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Tuesday, August 05, 2014

Stephen Meyer isn't keeping up

There are so many problems with Darwin's Doubt that one hardly knows where to begin. For me, the most important problem is that Meyer dismisses all the evidence for pre-Cambrian ancestors. These ancestors had most of the genes necessary to make all the animals that arose during the Cambrian explosion.

Our current model for evolution and development is that small changes in the regulation and timing of key developmental genes are responsible for big phenotypic differences, including new animal body plans. The data shows that all the animal phyla have similar genes and that there aren't very many genes whose origins can be traced to the Cambrian.

... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.

Stephen Jay Gould
Ontogeny and Phylogeny (1977)
This model was popularized by Stephen Jay Gould in his 1977 book Ontogeny and Phylogeny. Meyer disputes this model. He claims that massive amounts of new information (= new genes) arose at the time of the Cambrian explosion. He claims that this cannot be explained by any naturalistic means; therefore, god(s) must have made those strange Cambrian animals. (Presumably, the gods are also responsible for making them go extinct.)

Charles Marshall, a paleontologist at UC Berkeley (USA) wrote a critical review of Darwin's Doubt [When Prior Belief Trumps Scholarship]. Here's part of what Marshal wrote in September 2012.
His [Meyer's] case against current scientific explanations of the relatively rapid appearance of the animal phyla rests on the claim that the origin of new animal body plans requires vast amounts of novel genetic information coupled with the unsubstantiated assertion that this new genetic information must include many new protein folds. In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes (1). Now Meyer does touch on this: He notes that manipulation of such networks is typically lethal, thus dismissing their role in explaining the Cambrian explosion. But today's GRNs have been overlain with half a billion years of evolutionary innovation (which accounts for their resistance to modification), whereas GRNs at the time of the emergence of the phyla were not so encumbered. The reason for Meyer's idiosyncratic fixation with new protein folds is that one of his Discovery Institute colleagues has claimed that those are mathematically impossibly hard to evolve on the timescale of the Cambrian explosion.

As Meyer points out, he is not a biologist; so perhaps he could be excused for basing his scientific arguments on an outdated understanding of morphogenesis. But my disappointment runs deeper than that. It stems from Meyer's systematic failure of scholarship. For instance, while I was flattered to find him quote one of my own review papers (2)—although the quote is actually a chimera drawn from two very different parts of my review—he fails to even mention the review's (and many other papers') central point: that new genes did not drive the Cambrian explosion. His scholarship, where it matters most, is highly selective.
A Christian radio station in the UK decided to host a debate between Stephen Meyer and Charles Marshall. The full debate can be seen in the video at the bottom of this post.

At one time during the debate, Marshall says that Meyer's view of molecular biology is stuck in the 1980s. What he means is exactly what he wrote in his review. Meyer simply doesn't understand the key aspects of modern EvoDevo and he certainly doesn't understand the massive amounts of evidence supporting that model. Marshall is right. Meyer read some of the 1980s papers on regulatory genes in Drosophila but he completely missed the point. Here's what Meyer says in his book (page 315),
Despite the enthusiasm surrounding the field, evo-devo fails, and for an obvious reason: it's main proposal, that early-acting developmental mutations can cause stably heritable, large-scale changes in animal body plans, contradicts the results of one hundred years of mutagenesis experiments. As we saw in Chapter 13, the experiments of scientists like Nüsslein-Volhard and Wieschaus have shown definitively that early-acting body-plan mutations invariably generate embryonic lethals—dead animals incapable of further evolution, The results of these experiments have generated the dilemma for evolutionary biologists that John McDonald aptly described as the "great Darwinian paradox." Recall that McDonald noted that early-acting regulatory mutations do not produce viable alterations in form that will persist in populations, as evolution absolutely requires. Instead, these mutations are eliminated immediately by natural selection because of their invariably destructive consequences.
During the debate, Meyer seems to concede that there are reasonable models of the evolution of animals that do not require explosive amounts of new information during the Cambrian. This contradicts and refutes the key argument of his book.

Watch this video (below) of Stephen Meyer explaining what happened during the debate [Video: Stephen Meyer Reflects on the Debate with Charles Marshall]. You will see a typical IDiot strategy at work. Whenever an important, credible scientific expert takes notice of their views, that counts as vindication of a sort. It means that what they (IDiots) are saying must be scientific. It means that their crazy ideas must have some respect in the scientific community. (Marshall was too polite for my taste, although he did make the point that Stephen Meyer is not a biologist.)

This is one of the reasons why you should not debate IDiots. It just makes them look good. The other reason is that they will always spin the results in subsequent publicity campaigns in order to make it look like they did much better than they really did.

Here's the debate...


Diogenes said...

Marshall was too polite and did not accuse Meyer of lying, even when Meyer was clearly lying about information theory. Meyer says information theory says only "intelligent agents" can create information-- ridiculous-- and Marshall does not challenge this lie.

