Nowhere in my post did I imply or state that Dr. Korthof agreed with my views on evolution. The commenter who wrote, “Gert strongly opposes creationists on his blog, so it is funny to see Vincent Torley quote him in defense,” was therefore completely missing the point I was making.

3. The reason why I quoted Dr. Korthof was very simple: to illustrate the point that I was making – namely, that a theory which “is not sufficient to explain complex life and adaptations” cannot be properly described as “a theory of evolution.” Evolution is by definition an all-encompassing theory of biology, as atomic theory is to chemistry. Any biological theory (such as the neutral theory) which does not even attempt to account for key aspects of our biology – such as “the vast majority of complex structures” (to quote Professor Moran’s own words) cannot be accurately called “a theory of evolution.” At best, one might call it “a theory of molecular evolution.”

4. Dr. Gert Korthof apparently thinks that I should have appended the following sentence from his review to my original quote: “However it is accepted that the neutral theory explains a lot of differences in DNA.” The reason why I didn’t quote that sentence is that it’s fairly non-controversial, and obvious to nearly everyone. I myself would agree with it, as would Professor Moran. Why belabor the obvious?

5. Dr. Korthof also chides me for omitting the following quote from Motoo Kimura:

Of course, Darwinian change is necessary to explain change at the phenotypic level – fish becoming man – but in terms of molecules, the vast majority of them are not like that. (7)

But if Dr. Korthof had bothered to read my post, he would have seen that I did quote this passage, in an earlier paragraph. I even provided a link to Dr. Korthof’s review for a citation of this passage, for the benefit of those readers who don’t own back issues of New Scientist magazine, where the quote originally appeared!

In other words, my original post correctly quoted the substance of Dr. Korthof’s views, as well as quoting Motoo Kimura in context.

6. For the benefit of commenters over at the Sandwalk blog who have trouble appreciating what a quote mine is, here’s an example. Suppose that in my original post, I had simply quoted Dr. Korthof as stating that “‘the neutral theory of evolution’ … is not a theory of evolution.” Now that would have been quote mining, as it fails to supply the proper context. The following quote supplies the relevant context, and is therefore a legitimate quote:

Please note that ‘the neutral theory of evolution’ is not sufficient to explain complex life and adaptations. In that sense it is not a theory of evolution. (Italics mine – VJT.)

7. The whole point of my quoting from Dr. Korthof was to put forward an embarrassing criticism of the neutral theory of evolution, from someone who is clearly in a position to understand it – namely, a Dutch biologist who has read hundreds of books relating to evolution, and who vocally supports evolution in his blog posts. Quoting highly credible people who hold views very different to your own, but who nevertheless agree with you on a vital point that you wish to argue for, is not quote mining. It’s simply smart tactics.

Dr. Nick Matzke’s amusing rant

The first person to comment on Professor Moran’s blog post was Dr. Nick Matzke, who wrote what he himself described as a “rant.” This one’s a beauty:

Creationists seem unable to hold in their heads the idea that multiple natural processes can be in operation, and that some of those processes can explain one class of observations, and other processes can explain other classes of observations.

Earth to creationists/Sal/vjtorley: natural selection is the main explanation of complex adaptations (e.g., eyes). Neutral processes are the main explanation of non-adaptive changes (e.g., sequence change in junk DNA). The fact that most molecular evolution is neutral makes sense because most of the genome of humans (and other large-genomed organisms) is junk. This statement does NOT mean ALL genomic change is neutral, and basically any evolutionist would agree that selection plays an important role when it comes to adaptive changes in functional DNA such as genes. Also, most molecular evolution being neutral says nothing in particular about the evolution of morphology, which is controlled by non-junk DNA.

There is more that could be said (as always; see in particular Michael Lynch), but that’s a good first approximation. This should have been obvious to you guys from the beginning, if you had bothered to think and read about it for 5 minutes, rather than trumpeting your ignorance in blogposts. Don’t you ever get embarrassed about getting such fundamental basics wrong? Don’t you see why this level of ignorance, when coupled with accusations that it is the evolutionists who are wrong / evil / misleading the world, is totally infuriating to professional biologists and guarantees that you will be seen as nothing but malicious, intellectually lazy cranks?

(end rant)

Here’s a piece of advice for Dr. Matzke: you really need to take a long, cold shower.

And here’s a question for Dr. Matzke: how do you reconcile your statement that “most molecular evolution being neutral says nothing in particular about the evolution of morphology” with Professor Masatoshi Nei’s claim in his paper, Selectionism and Neutralism in Molecular Evolution (Molecular Biology and Evolution, December 2005, Volume 22, Issue 12, doi: 10.1093/molbev/msi242, pp. 2318-2342): “It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels” (italics mine)? In his latest book, Mutation-Driven Evolution (Oxford University Press, 2013), Professor Nei is even more direct:

…[M]any evolutionists including Motoo Kimura and Jack King believe that mutation phenotypic evolution is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. (p. 9)

For that matter, Dr. Matzke, how do you reconcile your position with that of Professor PZ Myers, who in a post titled, Complexity is not usually the product of selection (11 December 2012), wrote:

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.

Here’s a final question for Dr. Matzke. You refer to me, Sal Cordova and unspecified “creationists” as getting the “fundamental basics” wrong. Very well, then: what “fundamental basics” did I get wrong in my post? I took great pains to accurately characterize the views of Motoo Kimura: I quoted him as saying that “The Darwinian theory of evolution by natural selection has served as a great unifying principle in biology,” and that his own neutral theory “does not deny the role of natural selection in determining the course of adaptive evolution, but it assumes that only a minute fraction of DNA (or RNA) changes are adaptive.” I also described Kimura as claiming that “molecular evolution was dominated by neutral evolution, but at the phenotypic level, natural selection probably accounted for most changes in characteristics, rather than genetic drift.” I quoted the exact words of Motoo Kimura’s colleague, Professor Masatoshi Nei, and I also took great care not to put words into the mouths of Professors PZ Myers and Larry Moran: I described them as arguing that “most of the complexity that we see in the biological world could be largely the result of chance, although they do not wish to rule out a role for natural selection.” Given that I took such pains to accurately represent the views of the key protagonists in the current debate on what the neutral theory of evolution can and cannot explain, why do you continue to accuse me of being wrong in my facts? Is it not you who are wrong in yours, Dr. Matzke?

84 Replies to “The much-disputed neutral theory of evolution and the book that Professor Moran refuses to review: Larry Moran responds to my questions

  1. 1
    Joe says:

    What is “negative natural selection”? If natural selection is the elimination of the less fit does that mean that negative natural selection is the non-elimination of the less fit?

    Does Larry Moran even understand what natural selection is? Apparently not.

  2. 2
    gpuccio says:

    VJ:

    I hate that in the end I have to be right!

    So, NS is still the only game in town. QED. 🙂

  3. 3
    Mung says:

    I did some research, and came across a very revealing interview which Professor Nei gave to Gemma Tarlach, in Discover magazine (“Mutation, Not Natural Selection, Drives Evolution,” March 16, 2014)

    nice find vjt! thanks!

    perhaps we’ll be again blessed by a drive by nicking.

    Even better, maybe Nick will write a review of the book!

  4. 4
    Barry Arrington says:

    VJ, Nick Matzke is really quite shameless as we all know. Let me repeat his famous “not really”:

    Barry Arrington: “If you came across a table on which was set 500 coins (no tossing involved) and all 500 coins displayed the ‘heads’ side of the coin, would you reject ‘chance’ as a hypothesis to explain this particular configuration of coins on a table?”

    Mark Frank: “. . . they might have slid out of a packet of coins without a chance to turn over.”

    Sal Cordova: “Which still means chance is not the mechanism of the configuration.”

    Matzke: “Not really.”

    Anyone who will say that will say anything. Don’t hold your breath while waiting for answers to the questions you pose at the end of your post.

  5. 5
    Joe says:

    Nick Matzke:

    Earth to creationists/Sal/vjtorley: natural selection is the main explanation of complex adaptations (e.g., eyes).

    It is an evidence-free explanation which means it doesn’t belong in science text books.

  6. 6
    JoeCoder says:

    Perhaps the reason for the ambiguous “sometiems this” and sometimes that” answers from Dr. Moran were because the questions weren’t specific enough? A month ago I asked him for some exact numbers since a chimp divergence and he responded:

    Updated numbers suggest 44 million point mutations and something like 2 million insertions/deletions for a grand total of 46 million mutations.

    We don’t know how many of those were beneficial (adaptive) leading to ways in which modern chimps are better adapted than the common ancestor. (Same for humans.) My guess would be only a few thousand in each lineage.

    So three thousand out of 23 million is 0.013% of mutations being fixed by selection and the rest by drift, or a little more than one out of ten thousand mutations by selection. With of course selection also removing the more deleterious mutations.

  7. 7
    JoeCoder says:

    Also, who wrote this post? The author is vjtorley but halfway through I see “You refer to me, Sal Cordova”.

  8. 8
    wallstreeter43 says:

    Can someone explain to me what this article has if anything to did with intelligent design?

  9. 9
    Mung says:

    Can someone explain to me what this article has if anything to did with intelligent design?

    Sure. “It just happened, that’s all,” is not a scientific theory. Intelligent design is an attempt to offer a rational alternative.

    Hope that helps!