In fact, Meyer backed up his claim by dragging out his dishonest quote mine of information theorist Henry Quastler. If you recall, in the previous thread about Meyer, I copied in Quastler's actual quote and showed that Meyer has alternately doctored the quote, or taken it out of context so as to totally reverse Quastler's clearly intended meaning: accidental processes create information.

How should we handle anti-evolutionists who lie about everything, and quote out of context like Meyer's Quastler fakery? We disagree how to handle lying-- but Charles Marshall's respectful approach is disastrous.

Diogenes said...

Here's another example of IDiot dishonesty in this radio "debate." At one point Marshall says of Meyer's book, "It *seems* like good science..." and then he is cut off; but his extremely dubious tone of voice, and his emphasis on the word "seems", made it clear Marshall was about to assert that reality was the opposite of appearance.

You know where the story is going. Yes, the IDiots went there. Immediately after the debate was over, Klinghoffer was crowing, over at ENV, about how Marshall had said Meyer's book "seems like good science."

Galling. In any debate with anti-scientists, when they are lying, tell the audience they are lying.

Diogenes said...

Here is my analysis of the Henry Quastler quote mine and how Meyer has faked it or quoted it out of context.

Unknown said...

Have you seen Meyers' response to Prothero?

Diogenes said...

Meyer quote mines Quastler at time stamp 17:28.

All these features that make life so phenomenally interesting and complex are also things that we know arise from one and only one type of cause in our experience of the cause and effect structure of the world and that cause is intelligence.

There’s a famed information scientist called Henry Quastler who’s a pioneer in applying information science to molecular biology and he said that the creation of new information is habitually associated with conscious activity. And of course that’s right. If we see digital code in a software program or heiroglyphic inscription or information embedded in a radio signal or a headline in a newspaper, if we trace information back to its source, we always come to a mind not a material process.

This, again, is the opposite of what Quastler wrote in his book.

Diogenes said...

Here's the "looks like good science quote" from Marshall, and what Casey Luskin does with it (I was wrong, it was Luskin not Klinghoffer who quote-mined Marshall).

Charles Marshall, timestamp 26:05: "And so, I felt a little frustrated because I actually discussed this in a review that I wrote in 2006 summarizing and integrating some of this information [about morphological evolution not requiring new genes nor proteins]. And, and Stephen’s… you know, the first third of his book… Umm… I mean, I really enjoyed reading it, and it’s, its good scholarship, and it looks like good science… [sotto voce] that’s a description of somebody’s science, as a description of science… and then I found, I outlined these arguments [about morphological evolution not requiring new genes nor proteins], and it’s completely missed in the book. The overall emphasis of the books is centered around the origins of brand new genes to explain the Cambrian explosion-- and yet, the papers that I had written, and people Jim Valentine and Sean Carroll and Eric Davidson and Doug Erwin, suggest that in fact that isn’t what we currently believe is required for the Cambrian explosion... But just speaking as someone committed to understanding the Cambrian explosion, I found myself disappointed that the arguments that were made in the papers that he cited weren’t the ones that he confronted directly. He confronted a different set of problems that I think harked back to an older age. And I attributed it.. to the fact that he’s not a biologist, he’s a philosopher, um, and it’s very very hard to keep up with the fire hydrant of new conceptual data that’s coming in."

Leave it to Luskin to spin what Marshall said into something positive. Luskin actually put the "good scholarship" bit in the title of his post: In Radio Debate, Darwin's Doubt Critic Charles Marshall Acknowledges Meyer's Fossil Treatment Is "Good Scholarship".

Casey Luskin: "As David Klinghoffer noted yesterday, the subject of the debate was Meyer's book Darwin's Doubt... It was an excellent debate, with both participants offering important insights and good arguments, though in my opinion Meyer unquestionably had the better of it, especially concerning the key scientific question of the origin of the information necessary to build the Cambrian animals. Nevertheless, both parties came to the table ready to engage in serious, thoughtful, and civil discussion about the core issues raised in Darwin's Doubt, and we commend Marshall not only for participating, but for focusing his critique of the book on the central scientific issues, something other critics have conspicuously failed to do.

...Both parties complimented, as well as critiqued, the work of the other. Marshall, for example, described the first third of Darwin's Doubt -- the section that discusses the Cambrian and Precambrian fossil record, Marshall's own area of principle expertise -- as "good scholarship." He also said it "looks like good science" and that Meyer "writes well," and that he (Marshall) "really enjoyed reading" Darwin's Doubt." [In Radio Debate, Darwin's Doubt Critic Charles Marshall Acknowledges Meyer's Fossil Treatment Is "Good Scholarship". Casey Luskin. ENV. December 3, 2013]

Mikkel Rumraket Rasmussen said...

Having read the book, a recurring phenomenon is that Meyer time and again makes claims without providing any references for them. Take for instance the claim that the Cambrian explosion requires lots of new protein folds, from Chapter 10 The Origin of Genes and Proteins:

"Axe had a key insight that animated the development of his experimental program. He wanted to focus on the problem of the origin of new protein folds and the genetic information necessary to produce them as a critical test of the neo-Darwinian mechanism. Proteins comprise at least three distinct levels of structure:4 primary, secondary, and tertiary, the latter corresponding to a protein fold. The specific sequence of amino acids in a protein or polypeptide chain make up its primary structure. The recurring structural motifs such as alpha helices and beta strands that arise from specific sequences of amino acids constitute its secondary structure. The larger folds or “domains” that form from these secondary structures are called tertiary structures (see Fig. 10.2).
Axe knew that as new life-forms arose during the history of life—in events such as the Cambrian explosion—many new proteins must also have arisen. New animals typically have new organs and cell types, and new cell types often call for new proteins to service them. In some cases new proteins, while functionally new, would perform their different functions with essentially the same fold or tertiary structure as earlier proteins. But more often, proteins capable of performing new functions require new folds to perform these functions. That means that explosions of new life-forms must have involved bursts of new protein folds as well."

In the whole section Meyer dedicates to the origin of novel folds, he makes zero references that actually substantiates that the cambrian diversification, or indeed any kind of speciation, or the that new cells types or organs, requires new protein folds. ZERO. Not one single reference that supports that these claims. He cites the work of Douglas Axe that attepts to address how hard it is to evolve new folds(and that work has it's own set of problems, but never mind that). Axe makes the same claim in his ID-journal Bio-complexity papers (which Meyers cites), but in Axe's papers, that claim is not supported by any reference either. It's simply asserted as fact.

Meyer mentions Ohno: "The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures. When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life such as sponges or one-celled organisms. Thus, Axe was convinced that explaining the kind of innovation that occurred during the Cambrian explosion and many other events in the history of life required a mechanism that could produce, at least, distinctly new protein folds."

No reference is given here either. The claim is simply made, so it's hard to check.

Mikkel Rumraket Rasmussen said...

Oddly enough, neither Axe or Meyer have apparenly ever heard of duplication and shuffling. Segments of proteins, such as the secondary structures, can be shuffled around and recombined. These secondary structures don't need to be generated de novo all over again, amino acid by amino acid, to get a brand-spanking new protein fold.
I also maintain that it is highly doubtful the Cambrian explosion required much innovation at the fold level that didn't have any structure-function homologues in precambrian life.

Is Meyer and Axe willing to bet that a preceding evolutionary history of, for example, Lysyl oxidase cannot be found in structure and sequence of related molecules? That there ARE no related molecules? Is that his claim? That the Cambrian explosion required tonnes of bona fide Orphan proteins with no preceding history? Where are the references that support this? Did Meyer or Axe look for homologues of Lysyl Oxidase and found none?

judmarc said...

New animals typically have new organs and cell types

That is All Ye Need To Know, right there. No evolution, but whole new organs and new cell types to comprise them, every time there's a new animal. (Plants and other life are perhaps exceptions?)

Diogenes said...

Virtually everything that Meyer wrote in that passage is false-- not just not cited to scientific references (BIO-complexity doesn't count), but demonstrably false.

To start with, lysyl oxidase! No, Meyer did not google it, did not do a PubMed search!

Meyer is saying that God created lysyl oxidase 525 million years ago de novo to help arthropods make their exoskeletons! But Meyer didn't know that lysyl oxidase is also found in all animals, including humans who have four copies (did we need it to build an exoskeleton?), as well as non-animals like yeast, mushrooms and fungi, so it must have evolved in the common ancestor of animals and fungi, long before Meyer thinks God zapped it into existence in the Cambrian era.

Marshall made this point in the debate.

[Charles Marshall, timestamp 1:22:20] In his criticism of my review and in his book, when he talks about the origin of new genes, he talks about lysyl oxidase and points out that that’s a very important gene that arthropods… need to make their skeletons. So it looks like a brand new gene comes into existence in that phylum. And so a scientist would have said, hmm, that’s seem to be a problem, let’s explore that a little bit further… and so I did that.. and what I found is that it’s four copies in humans, all animals, good heavens! It’s also in yeast, fungi, mushrooms. So it turns out that this key gene that seems so important to Stephen in the establishment of an arthropod body plan, it preexists animals by a long shot, it’s been simply co-opted to stiffen the collagen to lead to the chitin.


Diogenes said...

There is so much wrong with that one passage from Meyer, I don't have time to point out all his factual blunders and falsehoods. But to point out that Meyer does not understand the jargon he's using:

Meyer: The recurring structural motifs such as alpha helices and beta strands that arise from specific sequences of amino acids constitute its secondary structure. The larger folds or “domains” that form from these secondary structures are called tertiary structures

Ugh. A domain and a fold are not the same thing. A domain is a blobby part of a protein chain, often called "globular domain" if it's water-soluble, where a bunch of amino acids glob together around a hydrophobic core. A domain may have anywhere from 30 to ~300 amino acids, and a protein molecule may have 1 or dozens of domains along its length.