  10. 10
    bornagain77 says:

    Dr. Torley, it might be of interest to note that ‘form’ is not even reducible to mutations in the DNA in the first place, whether neutral or not:

    “Although this theory [neo-Darwinism] can account for the phenomena it concentrates on, namely, variation of traits in populations, it leaves aside a number of other aspects of evolution… Most important, it completely avoids the origination of phenotypic traits and of organismal form. In other words, neo-Darwinism has no theory of the generative.”
    – Gerd B. Muller & Stuart A. Newman – Origination of Organismal Form, p.7

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    https://vimeo.com/91322260

    Dr. Stephen Meyer comments at the end of the preceding video,,,
    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’
    Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009)

    Darwin’s Doubt narrated by Paul Giem – The Origin of Body Plans – video
    http://www.youtube.com/watch?l.....page#t=290

    Body Plans Are Not Mapped-Out by the DNA – Jonathan Wells – video
    http://www.youtube.com/watch?v=meR8Hk5q_EM

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences
    http://musicoflife.co.uk/

    “Live memory” of the cell, the other hereditary memory of living systems – 2005
    Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.
    http://www.ncbi.nlm.nih.gov/pubmed/15888340

    Response to John Wise – October 2010
    Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

  11. 11
    Mung says:

    …I realized that mutation is the driving force of evolution. Yet, this view was regarded as a heresy at the time when neo-Darwinism dominated the field. In the meantime the neutral theory of molecular evolution was proposed to explain the evolution of genes and proteins. This theory clearly showed that the evolution of nucleotide sequences has occurred mainly by random fixation of neutral mutations. However, most neo-Darwinians did not pay much attention to this discovery, because they believed that neutral evolution has nothing to do with phenotypic evolution, in which most evolutionists are interested. In fact, even the proponents of the neutral theory of molecular evolution stated that phenotypic evolution occurs mostly by natural selection…

    …my conception of evolutionary biology is different from the currently popular views. – Masatoshi Nei

    Is it any wonder why Larry, PZ, Nick and crew don’t want to touch this book with a ten foot pole?

    The Changing Face of Evolutionary Thinking

  12. 12
    jerry says:

    Allen MacNeill has been saying for years that neo-Darwinism is dead. I have cited this comment below about 4-5 times in the last few months. It is from years ago. This is exactly what Nei is talking about.

    This quote demonstrates a basic misunderstanding of the process of natural selection. According to Darwin (and virtually all evolutionary biologists), natural selection has three prerequisites:

    1) Variety (generated by the “engines of variation”

    2) Heredity (mediated by the transfer of genetic material, either vertically – from parents to offspring – or horizontally – via viral transduction, retrotranscription, etc.)

    3) Fecundity (reproduction, usually at a rate that exceeds replacement).

    Given these three prerequisites, the following outcome obtains:

    4) Demography: some individuals survive and reproduce more often than others. Ergo, the heritable variations of such individuals become more common over time in populations of those organisms.

    Natural selection is synonymous with #4; it is an outcome of the three processes listed first, not a “mechanism” in and of itself.

    Ergo, the real dispute here is not over natural selection per se, but rather the properties and capabilities of the “engines of variation”. I have written extensively about these here:

    http://evolutionlist.blogspot......ution.html

    and here:

    http://evolutionlist.blogspot......awman.html

    Yes, natural selection (i.e. #4, above) is conservative not creative. It produces no new genetic nor phenotypic information, which is why Darwin eventually came to prefer the term “natural preservation” rather than “natural selection”.

    However, it is also abundantly clear that the “engines of variation” – that is, the processes the produce phenotypic variation among the members of populations of living organisms – are both extraordinarily creative and extraordinarily fecund. The real problem in biology is not producing new variation, but rather limiting the production of new variation to the point that the “engines of variation” do not cause the rapid disintegration of living systems.

    As just one example of this problem, the genetic elements known as transposons generate a huge amount of new genetic variation, much of which is either phenotypically neutral or deleterious to the organism. There are biochemical mechanisms by which cells can monitor the incidence of transposition in themselves, and limit its consequences (up to and including the active self-destruction of the cell via apoptosis).

    At the same time, there is very good evidence in the genomes of many organisms that retrotransposition events mediated by transposons have produced genetic changes that have resulted in increased survival and reproduction of the organisms in which such events have taken place. There is a large and growing literature on this phenomenon, all of which points to the inference that retrotransposition via transposons both creates new genetic and phenotypic variation, and that in some cases such variation can provide the raw material for evolutionary adaptations, which are preserved via natural selection.

    So, if you really want to find out where the “intelligent designer” might create new variations, you should follow the lead of Darwin’s good friend, Asa Gray, and look for the telltale evidence for such intervention in the “engines of variation”. Of course, you will have to show pretty conclusively, using empirical investigations and statistical analysis, that such “creation events” are not the result of purely natural, unguided processes. If you can do this, you will undoubtedly win a Nobel Prize and a Crafoord Prize (plus a MacArthur or two).

    Notice that this will involve looking carefully into the mechanisms by which new variations are produced, rather than pointing to the outcomes of such processes (i.e. natural selection) and simply asserting that “you can’t get here from there”. Simply asserting (without empirical evidence) that something can’t happen isn’t “doing science” at all. In fact, it’s doing just the opposite…

    This must be pretty much of what the evolutionary biologist at Cornell must think. He points out various researchers, mainly disciples of Stephen Gould who share his view.

    Notice how Allen tells the ID people how to support their position. All this is testable especially with the exponential increase of genomes being sequenced and analyzed. It is only a matter of time before we have many of the answers.

  13. 13
    jerry says:

    Here is something someone explained to me several years ago. I didn’t really understand it in terms of the debate at that time.

    What the advocates in the creativity of natural selection mainly believe is that the gene pool is incredibly flexible in what can be produced from it. You have to first look at processes such as dog and pigeon breeding, or artificial selection, especially dogs. We see amazingly different phenotypes, all hidden in a basic dog genome. The right combination of alleles will produce a great dane while another combination will produce a dachshund. Darwin uses artificial selection in the Origin to hook his reader.

    Darwin and people like Dawkins believed that all the variations was hidden in the genome and the right type of selection would bring out the right type of alleles that could produce any phenotypes we see (of course Darwin knew nothing about anything specific within the organism such as alleles) . In other words, there was once a gene pool that with the proper sequence of environmental changes would produce all the organisms we see.

    It is that the phenotype seemed to be plastic and could be molded into almost anything. This is why they worship NS and genetic drift. All that is necessary is for the right combinations of alleles to arise. The right combinations will create or form the intricate morphological characters.

    One of the concepts in the new Nicholas Wade book is that most characteristics and traits in humans are the result of a suite of alleles and not a single one. So it is the right combination that will produce the trait or characteristic. Mutations play a role but more so in the creation of new alleles as opposed to entirely new coding sequences and new proteins. Humans and the chimps deviate as different alleles develop in the human and the chimp after they diverged.

    MacNeill and Nei are saying that you must have new variation constantly arising and some of it is very complex. Thus, there is another school of evolutionary biologists who believe natural selection is essential but secondary to new variation. We seem not to be aware of them despite MacNeill talking about it for years.

    If this is reading Moran and Dawkins wrong, I would be interested just what they are saying that is different but it seems to be what they are advocating.

  14. 14
    vjtorley says:

    Hi jerry,

    Thanks very much for the quote from Allen MacNeill, a man whose opinions I respect. I was especially interested in the following passage:

    So, if you really want to find out where the “intelligent designer” might create new variations, you should follow the lead of Darwin’s good friend, Asa Gray, and look for the telltale evidence for such intervention in the “engines of variation”. Of course, you will have to show pretty conclusively, using empirical investigations and statistical analysis, that such “creation events” are not the result of purely natural, unguided processes. If you can do this, you will undoubtedly win a Nobel Prize and a Crafoord Prize (plus a MacArthur or two).

    Well, there’s a research goal for the ID movement. Food for thought.

    Thanks once again.

  15. 15
    vjtorley says:

    Hi Mung,

    Thank you very much for your helpful comments, and for the enclosed link to Gunter P. Wagner’s review of Masatoshi Nei’s Mutation-Driven Evolution. I was especially struck by this sentence from the review:

    As far as I can see, the core idea in Nei’s book, to which evolutionary biologists need to pay attention, is constraint-breaking mutations.

    Wagner has hit the nail on the head. What I think we in the Intelligent Design movement need to focus on is the mathematics of these mutations. Thanks once again, Mung.

  16. 16
    vjtorley says:

    JoeCoder,

    In answer to your question, I wrote this post. In the passage you quoted, I wrote: “You [Dr. Matzke] refer to me [vjtorley], Sal Cordova and unspecified ‘creationists’ as getting the ‘fundamental basics’ wrong.” I hope that makes sense.

  17. 17
    Mung says:

    More from Nei:

    …he [Darwin] never implied that natural selection has creative power … he stated: “Several writers have misapprehended or objected to the term Natural Selection. Some have even imagined that natural selection induces variability, whereas it implies only the preservation of such variations as arise and are beneficial to the being under the conditions of life.

  18. 18
    Mung says:

    Conceptually his [Darwin’s] theory of evolution consists of two proceses: (1) the generation of new variations and (2) natural selection of favored variations. In this sense his view is similar to the modern concept of evolution. Darwin provided strong arguments for the second process (not evidence), but he could not give satisfactory explanations for the first evolutionary process.

  19. 19
    Mung says:

    VJT, thank you. I wish you had access to my library. You seem to have a lot more time for this than i do, lol.

    I live in the Seattle area. Speak to your friends at the DI about setting up a lending library for ID research 🙂

  20. 20
    Mung says:

    To avoid the reduction of variation, there was a need for finding mechanisms that generate new variation.

    – Nei p. 3

    If mechanisms that generate new variation are so important to evolutionary theory, how is the origin of those mechanisms explained by evolutionary theory?

    How is the existence of mechanisms that generate new variation an argument against intelligent design?

  21. 21
    jerry says:

    Dr. Torley,

    There is a lot being published on the origin of variation. One of the books recommended by MacNeill was titled “Macroevolution” by Vrba and Eldredge who were colleagues of Stephen Gould. The book was series of papers from (Paleobiology 31(sp5):1-16. 2005) and was a tribute to Stephen Gould.