A "fold" is not a domain-- it's a generalized, abstract description of class or type of tertiary structure, like "alpha-beta barrel" fold which describes alternating alpha helices and beta strands arranged in a barrel shape.

And the word "recurrent" should be "repetitive" or better, "periodic."

Mikkel Rumraket Rasmussen said...

It gets much worse, turns out Meyer is making assertions diametrically opposite to what his references say. Remember the what Meyer wrote above? "The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures."

Well, much later in the same chapter, Meyer finally references Ohno: "Third, building new animal forms requires generating far more than just one protein of modest length. New Cambrian animals would have required proteins much longer than 150 amino acids to perform necessary, specialized functions.21"

What is reference 21? It's "21. Ohno, “The Notion of the Cambrian Pananimalia Genome.”"
What does that reference say? Let's look: "
Reasons for Invoking the Presence of the Cambrian Pananimalia Genome.
Assuming the spontaneous mutation rate to be generous 10-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million years in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the kingdom Animalia within the time span of 6-10 million years can't possibly be explained by mutational divergence of individual gene functions. Rather, it is more likely that all the animals involved in the Cambrian explosion were endowed with nearly the identical genome, with enormous morphological diversities displayed by multitudes of animal phyla being due to differential usages of the identical set of genes. This is the very reason for my proposal of the Cambrian pananimalia genome. This genome must have necessarily been related to those of Ediacarian predecessors, representing the phyla Porifera and Coelenterata, and possibly Annelida. Being related to the genome - possessed by the first set of multicellular organisms to emerge on this earth, it had to be rather modest in size. It should be recalled that the genome of modern day tunicates, representing subphylum Urochordata, is made of 1.8 x 108 DNA base pairs, which amounts to only 6% of the
mammalian genome (9). The following are the more pertinent of the genes that were certain to have been included in the Cambrian pananimalia genome."

Oops Meyer. So, Meyer makes a single goddamn reference to support the claim that the Cambrian explosion required a lot of innovation of new proteins, folds, cell-types and so on. What do we find in that references? That Ohno is suggesting the direct opposite, that he is in fact supporting the standard evo-devo view that few regulatory changes were what happened.

Later Meyer gets a ID-complexitygasm when he asserts, again without any support, that: "The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions."

Where does he get this? His ass, that's where.

Diogenes said...

Good catch Rumraket.

Ted said...

Meyer concedes that the genetic information may have originated in the pre-Cambrian but complains that this merely pushes back the origin of the information. But doesn't that eliminate the Cambrian "explosion" and thereby destroy the ostensible point of his book that the Cambrian is too short a time for so much new information to appear?

judmarc said...

It all goes back to the idea that it's "typical" for a "new animal" to have entire new organs and new cell types. Where are the new organs and new types of cells in each of Darwin's finches? All Meyer, et al. are doing is making evolution one explosion after another by saying that every new species must undergo leaps at the genomic, cellular and organ level more typical of differences between orders or even higher taxonomic ranks than between species.

NickM said...

"Meyer concedes that the genetic information may have originated in the pre-Cambrian but complains that this merely pushes back the origin of the information. But doesn't that eliminate the Cambrian "explosion" and thereby destroy the ostensible point of his book that the Cambrian is too short a time for so much new information to appear?"


Diogenes said...

It's true. When Meyer conceded that point, he simply contradicted the "sexiest" and most original (though also most stupid) claim in the book.

Meyer revealed that the "Cambrian Explosion" was just a sexy marketing gimmick that he didn't really believe in, like "Explosion of Flavor" in Starburst Candy, which also doesn't explode.

Robert Byers said...

if new powerful ideas come along in some subject of science and people refuse to debate then they must watch the powerful idea that seed and root and grow. this forum exists because a threat is noticed and a response is thought needed.
its simple really.
Behe says a explosion of complexity is shown by this fossil assemblage and fossil evidence shows nothing before this to explain this explosion.
Yet its on fossils that evolution rests its case greatly.
Behe just then proves further how unlikely complexity could pop out without previous evidence when the fossil stratas are the whole evidence.
Evolutionists can't say WELL we just didn't find it. its there somewhere!

By the way. its just a accusation that prior beliefs mean scholarship was not the origin for behe book.
Its a serious accusation that Mr Behe is a liar or a fool since obviously he means to be a scholar in good respect and good credibility.
The book reviewer seems to make a serious accusation without expecting anyone to question him in his book review circles. I suspect his motives are affected by the bigger issue about God and Christianity. however suspicion is just that.

Unknown said...

"Oddly enough, neither Axe or Meyer have apparenly ever heard of duplication and shuffling."

you said you read the book. There is a chapter dedicated to gene duplications, reshuffling and all other evolution magic.

Mikkel Rumraket Rasmussen said...

Yes and it's just as bad as this one, and you probably uncritically gobbled it up just like you did chapter 10. Am I right? Did you check all Meyer's claims for supporting references, did you then actually check those references? No, you didn't.

The same theme runs throughout the entire book. Lots of assertions, little to no support for them. Some times the "support" turn out to be saying the opposite of what Meyer is attempting to prove. That's not just shoddy scholarship, that's deliberate misinformation. But never mind that, because Meyer is some one you agree with, he's arguing for a conclusion you want and like, so he's just right when he asserts stuff.

Mikkel Rumraket Rasmussen said...

The hilarious thing is that the examples Meyer mention as molecules that could not have evolved in the short period of the cambrian, like Lysyl Oxidase, have almost 3 billion year preceding evolutionary histories. Why does Meyer then think this molecule had to magically and instantaneously appear de novo in the cambrian? Funny thing is the only one suggesting that it did is Meyer himself, who then turns around and complains that the cambrian doesn't have enough time to do it.

It's nothing short of deliberate misinformation by Meyer, and he can get away with it because he knows his blinders-on-fanbase in the ID community don't bother actually checking this stuff.

Uncivilized Elk said...

I always find it funny how to disprove "evolution magic" the IDists try to cite actual scientific literature.

This scientific literature typically does not claim what they say it claims, and often even claims the exact opposite.

That sounds like a winning strategy Unknown! Keep with it! ID will surely never die!

Uncivilized Elk said...

Babyfuckingjesus, the book author's name isn't just in the picture of this blog post, it's also the first two words of the fucking TITLE.

Diogenes said...

As we see from our friend Unknown, above, who robotically copies and pastes long passages from IDiots like Michael Behe-- full of predictions and statements already falsified, and dissected in gruesome detail on this website-- not realizing that by quoting them saying already-falsified things, he's undermining their authority.

Diogenes said...

I find it funny that IDiots use words like "magic" to describe falsifiable, tested evolutionary models, whereas their hypothesis really IS magic. Michael Behe stated directly that his hypothesis is that a magic "puff of smoke" (his words) created irreducible complexity. No word on whether it was sparkly.

So when creationists say things like "you believe it evolved by magic", it's just a conversation with a Klansman who starts out by accusing YOU of racism. Uh huh. Sure. Propaganda 101. Yeah, you been schooled in propaganda techniques, we been schooled in science. Let's dance @$$h07€.

Here we caught Stephen Meyer Shameless Liar lying in all of his key assertions in his book, but Unknown don't have shit to say about that.

Magic, magic!! he says. By the way, by what mechanism was biological complexity created? Same, or different mechanism as the one used when Jesus multiplied loaves and fishes?

Unknown said...

Ted Lawry:
"Meyer concedes that the genetic information may have originated in the pre-Cambrian but complains that this merely pushes back the origin of the information. But doesn't that eliminate the Cambrian "explosion" and thereby destroy the ostensible point of his book that the Cambrian is too short a time for so much new information to appear?"

1. He didn't concede, he said "even if"
2. You missed the context. The context was the origin of information.

Meyer in response to Ch. Marshall's review

"Nevertheless, this question-begging assumption does not solve the central problem posed by Darwin's Doubt -- that of the origin of the genetic (and epigenetic) information necessary to produce the Cambrian animals. It merely pushes the problem back several tens or hundreds of millions of years, assuming that such a universal genetic toolkit ever existed. (Marshall also makes no attempt to rebut my argument about the inability of the mutation/selection mechanism to generate new epigenetic information, a problem that has led other prominent evolutionary biologists to express skepticism about the adequacy of the neo-Darwinian mechanism.19) In any case, Marshall does not explain how the neo-Darwinian mechanism could have overcome the combinatorial search problem described in Darwin's Doubt to produce even the new genetic information necessary to build new proteins and Cambrian animals.

In any case, the experimentally based calculations in Darwin's Doubt show that neither ten million, nor several hundred million years would afford enough opportunities to produce the genetic information necessary to build even a single novel gene or protein, let alone all the new genes and proteins needed to produce new animal forms. Indeed, neither stretch of time is sufficient to allow the mutation/selection process to search more than a tiny fraction of the relevant sequence spaces. Marshall's review does not even allude to a solution to this longstanding mathematical,21 and now experimentally based,22 challenge to the efficacy of the neo-Darwinian mechanism. Instead, his proposal merely presupposes the prior existence of the genetic information necessary to produce the Cambrian animals. "

Mikkel Rumraket Rasmussen said...

I love how Meyer just endlessly repeats the unsupported and evidently false assertion that the cambrian explosion required lots of novel genes, proteins and information.

Meyer, repeat until it sinks in: You're the only one who thinks the diversification in the cambrian required "new genetic information necessary to build new proteins and cambrian animals".

The "necessity" you speak of is of your own invention. It is a carefully constructed LIE you tell to impress your deluded audience.