    The lead author in this book and journal issue was Jurgen Brosius who is at the University of Münster in Germany. They are heavily into the origin of new proteins via natural means. Here is a page of their activity.

    http://zmbe.uni-muenster.de/in.....chmitz.htm

    And here are three relevant publications:

    Exonization of transposed elements: A challenge and opportunity for evolution – http://zmbe2.uni-muenster.de/e.....iochim.pdf

    Book chapter Repetitive DNA: SINEs as driving forces in genome evolution – http://zmbe.uni-muenster.de/in.....n_2012.pdf

    Genomic impact of eukaryotic transposable elements – http://zmbe.uni-muenster.de/in.....a_2012.pdf

    These articles are direct challenges to Axe and Durston. It is hard to tell just how much of a challenge they are since they may be claiming much more than they can show.

  22. 22
    jerry says:

    How is the existence of mechanisms that generate new variation an argument against intelligent design?

    Essentially they are not arguments against ID and in fact may be great design.

  23. 23
    wallstreeter43 says:

    Mung “”Sure. “It just happened, that’s all,” is not a scientific theory. Intelligent design is an attempt to offer a rational alternative.

    Hope that helps!”””

    Yea it helps a lot . I guess Darwinists won’t stop trying to push their religious beliefs on us all no matter whether it makes sense or not.

  24. 24
    Mung says:

    jerry:

    There is a lot being published on the origin of variation. One of the books recommended by MacNeill was titled “Macroevolution” by Vrba and Eldredge who were colleagues of Stephen Gould. The book was series of papers from (Paleobiology 31(sp5):1-16. 2005) and was a tribute to Stephen Gould.

    “Many of Gould’s ideas generated controversy, but one for which he was never criticized was being a neutralist, which he most definitely was not. On the contrary, Gould argued that patterns of of punctuated equilibria in phylogeny can be explained only if natural selection operates not just among individuals within populations, but also among species and higher taxon levels (Gould 2002).”

    Macroevolution: Diversity, Disparity, Contingency, p. 122

  25. 25
    Mung says:

    Mung’s neutral theory of dumpster diving.

    jerry:

    We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion.

    It seems to me that by analogy you are asserting that we can’t argue for junk in the local landfill because we haven’t taken into account dumpster diving.

  26. 26
    jerry says:

    Many of Gould’s ideas generated controversy, but one for which he was never criticized was being a neutralist

    Depends what you mean by a neutralist. I suggest you read the articles by Brosius if you can get them. Both Vrba and Brosius worked with Gould and of course Eldredge was his partner. Here is a quote from the article by Brosius which is the lead article in the book.

    An extension of Wally Gilbert’s metaphor “exons in a sea of introns” (Gilbert 1978). Functional nuons are is lands in a sea of nonfunctional (nonaptive) sequences. Nevertheless, any of those sequences has the potential to be exapted into novel functions (Brosius and Gould 1992; Balakirev and Ayala 2003). While “plate tectonics,” or exon shuffling, occasionally leads to rearrange ments of existing functional nuons (Gilbert 1978), retro position, the major force in the plasticity of genomes, which in our analogy is more akin to volcanic eruptions, frequently creates new nuons. Initially, most nuons (is lands) are barren (nonfunctional, nonaptive) but have the potential to be fertilized by some microevolutionary base changes or short indels and exapted as functional nuons. Nonfunctional nuons erode over time and the is lands disappear in the sea of anonymous sequences. An interesting example is the recruitment of part of an Alu retronuon as an alternative exon in an isoform of the cytokine tumor necrosis factor receptor. Insertion of the Alu element occurred after Anthropoidea split from pro simians and a subsequent point mutation generated an ATG start codon. This base substitution alone, however, was not sufficient for exaptation of the Alu element as a protein-coding exon, as this sequence is nonaptive (not used as part of an alternative mRNA) in Platyrrhini. Only two additional small changes in the lineage lead ing to Catarrhini including apes, a C->T transition to generate a GT 5? splice site and a 7-bp deletion to pro vide translation into the next exon in the correct reading frame, led to generation and exaptation of this alternative exon (Singer et al. 2004).

    ———- from another part of the article

    A nuon is any distinct nucleic acid, a defined sequence module (Brosius and Gould 1992). The term can be used with a prefix (e.g., retronuon) to designate any DNA module that was generated by retroposition. I prefer retronuon over retroposon and especially over transposable element (TE) or mobile element (ME). In fact, any RNA is a potential mobile element: if a segment of the genome is transcribed in the germline it has the potential to serve as template for retroposition (hence, RNA might be considered the ultimate selfish unit). However, upon integration into the genome, there is no guarantee for autonomous transcription in the germline, which results in a loss of mobility. The original transcript, how ever, can serve as a template for retroposition multiple times. In contrast to TE or ME, the term “retronuon” solely indicates the mode of origin, but not the potential for successive amplification. Only a minority of retronuons are true TEs or MEs, such as endogenous retroviruses or intact LINE elements [see Brosius 2003a]).

    Here is a link to a study by Gould and Brosius from over 20 years ago.

    http://www.pnas.org/content/89/22/10706.full.pdf

    ———-

    We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion.

    I never said anything like this. Maybe you have me confused with someone else.

  27. 27
    Mung says:

    Since we’re quoting Brosius:

    Life depends on stable, efficient, high-capacity systems of information storage and on information that replicates at high fidelity.

    Maybe that’s why MacNeill is recommending the book. 🙂

    I’m still at a bit of a loss to find a connection between this book and alternatives to neo-Darwinism.

    Chapter 11 (author: Daniel W. McShea) is titled: The evolution of complexity without natural selection

    The internal-variance principle identifies an evolutionary vector, a kind of pervasive force pushing complexity – understood as differentiation among parts – upward.

    Wasn’t it Gould who proposed that life couldn’t help but get more complex? But so what?

    …it is unclear whether selection will enhance this vector, act neutrally, or oppose it, perhaps negating it.

    So it still comes down to selection?

  28. 28
    Mung says:

    jerry:

    I never said anything like this. Maybe you have me confused with someone else.

    You are correct. My apologies. I accidentally cross-posted this to the wrong thread under a quote box I had created to respond to you. That’s what I get for trying to multitask. 🙂

    It was Dr JDD

  29. 29
    NickMatzke_UD says:

    Here’s a piece of advice for Dr. Matzke: you really need to take a long, cold shower.

    As usual, you need to do your due diligence, science-wise, and make sure you understand the basics of what people are talking about, before proclaiming that well-established fields of science are seriously doubtful.

    And here’s a question for Dr. Matzke: how do you reconcile your statement that “most molecular evolution being neutral says nothing in particular about the evolution of morphology” with Professor Masatoshi Nei’s claim in his paper, Selectionism and Neutralism in Molecular Evolution (Molecular Biology and Evolution, December 2005, Volume 22, Issue 12, doi: 10.1093/molbev/msi242, pp. 2318-2342): “It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels” (italics mine)?

    Simple. Nei is talking about whether morphological/phenotypic evolution is

    (a) mostly a matter of random drift,
    (b) mostly a matter selection acting on preexisting genetic variation, or
    (c} mostly selection acting on rare mutations that are not usually sitting around in the population as polymorphisms

    He takes position (c}. I would take position (b) for most morphological evolution, e.g. body size and other quantitative characters where populations usually show substantial natural variability. Nei would almost certainly agree with (b) for things like body size, actually, since it is undeniable that natural variation exists in most populations. When it comes to major changes in development — e.g. the origin of turtle shells or something — Nei would probably argue (c}, that the ability of populations to change is limited by mutational availability. I would be less sure. One the one hand, it is undeniable that each species has many evolutionary changes that are mutationally unavailable — there is the famous quip about how humans can’t become angels because their tetrapod bodyplan is limited to 4 limbs. On the other hand, there is often more developmental variability available in populations than we realize, which we can see once it is unmasked by strong selection — e.g. dogs — and the origins of major developmental shifts are often much more gradual than they seem at naive first glance, once detailed phylogenetic comparative studies of living and fossil specimens have been done.

    Even if (c} is right, I still think that would be more properly described as “evolution is mutation-constrained”, rather than “evolution is driven by mutation”. It is natural selection, mostly, that is the cause of directional change in adaptive directions. This can be blocked if the mutations aren’t available, but if the mutations are available but natural selection was absent, you would get small change in random directions, not major adaptations. So the bit about mutations “driving” evolution is just a bit of hyperbole from Nei — neomutationism is his hobby horse, and one adopted mostly by him.

    What neither of us are saying is (a), but you nevertheless seem to think (a) is a live controversy. Nei even says it’s obvious that natural selection is more important on average in phenotypic evolution than molecular evolution. Read more of Nei’s article than the abstract!

  30. 30
    NickMatzke_UD says:

    In his latest book, Mutation-Driven Evolution (Oxford University Press, 2013), Professor Nei is even more direct:

    …[M]any evolutionists including Motoo Kimura and Jack King believe that mutation is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. (p. 9)

    He says “mutation is caused primarily by natural selection”? No one believes this. Mutations occur independently of selection. *Substitutions* can be strongly influenced by selection, or if selection is near 0, they are the product of neutral drift. Confusing mutations and substitutions is a bit of sloppiness common with certain molecular folks.

    The bit about “since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation.” This is mostly just a word game, Nei does it his article also. Arguing mutation *versus* selection as the cause of evolution is, except in special cases, like arguing about whether the water or the cliff is the cause of the waterfall. The most correct thing to say is that the cause is 100% both.

    For that matter, Dr. Matzke, how do you reconcile your position with that of Professor PZ Myers, who in a post titled, Complexity is not usually the product of selection (11 December 2012), wrote:

    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.

    PZ is talking about “complexity”, which is *not* the same thing as “adaptive complexity” or “complex adaptations”, even though I understand why quote-mining creationists would be unable to perceive these kinds of scientifically important distinctions, since creationists typically think basically all complexity is adaptive. Creationists have a huge problem with making naively broad interpretations of statements of scientists who are referring to something technical and specific.