Like Unknown here, who appears to be deeply infatuated with the phrase "origin of new information", because apparently, he swallowed it hook, line and sinker when you mindlessly asserted that the cambrian diversification required this.

Meanwhile, evolutionary biologists, including Susumo Ohno, whom you dishonestly cite in support of a claim he in fact argues against(as I documented above in this thread), have been saying now for decades that it was primarily rewiring of gene regulatory networks that "produced the cambrian animals".

On the topic of the origin of information, it is uber trivial to see that new genes arise primarily through gene duplication and subsequent mutational divergence, despite Axe et al's deliberately flawed studies.

We have superfamilies of proteins that have diverged in structure and function through this method over the entire history of life. Here's a paper that shows that around 71% of all known enzyme functions(we are talking tens of thousands of different chemical reactions catalyzed here) have evolved from a relatively small set of 276 enzyme superfamilies.

Mikkel Rumraket Rasmussen said...

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

In order to understand the evolution of enzyme reactions and to gain an overview of biological catalysis we have combined sequence and structural data to generate phylogenetic trees in an analysis of 276 structurally defined enzyme superfamilies, and used these to study how enzyme functions have evolved. We describe in detail the analysis of two superfamilies to illustrate different paradigms of enzyme evolution. Gathering together data from all the superfamilies supports and develops the observation that they have all evolved to act on a diverse set of substrates, whilst the evolution of new chemistry is much less common. Despite that, by bringing together so much data, we can provide a comprehensive overview of the most common and rare types of changes in function. Our analysis demonstrates on a larger scale than previously studied, that modifications in overall chemistry still occur, with all possible changes at the primary level of the Enzyme Commission (E.C.) classification observed to a greater or lesser extent. The phylogenetic trees map out the evolutionary route taken within a superfamily, as well as all the possible changes within a superfamily. This has been used to generate a matrix of observed exchanges from one enzyme function to another, revealing the scale and nature of enzyme evolution and that some types of exchanges between and within E.C. classes are more prevalent than others. Surprisingly a large proportion (71%) of all known enzyme functions are performed by this relatively small set of 276 superfamilies. This reinforces the hypothesis that relatively few ancient enzymatic domain superfamilies were progenitors for most of the chemistry required for life.


A significant proportion of the reactions required for life are performed by a relatively small number of superfamilies so it can be postulated that a few ancient enzymatic domain superfamilies were progenitors for most of the chemistry required for life, this considerably develops previous observations [37]. Using the phylogenetic trees to define the evolutionary route taken within a superfamily to change function, we were able to generate the E.C. change matrix. The large numbers of changes at the E.C. 4th level in the summary of E.C. changes in phylogentic trees compared to the low number of E.C. class changes indicates that changes in specificity occur mostly at the leaves of the trees, while more fundamental changes in chemistry occur at the root of the tree. Further work is required to ascertain when in evolution these changes occurred. Therefore a large amount of enzyme diversity occurs through evolution rather than de novo invention. Although, of course, new enzymes must have evolved at some stage, probably very early in the evolution of life. To identify the small number of ‘original’ enzyme progenitors requires more work and more experimental data."

Did you catch that? A protein superfamily is a large collection of structurally similar proteins that share common descent. As in, they all evolved from a common ancestral protein, where gene duplications and mutations subsequently spawned descendant proteins with different functions. Some of these proteins are now so different they have no sequence similarity. We are talking, from an informational standpoint, a totally new sequence wholly unlike it's most distant ancestor. The slow accumulation of mutations over the history of life have completely changed the amino-acid sequence of the protein. It only has structural similarities with it's distant ancestor. It is new information in any meaningful definition of the word.

But fuck that, keep drinking the ID coolaid. Meyer says it, he cites Axe, that settles it.

Diogenes said...

We're doomed. The Christians have mastered copy-and-paste technology.

If they ever learn what a URL is, Darwin is finished!

Diogenes said...

It's like the scene in Jurassic Park where the velociraptors learn to turn doorknobs.

NickM said...

I addressed the origin of new genes stuff here but the rebuttals in that point are nonexistent, I think their brains shut down long before they get there :

Diogenes said...

Rumraket, good job citing the paper by Janet Thornton. Janet [not to be confused with Joe Thornton, no relation, who also does great work on protein evolution] has worked for decades compiling numerous databases of protein structure and function.

If Doug Axe and Stephen Meyer really wanted to test their hypothesis that many new protein folds originated in the Cambrian explosion, they could start by running analyses of already existing databases of protein structure and function, which they could do in their living rooms, in their underwear. There are databases of protein 3-D structure [PDB], fold [SCOP], function [ENSEMBL], protein-proteiin interactions [DIP] and Janet Thornton's and others' databases of structure-function relationship.

So Doug Axe and Stephen Meyer could and should test their "protein folds appear magically all at the same time" hypothesis just by scanning already-existing databases. But no. Instead they just make bare assertions that they pulled out of their asses.

And even their bare assertions are easily refuted. The one example of a protein "fold" that they say appeared by magic in the Cambrian explosion is lysyl oxidase, which is not actually a fold, it's actually a functional class. Duh. And it must have pre-existed the Cambrian, because all animals have it today, along with fungi-- but animals existed before the Cambiran (Ediacarn biota), and they must have had lysyl oxidase, so it pre-existed Meyers' Cambrian magic puff of smoke.

Unknown said...

Before reading Behe and Meyer I thought that evolutionary claims were based on solid
evidence. What those two are saying is that there is absolutely no evidence for those claims.

I thought that reading their critics I would see some evidence presented but all
they say is what evolutionists always say : stories. Must have, might, maybe
translated we wish. When their stories are questioned they resort to excuses of why
there is no evidence. Just listen to Marshall in the debate, no reference to actual
evidence only excuses.

2. So the story says that long before there were animals random errors invented all the genes necessary to build animal proteins, cells, organs, body plans.? And that's science.

The facts are : There are no ancestral fossils
There is no mechanism
And that is not going to change.

As M Behe says
"My current thinking is that the limits to Darwinian evolution are much more severe
than I had envisioned in 1996, and even more severe than I discussed in my 2007
book, The Edge of Evolution. Random mutation and natural selection sometimes produce simple beneficial results for an organism, but usually by degrading some genetic feature the organism already had. Darwin’s mechanism cannot coordinate the many changes necessary to build even modestly complex systems."

"Well, to change my mind at this point would require Darwinists to produce actual
evidence that their theory can do what they claim for it. They aren’t used to doing
that, and I don’t expect that to change anytime soon."

Unknown said...

Robert Byers is so far out there that even UD has banned him from commenting.

Uncivilized Elk said...

When you realize that the book you love is full of citations to literature (containing evidence) that say the exact opposite of what the book claims they say, the next logical step is clearly to throw your hands in the air and shout "THERE IS NO EVIDENCE! THERE NEVER WAS ANY EVIDENCE! THE EVIDENCE IS JUST A MYTH!"

Robert Byers said...

Well put anf you put well some major themes of Behe.
Complexity can not be just assumed a easy matter to create by mutations being selected on. its so unlikely that this could happen and did happen and here we are.
Evolutionists must prove mutationism could arrange the glorious complexity of our immune system or any system in us.
by the way I say fossils are not in any way legit biological evidence for evolution or criticizing evolution.

Mikkel Rumraket Rasmussen said...

No evidence, Darwinists!.

Diogenes said...

Unknown says: "The facts are : There are no ancestral fossils
There is no mechanism
And that is not going to change."

How the %$&! would you know? You learned all the science you know from creationists, who have been shown, on this very page, to dishonestly misrepresent the scientific papers they cite. And when you issue universal negatives ("There are no ancestral fossils! There is no mechanism") you make yourself look like a boob, both because of the falsity of your allegations, and because a universal negative assumes a claim that you have encyclopedic knowledge. Thus, the actual facts that there are intermediate fossils and that there is a mechanism not only makes you wrong about important facts, but also means that you dishonestly representing your alleged encyclopedic knowledge of paleontology and genetics when you emit universal negatives, in fields about which you know nothing, and your trusted authorities know little.

You learned your "science" from Stephen Meyer who learned all his "science" from other creationists like Doug Axe. Let's review the content of your trusted authority, Stephen Meyer's, book, discussed on this very page:

1. Stephen Meyer quoted Henry Quastler out of context to reverse his meaning: Quastler said natural, accidental processes create information, Meyer says Quastler said "invariably" only intelligent agents create information. Creationist response: you support Meyer because he lies to you and you want him to.

2. Stephen Meyer "paraphrased" Susumu Ohno to reverse his meaning: Ohno said the Cambrian explosion involved old genes used in new ways, with few if any new genes; Meyer says Ohno said that many entirely new protein folds were necessary. Creationist response: you support Meyer because he lies to you, and you want him to lie to you.

3. In the debate, Charles Marshall accused Meyer of misrepresenting all the papers he was citing, and Meyer could not defend himself: "I outlined these arguments [about morphological evolution not requiring new genes nor proteins], and it’s completely missed in the book... I found myself disappointed that the arguments that were made in the papers that he cited weren’t the ones that he confronted directly. He confronted a different set of problems that I think harked back to an older age. And I attributed it.. to the fact that he’s not a biologist..." Marshall accuses Meyer of misrepresenting the literature he cited, and Meyer's response at the debate: none. He did however concede at the debate that new proteins didn't appear in the Cambrian, so he was bullshitting in his book.

Diogenes said...