  31. 31
    NickMatzke_UD says:

    A huge amount of biological complexity at the genomic level, in eukaryotes, is probably nonadaptive. Junk DNA, the elaborate exon/intron-splicing system, producing RNA and proteins which are immediately broken down again, etc. Similarly, there has been a fair bit of recent work suggesting that a lot of multiprotein systems could be done perfectly well by one protein, but gene duplication and reciprocal loss of functionality results in systems where multiple proteins are “required”.

    This is much more common in eukaryotes, especially multicellular eukaryotes, than prokaryotes. The population genetic explanation is that the strength of natural selection scales with effective population size. If you have a small effective population size (many large mammals have e.g. 10,000 or 100,000; I think 10,000 is the pre-civilization average for humans), drift is relatively much more important, thus a lot of weakly deleterious changes can get fixed in the genome. In bacteria, their population size is so huge that probably there is effective selection against extra DNA that isn’t doing much, just based on the tiny energetic cost of extra DNA. Thus their genomes are streamlined and “simple”, whereas eukaryotic genomes can get very “complex” — without all of this complexity necessarily being adaptive.

    This is argued at length by Michael Lynch in various works, and Lynch’s stuff is mostly what PZ is referring to. Unlike Nei, I would say most evolutionary biologists think that Lynch is mostly right and getting the relative emphases of things right as well.

    All of this is obvious, or should have been, to anyone deigning to denigrate major conclusions of evolutionary biology. I suppose this stuff could well seem confusing to someone who’s never taken college coursework in evolutionary biology or done equivalent detailed study, but then, most people would have better sense and learn their basics before pestering the scientific community.

  32. 32
    NickMatzke_UD says:

    Here’s a final question for Dr. Matzke. You refer to me, Sal Cordova and unspecified “creationists” as getting the “fundamental basics” wrong. Very well, then: what “fundamental basics” did I get wrong in my post? I took great pains to accurately characterize the views of Motoo Kimura: I quoted him as saying that “The Darwinian theory of evolution by natural selection has served as a great unifying principle in biology,” and that his own neutral theory “does not deny the role of natural selection in determining the course of adaptive evolution, but it assumes that only a minute fraction of DNA (or RNA) changes are adaptive.” I also described Kimura as claiming that “molecular evolution was dominated by neutral evolution, but at the phenotypic level, natural selection probably accounted for most changes in characteristics, rather than genetic drift.” I quoted the exact words of Motoo Kimura’s colleague, Professor Masatoshi Nei, and I also took great care not to put words into the mouths of Professors PZ Myers and Larry Moran: I described them as arguing that “most of the complexity that we see in the biological world could be largely the result of chance, although they do not wish to rule out a role for natural selection.” Given that I took such pains to accurately represent the views of the key protagonists in the current debate on what the neutral theory of evolution can and cannot explain, why do you continue to accuse me of being wrong in my facts? Is it not you who are wrong in yours, Dr. Matzke?

    It’s simple — as I discussed above:

    1. You confuse “complexity” and “adaptive complexity”. Presence of selection is an important part of the explanation of the latter, but not the former.

    2. You claimed in your post ‘Will the real Neutral Theory please stand up?’:

  33. 33
    NickMatzke_UD says:

    What kinds of structural, functional and behavioral complexity can the neutral theory of evolution account for, and what kinds of complexity can’t it account for? According to Professor Larry Moran, to evince confusion on these vital questions is a sure sign of being an “IDiot.” But it is the “neutralists” themselves who are confused on these issues, as I intend to show in today’s post.

    …but, in fact, there is widespread consensus that most molecular evolution (in large genomes) is neutral (since large genomes are mostly junk), but there is also consensus that natural selection is crucial to explain adaptive evolution in genes, gene regulation etc.,; and there is also widespread consensus that “most”* phenotypic evolution is controlled by selection rather than drift. Even Nei mostly agrees with most of this consensus most of the time, most of the difference that you perceive is hyperbole rather than some systematic, widespread doubt of the consensus I have described. In other words, there’s no confusion in the community — you’re confused, because you’re the one that thinks there is confusion.

    3. In this very thread, you claim in the title that neutral theory is “much-disputed”.

    This is just false. It’s an important piece of mainstream, modern evolutionary theory, part of the curriculum of any college course on evolution.

  34. 34
    NickMatzke_UD says:

    Despite all of the above, which all should have been obvious to any informed commentator, you’ve been spending weeks heaping doubt on evolutionary biology because of various things you don’t understand about neutral theory and the (very important, but also limited) role that this subfield plays in the overall field of population genetics and evolutionary biology. And then, you come at me, Larry Moran, etc., directly, pestering us with what really should be your homework.

    There, I just spent an hour I should have spent on something productive or fun explaining to you basics that you should have figured out yourself. Happy? Unfortunately, I think my previous rant was probably a better move — it also expresses annoyance and encourages people who don’t understand to do their homework, and most importantly, it was faster. Given previous history, probably neither strategy will have an impact on people with high confidence and low knowledge, so I might as well go with the faster strategy.

    (* By “most”, we mean body size, body shape, the fit between morphology and usage of environmental resources, etc. There is of course a list of things often effected by sexual selection, and various minor features — details of color patterns, vestigial traits of animals, whether or not human earlobes attach, etc., that could well be morphological features that are evolving neutrally. Quantifying “most” require some objective way to count all of these different kinds of morphological variation, which would be very difficult, so “most” just means “most things that seem to matter for organism ecology, function, survival, etc.”)

  35. 35
    Mung says:

    re Nick @ 30:

    The text should read:

    Yet, many evolutionists including Motoo Kimura and Jack King believed that mutation phenotypic evolution is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. (p. 9)

    Nick: “I would take position (b) for most morphological evolution…”

    And Nei would take not (b).

    Which is, i think, the point.

  36. 36
    kevnick says:

    NickM_UD, Can you please confirm your claims by either quotations from Neil’s book or his papers? To me you are making a lot of unfounded assumptions at best. I personally think you are writing fairytale.

  37. 37
    Mung says:

    Nei on complexity:

    Fisher’s theorem works only for limited cases of short-term evolution, and in the case of long-term evolution the biological meaning of the theorem is unclear.

    These observations suggest that evolution does not necessarily occur by the struggle for existence. In the presence of changeable environments, Fisher’s theorem does not work. Note also that the mean fitness is not a good quantity for measuring the extent of evolutionary change because we cannot compare the mean fitness of different species. Is there any way to define evolution in a reasonable way when long-term evolution is considered? In my view evolution should be defined as a process of increase of organismal complexity, as is generally believed by many biologists. Strictly speaking, this definition still does not always work well, because there are organisms that simplify their complexity to adapt to a particular environment. If we consider this possibility, we may define evolution as a process of increase or decrease of organismal complexity. However, how should we measure the extent of organismal complexity? This is not a simple problem, but there is a crude way to measure the extent. It is to use the number of cell types in the organism (Vogel and Chothia 2006). (p 10)

    Makes me wonder about these organisms that simplify their complexity. They reduce their number of cell types?

  38. 38
    Mung says:

    Nick Matzke:

    Nei would almost certainly agree with (b) [(b) mostly a matter selection acting on preexisting genetic variation] for things like body size, actually, since it is undeniable that natural variation exists in most populations.

    If there’s some doubt, Nick, you could read Chapter 9 of Nei’s book. Hey, maybe you and Larry Moran could do a review of it together!

    Chapter 9: Mutation and Selection in Evolution
    Section 9.5: Genetic Variation within Species

    Masatoshi Nei:

    Although genomic evolution is conservative, we are aware that a randomly mating species contains a large amount of phenotypic variation.
    …this large phenotypic variation is largely neutral or nearly neutral for two reasons.

    These observations suggest that phenotypic variation is generated largely by nonselective forces.

    This conclusion means that although there is an enormous amount of genetic variation within a species the fitness is nearly the same for most individuals except for those affected by deleterious mutations. (p 185-186)

  39. 39
    Mung says:

    Next up, constraint-breaking evolution.

  40. 40
    NickMatzke_UD says:

    Mung,

    You are confusing the statement “Phenotypic variation in a population is due to mutations” with the statement “Directional phenotypic change in a population is due to mutations”. Only the latter would help your/vjtorley’s argument. Nei is saying the former. The former is mainstream evolutionary theory (basically, more could be said about environment-caused variation, stabilizing selection, yadda yadda).

    But, score another one for creationists randomly throwing quotes around without bothering to understand them.

  41. 41
    bornagain77 says:

    Nick states,

    make sure you understand the basics of what people are talking about, before proclaiming that well-established fields of science are seriously doubtful

    Would not neo-Darwinian evolution actually have to be a ‘science’ before you proclaim any part of it to be a well-established field of science?

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

    The main problem for you Nick, despite your rampant literature bluffing in the past, is that you have no empirical evidence that Darwinian processes can produce functional information:

    Hopeless Matzke -David Berlinski & Tyler Hampton August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

    “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/

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    – per scitopics

    And when you ‘understand the basics’ Nick, it is really not all that hard to see why unguided Darwinian processes are unable to explain the ’emergence’ of functional information from a matter/energy basis. You see Nick, the ‘basics’ are that information is its own independent entity which is completely separate from matter and energy:

    John Lennox – Is There Evidence of Something Beyond Nature? (Semiotic Information) – video
    http://www.youtube.com/watch?v=F6rd4HEdffw

    “Information is information, not matter or energy. No materialism which does not admit this can survive at the present day.”
    Norbert Weiner – MIT Mathematician -(Cybernetics, 2nd edition, p.132) Norbert Wiener created the modern field of control and communication systems, utilizing concepts like negative feedback. His seminal 1948 book Cybernetics both defined and named the new field.

    Intelligent design: Why can’t biological information originate through a materialistic process? – Stephen Meyer – video
    http://www.youtube.com/watch?v=wqiXNxyoof8

    “One of the things I do in my classes, to get this idea across to students, is I hold up two computer disks. One is loaded with software, and the other one is blank. And I ask them, ‘what is the difference in mass between these two computer disks, as a result of the difference in the information content that they posses’? And of course the answer is, ‘Zero! None! There is no difference as a result of the information. And that’s because information is a mass-less quantity. Now, if information is not a material entity, then how can any materialistic explanation account for its origin? How can any material cause explain it’s origin?
    And this is the real and fundamental problem that the presence of information in biology has posed. It creates a fundamental challenge to the materialistic, evolutionary scenarios because information is a different kind of entity that matter and energy cannot produce.
    In the nineteenth century we thought that there were two fundamental entities in science; matter, and energy. At the beginning of the twenty first century, we now recognize that there’s a third fundamental entity; and its ‘information’. It’s not reducible to matter. It’s not reducible to energy. But it’s still a very important thing that is real; we buy it, we sell it, we send it down wires.
    Now, what do we make of the fact, that information is present at the very root of all biological function? In biology, we have matter, we have energy, but we also have this third, very important entity; information. I think the biology of the information age, poses a fundamental challenge to any materialistic approach to the origin of life.”
    -Dr. Stephen C. Meyer

    Thus when one ‘understands the basics’ Nick, it is not surprising that neo-Darwinian processes are completely inadequate to explain to ’emergence’ of functional information from a matter/energy basis, since information is not reducible to matter/energy in the first place. Moreover, if that was not bad enough for neo-Darwinists, it is now found that both matter and energy reduce to ‘non-local’, beyond space and time, ‘quantum’ information instead of information reducing to a matter/energy basis as is presupposed in neo-Darwinian thought:

    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.”

    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

  42. 42
    bornagain77 says:

    Moreover, as if that was not bad enough for neo-Darwinists, this ‘non-local’, beyond space and time, quantum information is now found in molecular biology on a massive scale,,

    Quantum Information/Entanglement In DNA – short video
    https://vimeo.com/92405752

    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

    Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012)
    Excerpt: The remaining option is to accept that (quantum) influences must be infinitely fast,,,
    “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,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,,
    http://www.sciencedaily.com/re.....142217.htm

    Of additional note, encoded ‘classical’ information such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of conserved ‘non-local’ (beyond space and time) quantum entanglement/information by the following method:

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    Moreover quantum information/entanglement is found to be conserved

    Quantum no-hiding theorem experimentally confirmed for first time – March 2011
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.
    http://phys.org/news/2011-03-q.....tally.html

    Quantum no-deleting theorem
    Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist.
    http://en.wikipedia.org/wiki/Q.....onsequence

    It is very interesting that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints (Bell, Aspect, Leggett, Zeilinger), 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? (A. Aspect) 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!

    The implication of finding conserved ‘non-local’, beyond space and time, quantum information/entanglement in our body on a massive scale is fairly self evident:

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

    Verse and Music:

    John 1:1-3
    In the beginning, the Word existed. The Word was with God, and the Word was God. He was with God in the beginning. Through Him all things were made; without Him nothing was made that has been made.

    Jason Kertson playing “Drifting” by Andy McKee
    https://www.youtube.com/watch?v=naYbJGlW-CA

  43. 43
    Mung says:

    Nick, I’m not the one confused about Nei’s position here, you are.

    Further from your post @ 29:

    Even if (c} is right, I still think that would be more properly described as “evolution is mutation-constrained”, rather than “evolution is driven by mutation”. It is natural selection, mostly, that is the cause of directional change in adaptive directions. This can be blocked if the mutations aren’t available, but if the mutations are available but natural selection was absent, you would get small change in random directions, not major adaptations. So the bit about mutations “driving” evolution is just a bit of hyperbole from Nei

    That’s your position, not Nei’s.

    Masatoshi Nei:

    If evolution is affected by so many random factors, why should we see that the evolutionary change of organisms appears to be so orderly and progressive when long-term evolution is considered?

    Some neo-Darwinians like Dawkins (1997) believe that evolution occurs progressively and it is caused by positive Darwinian selection. These authors often write as though natural selection has the power of determining the future direction of evolution whereas mutation merely provides raw material for evolution. However, we have seen in the previous chapters that at the molecular level the major force of evolution has been mutation and that there is little empirical evidence for natural selection to have determined the future direction of evolution.

    A more proper way of explaining the orderly evolution of organisms is to note that the evolutionary changes of genetic materials and phenotypic characters occur almost always in a conservative fashion, but the conservative characters are occasionaly subject to innovative changes and these changes result in improved phenotypic characters.

    …this form of evolution…may be called conservation-breaking or constraint-breaking evolution…

    His version is not “mutation-constrained,” but constraint-breaking.

    Nick Matzke:

    You are confusing the statement “Phenotypic variation in a population is due to mutations” with the statement “Directional phenotypic change in a population is due to mutations”. Only the latter would help your/vjtorley’s argument. Nei is saying the former.

    And you’re totally clueless and making things up.

    Who here is claiming that “Directional phenotypic change in a population is due to mutations”?

    Are you claiming that is Nei’s position? No, you plainly state that Nei is saying the former. But then you claim that because only the latter would help my argument that I am confusing the two statements. And that’s a non-sequitur.

    Since the second statement was never on the table, how did I manage to confuse the two, other than in your own mind?

  44. 44
    Mung says:

    The only gene for which the action of natural selection in the wild has been established unequivocally is the sickle cell anemia gene (S).

    – Masatoshi Nei

  45. 45
    vjtorley says:

    Hi Nick,

    Thank you for your posts. Before I go on, I’d like to clear one matter up. In my original post, I quoted Nei as writing:

    [M]any evolutionists including Motoo Kimura and Jack King believe that mutation is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. (p. 9)

    As Mung has pointed out above, the word “mutation” in the first sentence was incorrectly transcribed by me; what Nei wrote was that many evolutionists including Motoo Kimura and Jack King believe that phenotypic evolution is caused primarily by natural selection. The quote should read:

    [M]any evolutionists including Motoo Kimura and Jack King believe that phenotypic evolution is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. (p. 9)

    I’ve corrected my post accordingly.

    I’d now like to proceed to your substantive points.

  46. 46
    Mung says:

    Every biologist is aware that any evolutionary theory should be free of teleology if the theory is to be scientific.

    – Masatoshi Nei

  47. 47
    vjtorley says:

    Hi Nick,

    You write:

    Nei is talking about whether morphological/phenotypic evolution is

    (a) mostly a matter of random drift,
    (b) mostly a matter selection acting on preexisting genetic variation, or
    (c) mostly selection acting on rare mutations that are not usually sitting around in the population as polymorphisms.

    He takes position (c}. I would take position (b) for most morphological evolution, e.g. body size and other quantitative characters where populations usually show substantial natural variability…

    Even if (c} is right, I still think that would be more properly described as “evolution is mutation-constrained”, rather than “evolution is driven by mutation”. It is natural selection, mostly, that is the cause of directional change in adaptive directions. This can be blocked if the mutations aren’t available, but if the mutations are available but natural selection was absent, you would get small change in random directions, not major adaptations. So the bit about mutations “driving” evolution is just a bit of hyperbole from Nei — neomutationism is his hobby horse, and one adopted mostly by him.

    The position you attribute to Nei doesn’t represent his views. In the Conclusion to his book, from which I quoted extensively above, Nei writes:

    Mutation is the source of all genetic variation upon which any form of evolution is dependent… Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of a mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors… Evolution occurs primarily as a result of constraint-breaking mutations rather than as a result of the struggle for existence.

    And in his interview with Disover magazine, Nei is even more direct:

    I say mutation is the most important, driving force of evolution. Natural selection occurs sometimes, of course, because some types of variations are better than others, but mutation created the different types. Natural selection is secondary…

    Your attempts to minimize Nei’s position by representing him as holding that “evolution is mutation-constrained”, rather than mutation-driven, are tantamount to a distortion of his views. Nei does not hold the position you ascribe to him.

  48. 48
    Mung says:

    Nick Matzke:

    You are confusing the statement “Phenotypic variation in a population is due to mutations” with the statement “Directional phenotypic change in a population is due to mutations”. Only the latter would help your/vjtorley’s argument. Nei is saying the former.

    Let’s see what Nei has to say, shall we?

    Masatoshi Nei:

    It is often said that mutation is a random factor and cannot control evolutionary direction and that only natural selection can decide the evolutionary direction. This view is clearly based on the idea that any population contains all kinds of mutations and the evolutionary direction is determined only by natural selection. In practice, most mutations are deleterious or neutral and only a small proportion of mutations seem to be responsible for generating innovative characters. If this is the case, mutation must be important in determining evolutionary direction. (p. 183)

    Care to re-evaluate your representation of Nei’s position, Nick?

    And does that help vjtorley’s argument?

    Right now Nick, just so we’re clear, my argument is simply that you are misrepresenting Nei’s position, largely because you haven’t read the book we’re discussing, with an added touch of dismissal of relevant quotes as creationist quote-mining, and a liberal dose of “you don’t understand what the text plainly says” thrown in for good measure.

  49. 49
    jerry says:

    I pointed out in #13 that there are two camps in the naturalistic evolution debate. The first is represented by Dawkins, Moran and apparently Nick Matzke and zillions of others. Also within this camp there are I am sure many sub-camps.

    The second camp is represented by Allen MacNeill, Nei, Jurgen Brosius, many followers of Stephen Gould and zillions of others.

    The emphasis in the second camp is that environmental pressures is a weak force in creating novelty (natural selection) and must have substantial novel variation to produce anything novel, while the first camp seems to think all is in the gene pool and needs only minor mutations. The rest will be done by environmental pressures (natural selection) and drift.

    I am sure this is too a wide a cut at it but it seems to distinguish the two camps. Looking for any suggestions on how to modify this.

  50. 50
    jerry says:

    It seems that Nick Matzke is unaware of Allen MacNeill’s and Jurgen Brosius’s position on what is necessary for evolution.

  51. 51
    jerry says:

    I can understand body type, size, shape, color being in the gene pool and varying over time due to environmental pressures. I have a hard time believing that the eye just popped out of the gene pool without substantial new variation showing up.

  52. 52
    Mung says:

    : Constraint-Breaking Evolution (Part II)

    Nick Matzke:

    Even if (c} is right, I still think that would be more properly described as “evolution is mutation-constrained”, rather than “evolution is driven by mutation”. It is natural selection, mostly, that is the cause of directional change in adaptive directions. This can be blocked if the mutations aren’t available, but if the mutations are available but natural selection was absent, you would get small change in random directions, not major adaptations. So the bit about mutations “driving” evolution is just a bit of hyperbole from Nei

    Masatoshi Nei:

    …most genes evolve under functional constraints, so that the dN/dS ratio is much lower than 1, as we have seen in Chapter 4 (Fig. 4.4). This result indicates that evolution occurs by rare beneficial mutations rather than by abundant positive Darwinian selection whether we consider molecular or phenotypic characters … I would like to call this conservation-breaking or constraint-breaking evolution. In my view, this is the general principle that applies for the evolution of all organisms as well as for the origin of life. (p 184)

  53. 53
    Mung says:

    : Constraint-Breaking Evolution (Part III)

    Nick Matzke:

    Even if (c} is right, I still think that would be more properly described as “evolution is mutation-constrained”, rather than “evolution is driven by mutation”. It is natural selection, mostly, that is the cause of directional change in adaptive directions. This can be blocked if the mutations aren’t available, but if the mutations are available but natural selection was absent, you would get small change in random directions, not major adaptations. So the bit about mutations “driving” evolution is just a bit of hyperbole from Nei

    Masatoshi Nei:

    Some evolutionists still cling to panselectionism and state that natural selection is the only process by which species adapt to their environment. In the genomic era, this interpretation is clearly incorrect because without mutation no adaptation can occur and adaptation may occur by non-selective genetic processes, as discussed in the previous chapters. (p 180)

  54. 54
    vjtorley says:

    Hi Nick,

    Back again. You write:

    PZ is talking about “complexity”, which is *not* the same thing as “adaptive complexity” or “complex adaptations”, even though I understand why quote-mining creationists would be unable to perceive these kinds of scientifically important distinctions, since creationists typically think basically all complexity is adaptive…

    A huge amount of biological complexity at the genomic level, in eukaryotes, is probably nonadaptive. Junk DNA, the elaborate exon/intron-splicing system, producing RNA and proteins which are immediately broken down again, etc…

    You confuse “complexity” and “adaptive complexity”. Presence of selection is an important part of the explanation of the latter, but not the former.

    I”m well aware of the difference between complexity and adaptive complexity, thank you very much. And while I can’t speak for Professor PZ Myers, I noted in my post above that Professor Larry Moran, who usually sees eye to eye with PZ Myers on evolution, responded to my queries as follows:

    The vast majority of complex structures seem to be adaptations of one sort of another. I suspect there are many “functions” and “behaviors” that are neutral, or even detrimental, but it’s difficult to rule out any adaptive component…

    I have always contended that natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features.

    In other words, Professor Moran acknowledges that most complexity at the morphological level is adaptive complexity, and for all we know, a lot of functional and behavioral complexity may be adaptive, too. That’s quite an admission, coming from a self-described “mutationist.”

    Professor Moran does go on to say that “there are likely to [be] many ‘novel morphological features’ that are non-adaptive,” but since he has already conceded that “the vast majority of complex structures seem to be adaptations of one sort of another,” it is hard to take his last suggestion very seriously.

    You then attempt to shift the goalposts by arguing that “a huge amount of biological complexity at the genomic level, in eukaryotes, is probably nonadaptive” (italics mine), and then going on about junk DNA. Excuse me, but that wasn’t what my questions to Professor Moran were about. My questions were about the origins of ” complex structures, functions or behaviors,” as I put it. You’re changing the topic and talking about junk DNA instead. Well, of course junk DNA could be called “complex,” but so are random sequences of digits.

  55. 55
    vjtorley says:

    Hi Nick,

    Finally, you write:

    …[T]here is widespread consensus that most molecular evolution (in large genomes) is neutral (since large genomes are mostly junk), but there is also consensus that natural selection is crucial to explain adaptive evolution in genes, gene regulation etc.,; and there is also widespread consensus that “most”* phenotypic evolution is controlled by selection rather than drift. Even Nei mostly agrees with most of this consensus most of the time, most of the difference that you perceive is hyperbole rather than some systematic, widespread doubt of the consensus I have described. In other words, there’s no confusion in the community — you’re confused, because you’re the one that thinks there is confusion.

    You really believe that Nei would agree with the foregoing paragraph, Nick, after all the quotes we’ve produced from his writings? As he states in his interview with Discover magazine, he’s been banging on about this since 1975, but no-one has been listening, until recently. How much louder does he have to yell, before you acknowledge that there is a major controversy going on about the nature of evolution, among the world’s leading evolutionary biologists?

    You add:

    In this very thread, you claim in the title that neutral theory is “much-disputed”.

    This is just false. It’s an important piece of mainstream, modern evolutionary theory, part of the curriculum of any college course on evolution.

    For your information: when I described the neutral theory of evolution as “much-disputed,” I was not referring to any dispute as to whether it is an important part of modern evolutionary biology, but rather, I was referring to the enduring controversy over what the theory actually says. As we’ve seen, the way that Motoo Kimura interpreted it is completely different from the way in which Masatoshi Nei interprets it. Also, Nei’s opinions regarding the kinds of complexity that that undirected mutations are capable of explaining are very different from those of Larry Moran: Nei thinks that his neo-mutationist theory can account for even the evolution of the human brain, while Moran ascribes the brain’s evolution largely to natural selection.

    Those are substantive differences, Nick. Thanks for the exchange.

  56. 56
    gpuccio says:

    VJ:

    So, at least now we have a clear outline of Nick Matzke’s theory of evolution:

    a) Body size and other quantitative characters are mostly a matter of selection acting on preexisting genetic variation

    b) For turtle shells (and, I suppose, all qualitative characters) he is less sure, but essentially it is the same thing.

    c) A huge amount of biological complexity at the genomic level, in eukaryotes, is probably nonadaptive. That includes not only truly “junk” DNA (for which the term “complexity” could be considered maybe excessive, IMO), but also the exon-intron system with the splicing apparatus, protein cascades, and who knows what else.

    d) Such non functional “complexity” is not connected to selection, but to drift. “Adaptive complexity”, instead, is mainly explained by selection.

    e) A lot of multiprotein systems could be done perfectly well by one protein, if it were not for “gene duplication and reciprocal loss of functionality “.

    The last one is probably the most stunning statement in the pack. I suppose it includes:

    a) the coagulation and complement cascades:

    http://www.genome.jp/kegg-bin/.....y?hsa04610

    b) the major intracellular signal transmission pathways, like this one:

    http://en.wikipedia.org/wiki/MAPK/ERK_pathway

    c) the ubiquitine – proteasome system:

    http://www.nature.com/nrd/jour.....56_F1.html

    d) apoptosis (what a uselessly complex way to die):

    http://www.avivasysbio.com/res.....is-pathway

    e) admittedly, the spliceosome:

    http://fr.wikipedia.org/wiki/S.....e_new2.jpg

    and who knows what else. Practically, most of cellular pathways.

    Much ado about nothing!

    And all that is just the useless result of drift, and just because eukaryotes, metazoa, and especially mammals and humans, are few.

    Good to know. But I am probably quote mining. 🙂

  57. 57

    Darwinist definition of quote-mine: whenever an ID proponent uses a quote by a Darwinist to advance the ID position.

  58. 58
    gpuccio says:

    William J Murray:

    You are an optimist!

    I believe it is:

    “whenever an ID proponent uses a quote for any reason”

    or

    “whenever an ID proponent speaks or writes anything”. 🙂

  59. 59
    Joe says:

    Nick Matzke:

    It is natural selection, mostly, that is the cause of directional change in adaptive directions.

    That is the propaganda anyway.

    but there is also consensus that natural selection is crucial to explain adaptive evolution in genes, gene regulation etc.,; and there is also widespread consensus that “most”* phenotypic evolution is controlled by selection rather than drift.

    Evidence, not consensus, rules science, Nick. Nice to see that all you have is consensus.

  60. 60
    NickMatzke_UD says:

    Masatoshi Nei:

    If evolution is affected by so many random factors, why should we see that the evolutionary change of organisms appears to be so orderly and progressive when long-term evolution is considered?

    Some neo-Darwinians like Dawkins (1997) believe that evolution occurs progressively and it is caused by positive Darwinian selection. These authors often write as though natural selection has the power of determining the future direction of evolution whereas mutation merely provides raw material for evolution. However, we have seen in the previous chapters that at the molecular level the major force of evolution has been mutation and that there is little empirical evidence for natural selection to have determined the future direction of evolution.

    A more proper way of explaining the orderly evolution of organisms is to note that the evolutionary changes of genetic materials and phenotypic characters occur almost always in a conservative fashion, but the conservative characters are occasionaly subject to innovative changes and these changes result in improved phenotypic characters.

    …this form of evolution…may be called conservation-breaking or constraint-breaking evolution…

    His version is not “mutation-constrained,” but constraint-breaking.

    But…but…that’s what mutation-constrained evolution means! Evolutionary change in some feature X until some rare is constrained until some mutation comes along to break the constraint. Dear creationists: please read for comprehension, not for random quote-mines that seem like they conflict with each other until you think about it for 5 freakin’ seconds.

  61. 61
    NickMatzke_UD says:

    43
    Mung
    May 10, 2014 at 7:43 pm
    Nick, I’m not the one confused about Nei’s position here, you are.

    Further from your post @ 29:

    Even if (c} is right, I still think that would be more properly described as “evolution is mutation-constrained”, rather than “evolution is driven by mutation”. It is natural selection, mostly, that is the cause of directional change in adaptive directions. This can be blocked if the mutations aren’t available, but if the mutations are available but natural selection was absent, you would get small change in random directions, not major adaptations. So the bit about mutations “driving” evolution is just a bit of hyperbole from Nei

    That’s your position, not Nei’s.

    Masatoshi Nei:

    If evolution is affected by so many random factors, why should we see that the evolutionary change of organisms appears to be so orderly and progressive when long-term evolution is considered?

    Some neo-Darwinians like Dawkins (1997) believe that evolution occurs progressively and it is caused by positive Darwinian selection. These authors often write as though natural selection has the power of determining the future direction of evolution whereas mutation merely provides raw material for evolution. However, we have seen in the previous chapters that at the molecular level the major force of evolution has been mutation and that there is little empirical evidence for natural selection to have determined the future direction of evolution.

    A more proper way of explaining the orderly evolution of organisms is to note that the evolutionary changes of genetic materials and phenotypic characters occur almost always in a conservative fashion, but the conservative characters are occasionaly subject to innovative changes and these changes result in improved phenotypic characters.

    …this form of evolution…may be called conservation-breaking or constraint-breaking evolution…

    His version is not “mutation-constrained,” but constraint-breaking.

    Nick Matzke:

    You are confusing the statement “Phenotypic variation in a population is due to mutations” with the statement “Directional phenotypic change in a population is due to mutations”. Only the latter would help your/vjtorley’s argument. Nei is saying the former.

    And you’re totally clueless and making things up.

    Who here is claiming that “Directional phenotypic change in a population is due to mutations”?

    That’s what “mutation-driven evolution” most naturally means. Mutations giving a *direction* to evolution. Nei seems to use this phrase but just be referring to mutation-constrained evolution.

    Are you claiming that is Nei’s position? No, you plainly state that Nei is saying the former.

    No, you guys are trying to claim there is some huge dispute in the field because of Nei. This would only be true if he advocated the radical position you guys were originally claiming mutation-directed evolution was. But, the quote that was used in support of Nei being radical was just him talking about mere phenotypic variability, and the idea that populational variability is due (partially) to mutations is not radical, it’s the consensus!

    And, anyway, even if Nei’s view was radical instead of normal stuff with a bit of hyperbole, it would still just be one guy who is mostly ignored, not a huge dispute in the field.

    But then you claim that because only the latter would help my argument that I am confusing the two statements. And that’s a non-sequitur.

    Since the second statement was never on the table, how did I manage to confuse the two, other than in your own mind?

    I was answering vjtorley’s question in the OP:

    And here’s a question for Dr. Matzke: how do you reconcile your statement that “most molecular evolution being neutral says nothing in particular about the evolution of morphology” with Professor Masatoshi Nei’s claim in his paper, Selectionism and Neutralism in Molecular Evolution (is the driving force of evolution, December 2005, Volume 22, Issue 12, doi: 10.1093/molbev/msi242, pp. 2318-2342): “It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels” (italics mine)?

    I pointed out that Nei’s “mutation-driven evolution” is really just mutation-constrained evolution, which is a lot less radical than real mutation-driven evolution would be. Whether mutation-constrained evolution is true for X depends largely on whether or not X is variable in the population. I pointed out that for a lot of things, e.g. X=body size, shape, etc., it is undeniable that X is variable in the population, and thus directional selection has pre-existing variation to work on in these cases, therefore mutation-constrained evolution is not a major factor in those cases, and that even Nei would agree with this.

    You disagreed with my contention that Nei would agree on this point by quoting him:

    Although genomic evolution is conservative, we are aware that a randomly mating species contains a large amount of phenotypic variation.
    …this large phenotypic variation is largely neutral or nearly neutral for two reasons.

    These observations suggest that phenotypic variation is generated largely by nonselective forces.

    This conclusion means that although there is an enormous amount of genetic variation within a species the fitness is nearly the same for most individuals except for those affected by deleterious mutations. (p 185-186)

    …I responded by pointing out that this quote from Nei is just saying that variability in the population was ultimately due to mutations, which is what *everyone* in the field thinks, and is not some radical view of Nei’s. Now, apparently, you agree with me. Thanks for admitting you were wrong, although it would simpler if you just admitted up-front that you misunderstood that last Nei quote.

  62. 62
    Mung says:

    So, for the record, according to Nick, mutation-constrained evolution and Nei’s constraint-breaking evolution are one and the same.

    And yet Nick plainly tells us what he means by mutation-constrained evolution. Natural selection must wait for a mutation else at best you could get small changes in random directions but no major adaptation.

    Nick Matzke:

    Even if (c} is right, I still think that would be more properly described as “evolution is mutation-constrained”, rather than “evolution is driven by mutation”. It is natural selection, mostly, that is the cause of directional change in adaptive directions. This can be blocked if the mutations aren’t available, but if the mutations are available but natural selection was absent, you would get small change in random directions, not major adaptations.

    But that’s not what Nei means by conservation-breaking or constraint-breaking evolution. Therefore, it is not the same thing.

    And there’s nothing random about these quotes. They address specific claims you’ve made about what Nei’s position is. Claims you’ve made which are obviously not based on any reading of the text. So dear Nick: please read, period.

  63. 63
    NickMatzke_UD says:

    e) A lot of multiprotein systems could be done perfectly well by one protein, if it were not for “gene duplication and reciprocal loss of functionality “.

    The last one is probably the most stunning statement in the pack. I suppose it includes:

    a) the coagulation and complement cascades:

    http://www.genome.jp/kegg-bin/…..y?hsa04610

    b) the major intracellular signal transmission pathways, like this one:

    http://en.wikipedia.org/wiki/MAPK/ERK_pathway

    c) the ubiquitine – proteasome system:

    http://www.nature.com/nrd/jour…..56_F1.html

    d) apoptosis (what a uselessly complex way to die):

    http://www.avivasysbio.com/res…..is-pathway

    e) admittedly, the spliceosome:

    http://fr.wikipedia.org/wiki/S…..e_new2.jpg

    and who knows what else. Practically, most of cellular pathways.

    Much ado about nothing!

    And all that is just the useless result of drift, and just because eukaryotes, metazoa, and especially mammals and humans, are few.

    Good to know. But I am probably quote mining. 🙂

    No, here you’re just flat-out misunderstanding the basics. All of those systems required lots of selection to produce.

    The nonadaptive evolution of gene duplications etc. I was talking about is known as “constructive neutral evolution”. Google it. It might play a partial role in any system containing a lot of duplicated proteins, but amplification cascades etc. like blood-clotting are definitely most about the various duplicates *adding* to the function, and thus are mostly explained by selection.

    Constructive neutral evolution explains e.g. cases where it looks like the duplicates have just split up a function originally done by one protein — e.g., subfunctionalization.

    Undoubtedly there is a continuum between constructive selective evolution and constructive neutral evolution, and it’s even possible that some large systems with many duplicate proteins have some of both in their history, and that constructive neutral evolution might on occasion supply some nonadaptive complexity in the form of duplicate subfunctionalized proteins, some of which are later exapted to add some new function and thus increase the adaptive complexity of the system.

  64. 64
    bornagain77 says:

    Nick states:

    until you think about it for 5 freakin’ seconds

    But if neo-Darwinism is true how in blue blazes can I trust any of my ‘thinking’ in the first place?

    Sam Harris’s Free Will: The Medial Pre-Frontal Cortex Did It – Martin Cothran – November 9, 2012
    Excerpt: There is something ironic about the position of thinkers like Harris on issues like this: they claim that their position is the result of the irresistible necessity of logic (in fact, they pride themselves on their logic). Their belief is the consequent, in a ground/consequent relation between their evidence and their conclusion. But their very stated position is that any mental state — including their position on this issue — is the effect of a physical, not logical cause.
    By their own logic, it isn’t logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order.
    http://www.evolutionnews.org/2.....66221.html

    “Refuting Naturalism by Citing our own Consciousness” Dr. Alvin Plantinga – video
    http://www.youtube.com/watch?v=r34AIo-xBh8

    Physicalism and Reason – May 2013
    Summary: So we find ourselves affirming two contradictory propositions:
    1. Everything is governed by cause-and-effect.
    2. Our brains can process and be changed by ground-consequent logical relationships.
    To achieve consistency, we must either deny that everything is governed by cause-and-effect, and open our worldviews to something beyond physicalism, or we must deny that our brains are influenced by ground-consequence reasoning, and abandon the idea that we are rational creatures.
    Ask yourself: are humans like falling dominoes, entirely subject to natural law, or may we stand up and walk in the direction that reason shows us?
    http://www.reasonsforgod.org/2.....nd-reason/

    Evolutionists Are Now Saying Their Thinking is Flawed (But Evolution is Still a Fact) – Cornelius Hunter – May 2012
    Excerpt: But the point here is that these “researchers” are making an assertion (human reasoning evolved and is flawed) which undermines their very argument. If human reasoning evolved and is flawed, then how can we know that evolution is a fact, much less any particular details of said evolutionary process that they think they understand via their “research”?
    http://darwins-god.blogspot.co.....their.html

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?”
    – Charles Darwin – Letter To William Graham – July 3, 1881

    “Supposing there was no intelligence behind the universe, no creative mind. In that case, nobody designed my brain for the purpose of thinking. It is merely that when the atoms inside my skull happen, for physical or chemical reasons, to arrange themselves in a certain way, this gives me, as a by-product, the sensation I call thought. But, if so, how can I trust my own thinking to be true? It’s like upsetting a milk jug and hoping that the way it splashes itself will give you a map of London. But if I can’t trust my own thinking, of course I can’t trust the arguments leading to Atheism, and therefore have no reason to be an Atheist, or anything else. Unless I believe in God, I cannot believe in thought: so I can never use thought to disbelieve in God.”
    —C.S. Lewis

  65. 65
    NickMatzke_UD says:

    Correction: I just remembered that the spliceosome was in the list. That’s a well-known candidate for being mainly caused by constructive neutral evolution. The ubiquitine – proteasome system and apoptosis might be also for all I know but I haven’t researched it. The others — coagulation and complement cascades, the major intracellular signal transmission cascades — are definitely not, nor “most of cellular pathways.” Although constructive neutral evolution could play a partial role anywhere.

  66. 66
    Mung says:

    Nick Matzke:

    No, you guys are trying to claim there is some huge dispute in the field because of Nei.

    And this after I explicitly stated otherwise:

    Right now Nick, just so we’re clear, my argument is simply that you are misrepresenting Nei’s position, largely because you haven’t read the book we’re discussing, with an added touch of dismissal of relevant quotes as creationist quote-mining, and a liberal dose of “you don’t understand what the text plainly says” thrown in for good measure.

    Now I will admit, my curiosity was first piqued when I read the posts over at Sandwalk by Larry about the book. First he was going to review it, then he wasn’t.

    Me, I am just wondering why. VJT obviously, has his own agenda that he can answer for.

    But it is rather curious, from where I sit, that you would be making all this effort to tell us what Nei means but when I actually go red the text for myself that’s not what I find in the text.

    But there’s no controversy, right? That goes over real well here at UD. 🙂

  67. 67
    NickMatzke_UD says:

    You then attempt to shift the goalposts by arguing that “a huge amount of biological complexity at the genomic level, in eukaryotes, is probably nonadaptive” (italics mine), and then going on about junk DNA. Excuse me, but that wasn’t what my questions to Professor Moran were about. My questions were about the origins of ” complex structures, functions or behaviors,” as I put it. You’re changing the topic and talking about junk DNA instead. Well, of course junk DNA could be called “complex,” but so are random sequences of digits.

    But, vjtorley, YOU’RE the one who tried to cite PZ Myers’s post against the position that most morphological evolution was adaptive and controlled by selection:

    And here’s a question for Dr. Matzke: how do you reconcile your statement that “most molecular evolution being neutral says nothing in particular about the evolution of morphology” with Professor Masatoshi Nei’s claim in his paper, Selectionism and Neutralism in Molecular Evolution (Molecular Biology and Evolution, December 2005, Volume 22, Issue 12, doi: 10.1093/molbev/msi242, pp. 2318-2342): “It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels” (italics mine)? In his latest book, Mutation-Driven Evolution (Oxford University Press, 2013), Professor Nei is even more direct:

    …[M]any evolutionists including Motoo Kimura and Jack King believe that mutation phenotypic evolution is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. (p. 9)

    For that matter, Dr. Matzke, how do you reconcile your position with that of Professor PZ Myers, who in a post titled, Complexity is not usually the product of selection (11 December 2012), wrote:

    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.

    …but, PZ’s post was all about nonadaptive complexity in genomic evolution evolving through constructive neutral evolution. He used the same gene-duplication/subfunctionalization situation that I mentioned.

    Based on what you are saying now, you should retract your claim that PZ Myers’s post indicates significant conflict in the field over the mainstream position, which is that most molecular evolution is dominated by neutral processes, and most morphological/gross phenotypic evolution is dominated by selective processes.

  68. 68
    Mung says:

    Nick Matzke:

    No, you guys are trying to claim there is some huge dispute in the field because of Nei. This would only be true if he advocated the radical position you guys were originally claiming mutation-directed evolution was. But, the quote that was used in support of Nei being radical was just him talking about mere phenotypic variability, and the idea that populational variability is due (partially) to mutations is not radical, it’s the consensus!

    I’m not claiming Nei is radical. For all I know his views are now mainstream evolutionary biology, itself a remarkably adaptable theory.

    I probably disagree with your assertion highlighted in the bolded text about the quoted material, but it’s not easy to tell which quote you were talking about.

    Was it the one at the end of your post @ 61?

    thanks

  69. 69
    gpuccio says:

    NickMatzke_UD:

    You are the one who wrote:

    Similarly, there has been a fair bit of recent work suggesting that a lot of multiprotein systems could be done perfectly well by one protein, but gene duplication and reciprocal loss of functionality results in systems where multiple proteins are “required”.

    I simply quoted a few of the most important “multiprotein systems”, hoping that some neutral probability would include in the list at least one of your set of “a lot of multiprotein systems”. It seems that I have been very unlucky, and that out of 6 systems I quoted not even one was of the kind you referred to.

    Therefore, as I am obviously “just flat-out misunderstanding the basics”, as I usually do just to spend time and have fun, could you please be kind enough to detail your statement, and clarify which are the multiprotein systems that “could be done perfectly well by one protein”, and the recent work which proves it?

    Thank you for your attention.

  70. 70
    gpuccio says:

    NickMatzke_UD:

    I just read your post #65.

    OK, I was not so unlucky, after all, even “just flat-out misunderstanding the basics”. Luck is blind, and is no respector of merit.

    So, the scientific references, please?

  71. 71
    gpuccio says:

    To all:

    For convenience, I post again the link to the multiprotein system which, it seems, “could be done perfectly well by one protein”.

    http://fr.wikipedia.org/wiki/S.....e_new2.jpg

  72. 72
    Mung says:

    gpuccio,

    That’s funny. The one that caught my eye was ubiquitin.

    http://www.ncbi.nlm.nih.gov/pubmed/9759494

    But what Nick probably means is that once these systems were in place, then they became good candidates for their future evolution being mainly caused by constructive neutral evolution.

  73. 73
    gpuccio says:

    Mung:

    Ubiquitin in itself is ultraconserved in eukaryiotes. No neutral evolution after its appearance.

  74. 74
    gpuccio says:

    Mung:

    Ubiquitin in protozoa (plasmodium falciparum) and humans.

    Length: 76 AAs

    Identities: 75/76 (99%)

    Positives: 76/76 (100%)

    Expect: 8e-49

    Where is neutral evolution here?

  75. 75
    gpuccio says:

    Mung:

    The functional complexity for a molecule like ubiquitin, which has to be made of those exact aminoacids, and cannot be changed by neutral variation, is very easy to compute.

    Let’s compute it for 70 fixed AAs (allowing for the small variations observed in eukaryotes).

    Functional complexity = 20^70: 302 bits.

  76. 76
    kairosfocus says:

    Mung: False accusation of “quote mining” seems to now be a stock in trade by too many objectors to design being inferred on FSCO/I. KF

  77. 77
    kairosfocus says:

    Mung: I make it 302.5 bits, but let’s be generous. This is of course well beyond the blind search capability on chance and necessity of the observed cosmos across its lifespan. Multiply this case by ever so many others and we see how the only empirically and analytically well warranted causal explanation for such FSCO/I is design. This is the central issue (and has been so for many years now), one that is independent of debates over whether or not quotes are in-context, it is decisive, and too many objectors to the design inference just outlined seem to be willing to say or do anything to distract, distort, demonise, dismiss. That speaks volumes about the root issue — a worldview driven a priori evolutionary materialist ideology dressed in a lab coat and with a by any means “necessary” agenda. KF

  78. 78
    gpuccio says:

    KF:

    OK, I had rounded half bit. I am always too good with our adversaries. 🙂

  79. 79
    Mung says:

    Nick’s charge of quote-mining is intended for the Darwinian faithful and his own self-delusion. If I was quote mining he could show the quote in it’s larger context and demonstrate how the quoted text was taken out of context in order to make it seem like the author said something other than what was intended. He won’t, because he can’t.

    Here’s a real quote-mine from Nei:

    …the driving force of evolution is natural selection…

    That quote is what Nei actually wrote. You can find it on page 39 of his book.

    Now Nick get’s to argue that is not a quote mine, because it does represent Nei’s actual views, lol!

    What is it Nick? A quote-mine? Or is Nei a “radical” after all?

    If natural selection is not the driving force of evolution, what is?

    Oh, right, what is the title of Nei’s book again?

    Mutation-Driven Evolution

    Let me channel Nick. All evolution is “mutation driven.” Nei isn’t saying anything all evolutionists don’t already agree with.

    Right.

  80. 80
    PaV says:

    Nick Matzke_UD:

    But…but…that’s what mutation-constrained evolution means! Evolutionary change in some feature X until some rare is constrained until some mutation comes along to break the constraint.

    I want to redefine ID: ID is “mutation-constrained” evolution!

    After all, when the Designer ‘intervenes’, then mutations appear out of nowhere, and they’re mutations that lie completely beyond the ‘constraints’ of ‘directed evolution’ (NS), subject, NOW, simply to ‘purifying’ selection.

  81. 81
    Mung says:

    When your bluff’s been called, it’s time to fold.

    Nick may be a Darvangelist, but he’s no IDiot!

  82. 82
    Mung says:

    Just found another reason Larry Moran wouldn’t want to review Nei’s book. It validates Walter ReMine’s claims about the cost of selection.

    Chapter 3 Section 3
    3.3 Cost of Natural Selection and Fertility Excess Required

    Haldane’s original paper has been misunderstood by a number of authors.

    Shades of Walter James ReMine!

    Of interest in the debate over neutral theory:

    As is well known, Kimura (1968a) used the argument of the cost of natural selection to propose his neutral theory of molecular evolution. (p. 47)

    And genetic drift:

    Haldane’s upper limit is useful for knowing what natural selection can do without the effect of genetic drift.

  83. 83
    Mung says:

    : Mutation-Driven Evolution
    : Chapter 3
    : Evolutionary Theories in the Neo-Darwinian Era
    : Masatoshi Nei

    …it is true that the current population genetics theory is not powerful enough to explain long-term evolution of morphological characters. p. 57

  84. 84
    Mung says:

    : Mutation-Driven Evolution
    : Chapter 3
    : Evolutionary Theories in the Neo-Darwinian Era
    : Masatoshi Nei

    During the twentieth century, an impressive amount of mathematical theories has been developed, but a large portion of them, including some of mine, have remained unused because they are not realistic. p. 58

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