As for your claim that there are no "ancestral fossils", there certainly are intermediate fossils in the pre-Cambrian and Cambrian: to name a few, Kimberella, Cambrian lobopods, halkieriids, onychophorans, pre-Cambrian shells and early Cambrian (pre-Explosion) trace fossils of worm-like bilaterians, and possibly the pre-Cambrian Parvancorina. In fact, the chief characteristic of the Cambrian explosion is that the animals are generally stem groups [Budd & Jensen, 2000], which means the phyla are not fully formed when we first see them differentiated unambiguously in the fossil record, but creationist "theory" says all "kinds" appear "fully formed." The phyla are not "fully formed" when we first see them, so creationist predictions are falsified.

For some fossil evidence, I will cite the review of Meyer's book by John Harshman, who once again points out that Meyer misrepresents the scientific literature, in this case, Budd and Jensen 2000:

Here we begin two major confusions that are repeated and amplified in succeeding chapters: first about when the Cambrian explosion happened, as any phylum with a first appearance in the Cambrian is counted in fig. 2.5 as part of the explosion, including phyla that appear in the 20+ million years of the Cambrian that he fails to mention before his explosion starts; second, confusing appearance in the fossil record with appearance on earth, as if the record were perfect.

...A major claim in this chapter is the idea of “top-down” appearance: phyla appearing before families, families before species, etc. He dismisses the idea that this is an artifact of classification, but makes no real argument. But phyla were defined based on extant species as the broadest classifications, and so must arise earliest in the history of life, before lower-level groups that they contain. His counter is that these early taxa all have the distinctive features of their modern relatives. Oddly enough, he frequently cites one of my favorite papers, Budd & Jensen 2000, which shows that nearly all Cambrian taxa are at best stem-members of their respective groups. And he relegates potential transitional fossils (Anomalocaris, Opabinia, halkieriids, etc.) either to extant phyla or to new phyla, again unrelated to any others. Each transitional fossil, in other words, just creates another gap.
[John Harshman's review of Darwin's Doubt]

Stephen Meyer engaged in cite-lying about the content of a scientific paper he was citing [Budd & Jensen 2000]? What a surprise! Iago the parrot responds to reports of Meyer's dishonesty:

judmarc said...

There are no ancestral fossils - the Neanderthal exhibits in natural history museums were made up by commie liberal university professors; the lab work that shows they share genes with us (they contributed a few percent to the modern human genome) was made up by socialist Germans; and those cave paintings in France were done with spray cans.

See? I can write "intelligent design science" too!

SRM said...

I find it funny that IDiots use words like "magic" to describe falsifiable, tested evolutionary models, whereas their hypothesis really IS magic.

Yes, always found that amazing. Problem stems from the fact that the entirety of their hypothesis is wrapped up in one word: God.

They mistake this one word for a explanation, for a mechanism. Or probably closer to the truth, they simply aren't interested in mechanism. The apparant simplicity of the god hypothesis is appealing to simple minds, with none of that complex DNA/mutation/time scientific ivory tower mumbo-jumbo stuff.

They do not perceive that ultimately God would have had to enact a mechanism that would look just like the result of natural evolution using - what else - magic powers.

Truth of the matter of course, positing a god grossly complicates matters but the inordinate complexity of their hypothesis is easily obscured if only you realize God loves you.

Anonymous said...

What's the cause of the Cambrian explosion...? Is it falsifiable...? ;-)

Mikkel Rumraket Rasmussen said...

The timing of the cambrian diversification has been linked to geological strata that shows substantial environmental change, which is thought to have played an important role in the origin and evolution of hard body parts: Bones, teeth, scales, shells and the like.

I'm not a geologist or ecologist, so you will have to check the extant litterature to get a more detailed answer.

Yes, it's falsifiable. That these environmental changes can affect the biosphere has good empirical support and fits pretty well with what we see happening in the late Ediacaran and early cambrian.

William Spearshake said...

"The facts are : There are no ancestral fossils"

The lack of fossils does not mean the lack of ancestors.

Robert Byers said...

Fine but also there being no ancestors would mean no fossils.
however this is all about fossils which has nothing to do with biological evidence.
Its only the faith in the deposition story of the fossils and them being a wee bit different from others lying over them that is what these contentions are settled on.
You can't do biology on rocks!!

The whole truth said...

Robert, are bones biological? Are the shells of mollusks biological? Are the exoskeletons of arthropods biological? Are teeth biological? Are feathers, scales, and hair/fur biological? Are plant parts biological? Is scat biological? Is tree sap biological? Are skin, blood, cartilage, horns, antlers, tusks, and internal organs biological?

Yes or no?

Robert Byers said...

No. They are the result of biology but are not biological agents in a process of biological action. They are no more biological then a picture of a biological thing IS!!
In these matters its processes that are being figured out and taking mere pieces of life is unrelated to demonstrating the biological relationship.
There is no evidence of the inbetweens of fossils. Its just guessing.
Anyways its unrelated to scientific investigation of biological processes.
why do you think it is?

The whole truth said...

Robert, name five things that are "biological agents in a process of biological action".

Unknown said...
This comment has been removed by the author.
Unknown said...

Complete tree with links to 764 organisms that produce Lysyl oxidase proteins: