The DI Strikes Back

"Ganfornina and Sánchez argue that any approach to co-option "by definition, has to be hypothetico-deductive." (p. 438) In other words, evolution by natural causes is assumed to be true, and inferences are then drawn from that assumption. "

— FOTCFSAC

...we need to convincingly detect co-option and duplication events along the history of genes, developmental modules, or morphologic structures. In general, it would be very difficult to catch evolutionary events of cooption or gene duplication in current populations to experimentally test the hypotheses proposed here. The approach, by definition, has to be hypothetico-deductive, as discussed by Larson and Losos [59]; that is, we need to derive hypotheses from our phylogenies and must be able to make testable predictions about the current use or current characteristics of our genes in extant species. (emphasis added)

When the truth or falsity of the theory itself is the issue, as it is here, working out its logical implications is a largely irrelevant exercise.

The idea behind this is that rather than just have the usual disorganized commenting free-for-all, the comments page will be semi-organized so that people can find various topics and see which ones have been addressed, and which not.

When one is questioning whether a biological pattern was produced by descent via natural causes (as Meyer 2004 asked), one is not answered by citing a paper that assumes the truth of the very theory at issue.

Ganfornina and Sánchez argue that any approach to co-option "by definition, has to be hypothetico-deductive." (p. 438) In other words, evolution by natural causes is assumed to be true, and inferences are then drawn from that assumption. As we noted in the first installment of our response to GME, it is philosophically legitimate to presuppose a theory as a guide to research, but this is not the same as providing evidence for the theory. When the truth or falsity of the theory itself is the issue, as it is here, working out its logical implications is a largely irrelevant exercise.

"When the truth or falsity of the theory itself is the issue, as it is here, working out its logical implications is a largely irrelevant exercise."

ZOMGWTFBBQ.

Unbelievable. Absolutely unbelievable.

So when Behe says that it is a logical implication of evolution that IC structures cannot exist, and when Dembski says that it is a logical implication of evolution that biological structures will not exhibit CSI, and when Johnson, Wells, and Meyer say that it is a logical implication of evolution that the Cambrian Explosion cannot have occurred, this is all "a largely irrelevant exercise"?

Do creationists *ever* stop to think about what their statements entail before they sling them out, or is "making evolutionists look bad at the moment" the sole motivator?

Some of commentators belong at NASA: The National Acronym Slingers Association.

Well, the FOTDICF(R)S&C started it, by referring to MOM as GME, but CTASOTPT and MOTMPDNCSE seem to have upped the ante. ;-)

That should have been MHM, not MOM.

The DI truth-squad piece says that "...beneficial mutations affecting early development have never been observed."

This statement is debatable, to say the least. One counterexample can be found here, in a paper from the 21 February 2002 issue of Nature, "Hox protein mutation and macroevolution of the insect body plan."

Here's the abstract: "A fascinating question in biology is how molecular changes in developmental pathways lead to macroevolutionary changes in morphology. Mutations in homeotic (Hox) genes have long been suggested as potential causes of morphological evolution, and there is abundant evidence that some changes in Hox expression patterns correlate with transitions in animal axial pattern. A major morphological transition in metazoans occurred about 400 million years ago, when six-legged insects diverged from crustacean-like arthropod ancestors with multiple limbs. In Drosophila melanogaster and other insects, the Ultrabithorax (Ubx) and abdominal A (AbdA, also abd-A) Hox proteins are expressed largely in the abdominal segments, where they can suppress thoracic leg development during embryogenesis. In a branchiopod crustacean, Ubx/AbdA proteins are expressed in both thorax and abdomen, including the limb primordia, but do not repress limbs. Previous studies led us to propose that gain and loss of transcriptional activation and repression functions in Hox proteins was a plausible mechanism to diversify morphology during animal evolution. Here we show that naturally selected alteration of the Ubx protein is linked to the evolutionary transition to hexapod limb pattern."

The full paper is available on-line from this page.

A UC San Diego press release on the work appears here. This has some pretty pictures.

The Discovery Institute knows about this work, and has dismissed it. Jonathan Wells initially said "A research team headed by William McGinnis at the University of California at San Diego has reported discovering a DNA mutation that produces shrimp without hind legs."

This comment appeared in a D.I. Press Release, long since scrubbed from the web. A copy was archived by the Intelligent Design and Evolution Awareness (IDEA) Club, and can be found here.

The NCSE responded, noting that "In a Discovery Institute press release dated Feb. 6, Jonathan Wells accuses three developmental biologists of making 'exaggerated claims' in a recent paper in Nature (advance online publication, Feb. 6, 2002). But it is Wells, in his zeal to criticize any research supporting evolution, whose claims are 'exaggerated.' One wonders whether he actually read the paper. For example, the press release states: 'William McGinnis at the University of California at San Diego just reported discovering a DNA mutation that produces shrimp without hind legs.' He did? If Wells has indeed read the paper, currently published on Nature's website, then he should know that no shrimp were mutated in the production of the research. Further, no mutant shrimp were mentioned in a UCSD press release announcing the Nature paper, which is what Wells apparently relied upon for his critique. Wells appears obsessed by illusory shrimp when he asserts: 'The mutation does not transform the embryo into anything like an insect, but only into a disabled shrimp.' ..."

Wells quickly responded, saying "In a press release issued by Discovery Institute on February 6, I stated that researchers at the University of California at San Diego (UCSD) had produced a mutant shrimp and exaggerated its significance to evolutionary biology. I was mistaken. No mutant shrimp were produced. Alan Gishlick of the National Center for Science Education (NCSE) was quick to point this out, calling my statements 'thinly disguised creationist pontifications.' In fact, I made the mistake because I gave the UCSD researchers more credit than they deserved. Their actual results provide even less evidence for evolution than I was initially led to believe. ..."

The bottom line, from the UCSD press release, is this: "...the scientists showed how modifications in the Hox gene Ubx---which suppresses 100 percent of the limb development in the thoracic region of fruit flies, while its crustacean counterpart from Artemia only represses 15%---would have allowed the crustacean-like ancestors of Artemia, with limbs on every segment, to lose their hind legs and diverge 400 million years ago into the six-legged insects."

Was there a mutation? Yes. The Ubx gene in insects is different from the corresponding gene in crustaceans.

Was the mutation in a developmental gene? Yes. Ubx is in the Hox cluster, and is clearly involved in developmental processes.

Was the mutation beneficial? Apparently so. Here in New Mexico, at least, we have TONS of six-legged insects.

Is the DI correct to claim "...beneficial mutations affecting early development have never been observed" ?

I don't think so.

We can quibble about "early" if you like, but it's plain that the development of LIMBS is a key part of embryonic growth.

More recently, in his 2004 book On the Origin of Phyla, paleontologist James Valentine evaluates various attempts to explain (or explain away) the origin of the body plans that arise in the Cambrian. He concludes that no current hypothesis provides a satisfactory account of the origin of the Cambrian phyla and that the problem of novel body plans remains unsolved---or, as he puts it "the underlying causes remain uncertain."

— DIS

Although resolution of many problems with the evolution of phyla is clearly still beyond our reach, it is at least possible to grapple with competing hypotheses with the evidence that is now available.

"When the truth or falsity of the theory itself is the issue, as it is here, working out its logical implications is a largely irrelevant exercise."

Discussion with the DI is annoying because their views are apologetics (a word they avoid) not science. Please use the word "apologetics" when you refer to DI communications. Otherwise they'll interpret your communication as legitimizing their "science".

Misrepresenting Prum and Brush 2002

DI quotes Prum & Brush 2002 as saying that the "conceptual basis of functional theories of the origin is weak because these theories rest upon hypotheses about the function of an ancestral structure whose morphology is unknown," (p. 267) and conclude that the authors "do not think that the origin of feathers can be explained by change-of-function." This is supposedly in contrast to Gishlick et al. who "claim that change of function by co-option solves the problems with neo-Darwinism that Meyer described in his essay."

But Prum & Brush were not saying co-option was unimportant in the derivation of feathers, but that as a matter of emperical investigation, one should start with morphology and from that, deduce function -- not the other way around.

This reasonable methodological point has nothing to do with co-option having acted in the history of feathers or anything else.

Nick wrote: If you comment on the DI piece elsewhere (e.g., another PT post or an online forum), please add a link or carbon copy the text into the comments on this page.

Is a new and specifically causal theory needed to explain the origination of biological form? Meyer, Stephen C. 2004. The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington 117(2):213-239

Meyer argues that the origin of body plans (and other morphological novelties) during the history of life is increasingly recognized as a fundamental and unsolved problem in theoretical and evolutionary biology. He also argues that there is a good reason for this. In particular, he notes that neo-Darwinism attempts to account for the origin of novel form as the result natural selection acting solely on genetic variations of different kinds. Yet the construction of novel body plans depends upon new sources of epigenetic (as opposed to just genetic) information, and genes alone do not generate this higher-level information and structure.

Specifically, it will treat the problem of the origination of the higher taxonomic groups as a manifestation of a deeper problem, namely, the problem of the origin of the information (whether genetic or epigenetic) that, as it will be argued, is necessary to generate morphological novelty

(GME) Below is a small sampling of the kinds of papers that Meyer would have had to address in this field in order to even begin to make a case that evolution cannot produce new morphologies: Ganfornina M. D., Sanchez D. 1999. "Generation of evolutionary novelty by functional shift." Bioessays. 21(5):432-9. PubMed

(G&S) First, we need to convincingly detect co-option and duplication events along the history of genes, developmental modules, or morphologic structures. In general, it would be very difficult to catch evolutionary events of co-option or gene duplications in current populations to experimentally test the hypotheses proposed here... Second, we need to search for the mechanisms responsible for the evolutionary processes of co-option and duplication. Although much is known about the former, almost nothing is known about co-option mechanisms.

The central issue: Is there a need for a new causal theory

If anyone's got a new causal theory, let's hear it. "Poof, there it is" is not causal.

(Meyer) Yet, DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins; still less does it solely determine how cell types, tissue types, and organs arrange themselves into body plans (Harold 1995:2774, Moss 2004). Instead, other factors--such as the three-dimensional structure and organization of the cell membrane and cytoskeleton and the spatial architecture of the fertilized egg--play important roles in determining body plan formation during embryogenesis

As Gishlick et al and others have shown, Meyer has failed to show that 1) (neo)-Darwinian/evolutionary theory cannot explain the origination of biological form

"Well, ... it was unlikely he died of flu, but he didn't die of smallpox either, so he must have died from flu." Sorry.

The conceptual problems of previous theories of the origin of feathers are reviewed, and the alternative developmental theory is presented and discussed. The developmental theory proposes that feathers evolved through a series of evolutionary novelties in developmental mechanisms of the follicle and feather germ. The discovery of primitive and derived fossil feathers on a diversity of coelurosaurian theropod dinosaurs documents that feathers evolved and diversified in nonavian theropods before the origin of birds and before the origin of flight. The morphologies of these primitive feathers are congruent with the predictions of the developmental theory. Alternatives to the theropod origin of feathers are critiqued and rejected. Hypotheses for the initial function of feathers are reviewed. The aerodynamic theory of feather origins is falsified, but many other functions remain developmentally and phylogenetically plausible. Whatever their function, feathers evolved by selection for a follicle that would grow an emergent tubular appendage. Feathers are inherently tubular structures. The homology of feathers and scales is weakly supported. Feathers are composed of a suite of evolutionary novelties that evolved by the duplication, hierarchical organization, interaction, dissociation, and differentiation of morphological modules. The unique capacity for modular subdivision of the tubular feather follicle and germ has fostered the evolution of numerous innovations that characterize feathers. The evolution of feather keratin and the molecular basis of feather development are also discussed.

Unfortunately, the development of a heuristic theory of the origin of feathers has been limited by many of the same conceptual problems faced by macroevolutionary biology over the last century. Early workers attempted to reconstruct primitive feather morphologies based on variations in feather structures found among "primitive" lineages of extant birds (reviewed in Dyck 1985). In absence of an explicit concept of phylogeny, these theories overlooked the fact that all modern birds share a common ancestor with Archaeopteryx that already had fully modern feathers. Therefore, extant variations were derived, secondarily simplified feather morphologies.

In contrast to neo-Darwinian approaches, and in congruence congruence with a macroevolutionary concept of novelty, the developmental theory of feather origins is focused specifically on reconstructing the transition of developmental novelties required for the origin and diversification of feathers (Prum 1999).

This failure reveals an inherent weakness of neo-Darwinian attempts to synthesize micro and macroevolution. In contrast, the developmental theory of the origin of feathers focuses directly on the explanation of the actual developmental novelties involved in the origin and diversification of feathers (Prum 1999). Restructuring the inquiry to focus directly on the explanation of the origin of the evolutionary novelties of feathers yields a conceptually more appropriate and productive approach.

A second conceptual current has been the development of functional theories of the evolutionary origin of feathers (reviewed in Dyck 1985; Feduccia 1999). These theories propose plausible initial functions for ancestral feathers, and then hypothesize a suitable ancestral morphology to fulfill that function. Plausible initial functions have been justified based on notions about the natural history and ecology of ancestral birds, and notions about what functional transitions in morphology are evolutionarily possible. Recent evidence of biologically convergent, analogous instances of the intermediate functional states proposed by the models have been used to support the plausibility of specific functional theories (e.g., the hairy arms of Propithecus lemurs as an aerodynamic model of early feather evolution: Feduccia 1993). The list of functional theories of feather origins includes the hypotheses that feathers evolved for flight (e.g., Steiner 1917; Heilmann 1926; Blaszyck 1935; Parkes 1966; Feduccia 1985, 1993, 1999), thermal insulation (e.g., Davies 1889; Ewart 1921), heat shielding (Regal 1975), water repellency (Dyck 1985), communication (Mayr 1960), and tactile sensation (Broman 1941). ... Alternative functional theories of the origin of feathers have been justified by restating the initial functional speculations in absence of supporting evidence from the organism's biology. Over the past 20 years, it has been recognized that historical analysis in evolutionary biology requires an independent documentation of the pattern of evolutionary events before testing alternative functional hypotheses about the evolutionary process that explain those events (Lauder 1981; Lauder and Liem 1989; 2001). Based on nonphylogenetic, neo- Darwinian evolutionary theory (e.g., Bock 1965), functional theories of the origin of feathers have failed because they attempt to do exactly the opposite: they use presumed knowledge of adaptive evolutionary process to reconstruct historical pattern.

We have recently proposed an alternative approach to the origin of feathers that uses the details of feather development to reconstruct plausible antecedent morphologies (Prum 1999; Brush 2000, 2001). This approach suggests that any theory of the origin of feathers should also provide a complete and consistent theory of the origin of the complex mechanisms of feather development. Furthermore, the details of feather development support an hypothesis of feather evolution that is independent of phylogenetic and functional assumptions.

Important support for the plausibility of the developmental model of the evolutionary history of feathers comes from extant feather diversity (Prum 1999). All the primitive feather morphologies proposed by the model exist among extant avian feathers.

As Xu et al. (2001) comment, the current paleontological evidence of theropod feathers provides some additional phylogenetic support for the transition series predicted by the developmental model for the origin and evolution of feathers (Figures 5 and 6).

With the development of phylogenetic methods, it has been established that phylogenetic pattern should be determined before the analysis of evolutionary process (e.g., Lauder and Rose 1996). Obviously, it is difficult to explain why or how some event has occurred in evolutionary history without actually knowing what has occurred. But this is exactly what functional theories of feather origins attempt to do.

With the startling discovery of primitive feathers in nonavian dinosaurs, we now have the first data that allow us to reevaluate proposed functional explanations. What does the first view of what happened imply about why and how feathers evolved?

Consequently, aerodynamic hypotheses for the initial function of feathers have been falsified.

Thus the developmental model could provide an extremely early potential origin for the feather movement system, as proposed by Homberger and de Silva (2000).

Prum (1999) concluded that numerous other proposed initial functions of plesiomorphic feathers are developmentally plausible because the simplest possible feathers could have performed these functions. These hypotheses include thermal insulation (Davies 1889; Ewart 1921), thermal shielding (Regal 1975), communication (Mayr 1960), water repellency (Dyck 1985), tactile organs (Broman 1941), and defense (Prum 1999). Each hypothesis constitutes a physically plausible selective advantage of the earliest feather, a hollow tubular filament. Of course, the width, length, and rigidity of the first feathers remain unknown. Based on our current knowledge of the biology and natural history of coelurosaurian theropods, it would be entirely speculative to maintain that any of these plausible functions actually was the selective function that led to the fixation of the first feathers.

There is, however, an important fundamental commonality among these plausible functional hypotheses that is congruent with the developmental theory of the origin of feathers (Prum 1999) and that provides a more fundamental explanation of the origin of feathers. Any selection for a substantial integumentary appendage that emerges from the skin or extends out of the skin would essentially constitute selection for the evolution of a tubular follicle, the initial event (Stage I) in the evolution of feathers (Figure 4). ... Whatever it was, the initial functional advantage of the earliest feathers constituted natural selection for an emergent appendage that then fostered the evolution of the feather follicle (Stage I). Although the original functional advantage of the first feathers remains a mystery, the ultimate explanation for the origin of the feather must have involved selection for epidermal appendages that emerged from the skin.

By focusing too intensely on singular functional explanations, functional theories of the origin of feathers have obscured the fact that the history of feather evolution is characterized by a continued diversification and novelty in development, form, and function that cannot be explained by natural selection for a single function.

An explicit, process-independent definition of evolutionary novelty (Mueller and Wagner 1991) permits us to examine which of the hypothesized mechanisms for the origin of evolutionary novelties may have been involved in the evolution of feathers. Mueller and Wagner (1991) propose three modes for generating novelties: hierarchical organization, interactivity and dissociability, and equilibria and thresholds. As documented by both Brush (1993, 1996, 2000, 2001) and Prum (1999), feather development is extraordinarily hierarchical. ... The origin and differentiation of hierarchically nested morphological modules in the feather have resulted in numerous evolutionary novelties in structure and development...

Other novelties within feathers are hierarchical duplications and alterations of these processes. For example, the development of an afterfeather---a second posteriorly oriented vane growing out of the same follicle and attached to the same calamus (Figures 1 and 2)---occurs as a consequence of a second opposing, posteriorly oriented direction of helical growth (Lillie and Juhn 1938; Lucas and Stettenheim 1972). As a consequence of duplication and redirection, the same mechanisms that produce the main vane of the feather result in the division of the posterior new barb locus into two laterally displaced new barb loci, the creation of a second rachis ridge (the hyporachis), and ultimately an entire second vane growing simultaneously from a single follicle.

Interactivity and dissociability refer to the ability of components to create new structures through changes in the interactions among tissues, or modules, which create the interconnectedness of ontogenetic networks. Most novelties in feather development arise as a result of such interactions and dissociations.

Raff (1996) recognized an additional mechanism for the origin of evolutionary novelties: duplication and divergence. Duplication and divergence have played fundamental roles in the evolution of feather structure and diversity. The duplication of keratin genes is one example at a molecular level (Brush 1978, 1993). At the morphological level, the duplication of numerous feather follicles over the body surface and subsequent divergence in morphology of different feathers have contributed greatly to the origin and maintenance of feather novelties.

The origin and diversification of feathers have been intractable questions in evolutionary biology for more than a century. Progress on these issues has been hampered by conceptual problems and the lack of fossils of primitive feathers. Both of these limitations have been overcome by the recent proposal of a developmental theory of the origin of feathers, and discoveries of primitive feather fossils from nonavian theropod dinosaurs. The developmental theory provides a heuristic model of the evolution and diversification of feathers that is entirely congruent with the known details of feather development (Prum 1999). The discovery of primitive fossil feathers documents that feathers evolved and diversified in nonavian theropod dinosaurs before the origin of birds and before the origin of flight (Chen et al. 1998; Ji et al. 1998; Xu et al. 1999a, 1999b, 2000, 2001; Ji et al. 2001). These primitive feathers are morphologically and phylogenetically congruent with the predictions of the developmental theory ( Ji et al. 2001; Sues 2001; Xu et al. 2001).

One has to wonder, therefore, why GME cited the article against Meyer. Did they even read it?

— DIS

Thus to say (as GME do) that this paper demonstrates that evolution produces new morphologies is false - because the paper actually assumes it.

— Creationist troll

Below is a small sampling of the kinds of papers that Meyer would have had to address in this field in order to even begin to make a case that evolution cannot produce new morphologies: Ganfornina M. D., Sanchez D. 1999. "Generation of evolutionary novelty by functional shift." Bioessays. 21(5):432-9. PubMed

— GME

GME claim that current evolutionary theory does account for the origin of morphological novelty. They also fault Meyer for not citing scientific papers that allegedly establish this claim

— DIS

(I) GME ignore the large body of peer-reviewed biological literature supporting Meyer's contention that the origin of morphological novelty is a fundamental and unsolved problem for evolutionary theory. (II) The literature that GME do cite to show that this problem has been solved is obsolete or irrelevant, or it actually supports Meyer's case. (III) GME fail to address, let alone rebut, Meyer's detailed analysis of why neo-Darwinism, self-organization theory and structuralism do not account for the origin of new forms and body plans

PvM: Three of your four objections above are basically, "Well, ID hasn't done any better." This does not constitute sound argument, for more than one reason.

— Creationist troll

Firstly, this was a review paper - it was not its role to offer new propositions.

— Creationist troll

And, in fact, given the opposition that it received (and continues to) from the evolutionist community even in its current form - even though the DI group are making a fair job of justifying the paper - I find it hard to believe that any paper that was more blatantly non-naturalist would have had any chance of publication in mainstream scientific journals.

Secondly, you can't justify evolution on the basis that ID doesn't seem to be proposing anything any better. That's logically like saying, "Well, we accept that it was unlikely that he didn't die of flu, but he didn't die of smallpox either, so he must have died from flu."

PvM: As Gishlick et al and others have shown, Meyer has failed to show that 1) (neo)-Darwinian/evolutionary theory cannot explain the origination of biological form Unless you can deal with the objections raised by the DI staff, this final objection can't stand, either.

— Creationist troll

"Well, . . . it was unlikely he died of flu, but he didn't die of smallpox either, so he must have died from flu." Sorry.

— Creationist Troll

More recently, in his 2004 book On the Origin of Phyla, paleontologist James Valentine evaluates various attempts to explain (or explain away) the origin of the body plans that arise in the Cambrian. He concludes that no current hypothesis provides a satisfactory account of the origin of the Cambrian phyla and that the problem of novel body plans remains unsolved---or, as he puts it "the underlying causes remain uncertain."

— DIS

The title of this book, modeled on that of the greatest biological work ever written, is in homage to the greatest biologist who has ever lived. Darwin himself puzzled over but could not cover the ground that is reviewed here, simply because the relevant fossils, genes, and their molecules, end even the body plans of many of the phyla, were quite unknown in his day. Nevertheless, the evidence from these many additional souces of data simply confirm that Darwin was correct in his conclusions that all living things have descended from a commmon anscestor and can be placed within a tree of life, and that the principle process guiding their descent has been natural selection. The data on which this book is based have accumulated over the nearly century and a half since Darwin published On the Origin of Species, some gradually, but much in a rush in the last several dedades. I have been working on this book for well over a decade, and much of that time has been spent in trying to keep up with the flood of incredibly interesting findings reported from outcrops and laboratories. I am stopping now not because there is a lull in the pace of new discoveries (which if anything is still picking up), but because there never will be a natural stopping place anyway, and because the outlines of early metazoan history have gradually emerged from mysteries to testable hypotheses.

The Cambrian explosion represents a remarkable jump in the specified complexity or "complex specified information" (CSI) of the biological world. ... One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93). Valentine, J. W. 1995. Late Precambrian bilaterians: grades and clades. Pp. 87-107 in W. M. Fitch and F. J. Ayala, eds., Temporal and mode in evolution: genetics and paleontology 50 years after Simpson. National Academy Press, Washington, D.C.

— Meyer2004

Cell-phenotype numbers in living phyla, and a model of cell-phenotype number increase, suggest an origin of metazoans near 600 my ago, followed by a passive rise in body-plan complexity. Living phyla appearing during the Cambrian explosion have a Hox/HOM gene cluster, implying its presence in the common ancestral trace makers. The explosion required a repatterning of gene expression that mediated the development of novel body plans but evidently did not require an important, abrupt increase in genomic or morphologic complexity.

— Valentine 1995

At present there is no evidence of a major step in body-plan complexity during the Cambrian explosion.

— Valentine 1995

The Cambrian explosion represents a remarkable jump in the specified complexity or "complex specified information" (CSI) of the biological world.

Did anyone hear about this? Not that I really care to go see it, because the Devil's got me by the brain and I don't ever think about the issue (or, maybe it's because I just don't want to waste my time)...

Evening on Mars Hill presents the satellite rebroadcast of "
The Case For a Creator".

This very special event will explore the latest scientific
evidence that refutes popularly accepted theories of
naturalism and instead points to a world created by an
intelligent designer.

The broadcast features the nationally recognized author, Lee
Strobel, and the Director and Senior Fellow of the Center for
Science and Culture at the Discovery Institute, Dr. Stephen
C. Meyer.

Please plan on joining us tomorrow evening, Wednesday,
October 13th, in the North Coast Calvary Chapel auditorium
from 7-9 PM.

Blessings,
Sheri Braun
North Coast Calvary Chapel
7188 Avenida Encinas
Carlsbad, CA 92009
760.929.0029 Ext 124

In other words, the variations upon which natural selection would have to work remain elusive, just as they were for Mayr and for Prum and Brush, and the mechanism of co-option remains hypothetical

— DIS

Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit. John R. True and Sean B. Carroll, "Gene Co-option in Physiological and Morphological Evolution." (2002).

When it comes to morphological novelties, however, the evidence isn't there. Assuming gene transposition and duplication, True and Carroll conclude: "The mechanisms by which duplication and transposition bring about co-option of novel gene functions have thus far been hidden from view because functionally important polymorphisms [i.e., variations] involving these events are difficult to identify. The next phase of evolutionary developmental biology research must address this paradox by investigating the levels, causes, and consequences of microevolutionary variation in developmental systems."

— DIS

I've got a PDF copy if you want to give me you email, Pim.

(Its too much for me to wade through, at the moment)

Sheri, with all respect, I don't think any of the professional scientists on this forum are likely to be swayed or even interested in the kind of "evidence" put forward by a journalist who relies on pro-creationist sources for his material.

All of Strobel's arguments are dealt with and refuted quite thoroughly on TalkOrigins.org

Mike

Why did Meyer quote Valentine?

Possibly because he has no idea what he's talking about.

Strange, how the reviewers failed to catch that.

When it comes to morphological novelties, however, the evidence isn't there. Assuming gene transposition and duplication, True and Carroll conclude: "The mechanisms by which duplication and transposition bring about co-option of novel gene functions have thus far been hidden from view because functionally important polymorphisms [i.e., variations] involving these events are difficult to identify. The next phase of evolutionary developmental biology research must address this paradox by investigating the levels, causes, and consequences of microevolutionary variation in developmental systems."

— DIS

There are three ways by which genes may evolve new functions, even in the presence of selection to maintain their current function (Figure 1): (a) Changes may occur in parts of the amino acid sequence not required for the current function; i.e., new or alternative protein domains may evolve (Figure 1A); (b) changes may occur in gene regulation, expressing a protein in novel tissues and/or developmental stages (Figure 1B); and (c) gene duplication events may occur, followed by divergence in the amino acid sequences and/or regulatory DNA sequences of the descendant paralogs (Figure 1C,D). This third mechanism was thought to be required for the evolution of most novel gene functions (Li 1980). However, there is now much evidence that the evolution of novel gene functions via co-option can take place with or without gene duplication and that the order in which duplication and adoption of novel functions takes place can vary in different evolutionary trajectories. A fourth mechanism involves cobbling novel genes together from genomic fragments. This phenomenon, of which there is an increasing number of known examples, can involve either exon shuffling (Long 2001; Gilbert 1978, 1985) or, in some cases, the fortuitous switching of DNA fragments from coding to non-coding and vice versa (e.g., Nurminsky et al. 1998, Long&Langley 1993). In this review we concentrate on co-option involving extant genes because this appears to be a major mechanism through which developmental diversity in multicellular organisms has arisen.

So we are left with a paradox: Comparative developmental and genomic data provide vast evidence that gene families have diversified and specialized into adaptively important roles, and theory suggests that once present, gene duplications have substantial probabilities of survival. However, the mechanisms by which duplication and transposition bring about co-option of novel gene functions have thus far been hidden from view because functionally important polymorphisms involving these events are difficult to identify.

Conclusions Our goals herein have been to summarize the empirical data on case studies of co-option and to examine the molecular events and evolutionary contexts in which genes have evolved new functions. It is clear that gene co-option has been rampant in the evolution of complex, multicellular organisms, and phylogenetic patterns strongly suggest that many of these events are associated with major changes in ecology and life history. Thus the processes of co-option and regulatory diversification, rather than invention of new genes, explain to a great degree why total gene number in the most complex organisms, such as mammals, does not greatly exceed that of simpler organisms such as flies and worms. Furthermore, the apparent facility and regularity with which some types of co-option have taken place, such as crystallins and antifreeze proteins, indicate that in some cellular and developmental contexts the ingredients for co-option have been plentiful during evolution. This strongly implies that variation, in the form of both noise in spatiotemporal gene expression patterns and transient functional redundancy of duplicated genes, has been readily available for natural selection to act upon. The present convergence of evolutionary developmental biology and genome level analyses provides the stage upon which a deeper understanding of gene functional and regulatory evolution can be played out. In order to better understand the evolutionary and functional mechanisms surrounding co-option, studies of the phenotypic effects and extent of developmental variation in natural populations are needed. This variation is expected to encompass both cis-regulatory and proteincoding DNA. Quantitative and molecular genetic approaches must be integrated and combined with transgenic techniques to understand genotype-phenotype relationships. Specialization among members of multigene families has already been widely implicated as central to co-optive evolution. Comparative genomics can provide an indication of how both small- and large-scale genomic changes fuel the evolution of novelties. Integrating this information across taxa will indicate the propensity for genetic and genomic experimentation to occur in extant organisms and will provide clues about the genomic and selective circumstances surrounding ancestral co-option events.

"Ironically, though, by publishing and then repudiating the Meyer paper, the BSW has done the seemingly impossible. Not only has it given ID proponents a publication in a peer-reviewed biology journal, it has also handed a smoking gun to those ID proponents who argue that the peer-review process is unfairly stacked against them. Quite a feat for a single journal." http://www.arn.org/docs/wedge/mh_wedge_041012.htm

— Bill Dembski

The paper by Stephen C. Meyer in the Proceedings ("The origin of biological information and the higher taxonomic categories," vol. 117, no. 2, pp. 213-239) represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history. It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors. We have met and determined that all of us would have deemed this paper inappropriate for the pages of the Proceedings.

"Ironically, though, by publishing and then repudiating the Meyer paper, the BSW has done the seemingly impossible. Not only has it given ID proponents a publication in a peer-reviewed biology journal, it has also handed a smoking gun to those ID proponents who argue that the peer-review process is unfairly stacked against them. Quite a feat for a single journal." http://www.arn.org/docs/wedge/mh_wedge_041012.htm

— Bill Dembski

The paper by Stephen C. Meyer in the Proceedings ("The origin of biological information and the higher taxonomic categories," vol. 117, no. 2, pp. 213-239) represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history. It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors. We have met and determined that all of us would have deemed this paper inappropriate for the pages of the Proceedings.

In the light of the actual paper the comment: DIS wrote: One has to wonder, therefore, why GME cited the article against Meyer. Did they even read it? seems particularly ironic.

— PvM

Wagner et al. 2000; Chiu and Wagner 2001) proposed that research on the origin of evolutionary novelties should be distinct from research on standard microevolutionary change, and should be restructured to ask fundamentally different questions that focus directly on the mechanisms of the origin of qualitative innovations. This view underscores why the traditional neo-Darwinian approaches to the origin of feathers, as exemplified by Bock (1965) and Feduccia (1985,1993, 1999), have failed. By emphasizing the reconstruction of a series of functionally and microevolutionarily plausible intermediate transitional states, neo-Darwinian approaches to the origin of feathers have failed to appropriately recognize the novel features of feather development and morphology, and have thus failed to adequately explain their origins. This failure reveals an inherent weakness of neo-Darwinian attempts to synthesize micro and macroevolution. In contrast, the developmental theory of the origin of feathers focuses directly on the explanation of the actual developmental novelties involved in the origin and diversification of feathers (Prum 1999). Restructuring the inquiry to focus directly on the explanation of the origin of the evolutionary novelties of feathers yields a conceptually more appropriate and productive approach.

IDers couldn't have put it any better than Prum and Brush did: "research . . . should be restructured to ask fundamentally different questions that focus directly on the mechanisms of the origin of qualitative innovations."

— Pasquale

"It must have been designed" is not a mechanism.

— Dave S

Hey Pasquale, three quick questions

1) Is ID a scientific theory?

2) If so, what testable, novel predictions does it make?

3) Recently there have been several finds of dinosaurs with what appear to be protofeathers. Regardless of what evolution would say about this, would ID predict this? Or not?

Let's just cut to the chase and be clear about where the "debate" stands at this point. Meyer and toadies, in their first installment, are basically arguing that neo-Darwinism hasn't yet given a complete, closed explanation of the origin of animal body plans during the Cambrian. This is an unremarkable statement, and not really worthy of detailed comment. Of course evolutionary theory hasn't given a detailed account of everything that happened during the Cambrian, nor should that come as any surprise. It happens to be the most ancient animal radiation and has left the least amount of evidence behind. We know more about it today than we did ten years ago, and we'll know more in the furture than we do today, but we don't yet know everything. What, then, was Meyer's point?

In order to have anything resembling a legitimate argument, Meyer has to make the case that neo-Darwinism (or any other mechanism for that matter) cannot, in principle, account for the origin of body plans during the Cambrian. This was afterall the whole point of saying hat there was no known mechanism for creating new biological "information". This argument is rather trivial to refute, because there are indeed known mechanisms (namely gene duplication and cooption) that can be seen in action today, that Meyer amazingly forgot to even mention. And how does he respond? Simply by saying that these mechanisms have not been used to explain, in detail, absolutely every step during the evolution of Cambrian body plans; and that that they are based in part on inference rather than direct observation (and I must say, insisting on direct observation for everything shows how scientifically clueless the DI people really are). In other words, Meyer and cohorts are not even trying to defend their original thesis; they have instead moved the goal posts to a weaker, completely irrelevant thesis that most people would find hard to object to. (And they predictably complain of misrepresentation because the original thesis, rather than the newer, more senseless one, was the one critiqued.)

So what's left of Meyer's "evidence" for ID? Pretty much nothing. Unfortunately, simply saying that something is an unsolved problem, or that there are details left to be worked out, cannot bolster a hypothesis that itself has no evidence. The fact that Meyer and other ID advocates base their arguments entirely on the supposed insufficiency of evolutionary mechanisms is an clear indication that they have no independent evidence for ID. That makes their failure to rule out evolutionary mechanisms in principle all the more glaring. Simply sniping at the edges won't do.

Cheerleading here: Excellent post, Steve.

The "mechanisms of the origin of qualitative innovations" that I quote from Prum and Brush, is a reference to Prum and Brush's critique of the "neo-Darwinian mechanism".  Their plea to "ask fundamentally different questions" would be, IMHO, the "upshot" of ID taken seriously.  As I've state in other posts, if you're dealing with a designer, then if you want to understand what's going on, you must in effect, "reverse engineer" the processes being studied.  This leads to a whole set of "different questions", and different approaches to what nature exhibits.

— Pasquale Vuoso

3) Recently there have been several finds of dinosaurs with what appear to be protofeathers. Regardless of what evolution would say about this, would ID predict this? Or not?

— Steve

"What with all these competing designers who work from beyond the sorry "naturalistic explanations" and ye olde pitiful weak "mechanisms", maybe a better question to ask would be: Is there anything ID does not predict?"

I'm sorry, 386sx, but you've made a fundamental methodological error here.

As any competent philosopher of science knows, when the truth or falsity of the theory itself is the issue, as it is here, working out its logical implications is a largely irrelevant exercise.

HTH.

Steve Reuland wrote: This argument is rather trivial to refute, because there are indeed known mechanisms (namely gene duplication and cooption) that can be seen in action today, that Meyer amazingly forgot to even mention.

As I've state in other posts, if you're dealing with a designer, then if you want to understand what's going on, you must in effect, "reverse engineer" the processes being studied. This leads to a whole set of "different questions", and different approaches to what nature exhibits.

The rationale for reverse-engineering living things comes, of course, from Charles Darwin.

Pasquale says:
"Prum and Brush, as the DIs pointed out, believe that natural selection, in the end, can explain the "evolutionary novelties" surrounding the development of the feather, but not in a "gradualistic" (my wording) way."

Gradual change is change by small degrees or gradations, rather than by large ones. What is non-gradual here?

Steve Reuland says:
"Unfortunately, simply saying that something is an unsolved problem, or that there are details left to be worked out, cannot bolster a hypothesis that itself has no evidence."

But politically and socially, this is just what does bolster ID. ID's core principle, the so called explanatory filter, openly substitutes "The Designer did it" in place of "Don't know (yet)"
as the default explanation. In other words, the argument from ignorance is ID's core principle.

Pim says:
"Why would the DI quote this paper?"

Because it has a few sentences which, taken out of context, can be used to political advantage.
Not that Pim & Steve are unaware of the above.

The existence of such mechanisms (like gene duplication and co-option) is a necessary condition, but it is not a sufficient condition by far.

I can appreciate your point of view, but I don't think that statement has correct logic.  The existence of such mechanisms (like gene duplication and co-option) is a necessary condition, but it is not a sufficient condition by far.  Therefore the claim, "it's trivial to refute", I don't this quite right.  However, to your credit, it may have helped Meyer's paper to have mentioned these considerations to anticipate such objections.

— Salvadore

The critque of ID is directed at pointing out the inadequacy of the neo-Darwinian approach while suggesting that the 'logic' behind ID be put to use as a guide to future research. IDers couldn't have put it any better than Prum and Brush did: "research . . . should be restructured to ask fundamentally different questions that focus directly on the mechanisms of the origin of qualitative innovations."

— Pasquale

Meyer's paper deals a lot with the Cambrian Explosion. A look at the actual data would be helpful.

Nevertheless, the evidence from these many additional souces of data simply confirm that Darwin was correct in his conclusions that all living things have descended from a commmon anscestor and can be placed within a tree of life, and that the principle process guiding their descent has been natural selection.

It must have been designed" is not a mechanism.

The "mechanisms of the origin of qualitative innovations" that I quote from Prum and Brush, is a reference to Prum and Brush's critique of the "neo-Darwinian mechanism". Their plea to "ask fundamentally different questions" would be, IMHO, the "upshot" of ID taken seriously. As I've state in other posts, if you're dealing with a designer, then if you want to understand what's going on, you must in effect, "reverse engineer" the processes being studied. This leads to a whole set of "different questions", and different approaches to what nature exhibits.

— Pasquale

I think that some are certainly too far in the materialist direction, and they claim that science backs them up on that. ID can at least serve a 'keeping em' honest' function, even if nothing else. I think that ID may very well have things to offer science, but I think that it is too early for ID to claim that it has done so. I don't think that it is just obvious that ID will contribute substantively to science, but I think it has that potential, and that it should be pushed as far as it can be made to legitimately go.

— Del Ratzsch

Prum and Brush, as the DIs pointed out, believe that natural selection, in the end, can explain the "evolutionary novelties" surrounding the development of the feather, but not in a "gradualistic" (my wording) way.

— Pasquale

I consider this a step forward. Likewise, in the context of this board, I don't think they've stated anything that undermines Meyer's paper, and, in fact, perhaps its critique of "neo-Darwinian" mechanisms tends to support Meyer's claims.

— Pasquale

As reported on ARN, Meyer is rumored to 'debate' his latest paper on Pax this saturday 10pm

According to my channel guide this is 'Faith under Fire' Talk/Religious/Other
TVPG, English

Quite appropriate.

Dr. Stephen Meyer, senior fellow and director of the Center for Science & Culture at the Discovery Institute and co-editor of Darwinism, Design, and Public Education, will defend the theory of intelligent design and its theistic implications against Darwinian evolutionist Dr. Michael Shermer, publisher of Skeptic Magazine and author of The Science of Good and Evil in a televised debate on the PAX TV show Faith Under Fire, hosted by Lee Strobel. The program airs at 10pm PST/EST (9pm CST) on Saturday evening, October 16. Check your local listings to find out what cable station PAX is on in your area, or visit www.faithunderfire.com to find a station.
[/quote[

Dr. Stephen Meyer, senior fellow and director of the Center for Science & Culture at the Discovery Institute and co-editor of Darwinism, Design, and Public Education, will defend the theory of intelligent design and its theistic implications against Darwinian evolutionist Dr. Michael Shermer, publisher of Skeptic Magazine and author of The Science of Good and Evil in a televised debate on the PAX TV show Faith Under Fire, hosted by Lee Strobel. The program airs at 10pm PST/EST (9pm CST) on Saturday evening, October 16. Check your local listings to find out what cable station PAX is on in your area, or visit www.faithunderfire.com to find a station.

Dr. Shermer received his B.A. in psychology from Pepperdine University,his M.A. in experimental psychology from California State Univesity, Fullerton, and his Ph.D. in the history of science from Claremont Graduate School.

Whatever their function, feathers evolved by selection for a follicle that would grow an emergent tubular appendage.

p 275 These extant feathers are secondarily derived or simplified, however, and their existence does not constitute evidence that primitive feathers actually had these predicted morphologies. For these inferences, paleontological data are required to document plesiomorphic feather morphologies (see below).

Dr. Prum (of Prum & Brush 2002) asked to have the following posted:

Response by R. O. Prum to Fellows of the Center for Science & Culture

A complete and detailed rebuttal of the Fellows description of my research is probably not worth the effort, since it is clear from their rhetoric that they are not actually engaged in a sincere scientific effort to explain the origin of biodiversity. But I would like to be sure to point out several major disagreements I have with their characterization of our work on the evolution of feathers.

First, they eagerly quoted our criticisms of late-20th century neo-Darwinian functional attempts to explain the origin of feathers. Obviously, they are trying to represent criticisms of various approaches within the discipline of evolutionary biology as evidence that the entire field is corrupt. Traditionally, this rhetorical method then proceeds by citing the opponents of the first critic as evidence of the corruption of both world views, and this is followed by the satisfied conclusion that the entire discipline is without merit.

Since there haven't been any substantive published criticisms of our theory (isn't that nice!), they are forced to give their own unenthusiasitc, incomplete, and inaccurate representation of our alternative proposal to traditional, functional theories of the evolution of feathers.

I won't review our entire model, but I will state that our developmental theory uses the details of extant feather growth to predict an evolutioanry transition series in feather morphology from the most primitive to the most advanced forms. The predictions of the transition series have been tested comparatively using the morphology of integumentary appendages of theropod dinosaurs: e.g. (Xu et al., 2001). Further, we have also tested the model by examination of the patterns and function of signaling molecules during feather development: e.g. (Harris et al., 2002). These molecular data independently support both the morphologies and the sequence of stages in the developmental model.

In conclusion, the model is testable, and has been corroborated by analyses from vastly different levels of analysis- paleontology and molecular development. I remain agnostic about the actual functions involved in the evolution and diversification of feathers because: (1) feathers actually evolved through a number of different stages each of which likely evolved for different of functional reasons, (2) because of the ambiguity in the fossil record (fossil feathers are rare!) we are not actually sure about the actual lineage in which feathers did originally evolve. So concluding WHY feathers evolved without having a clear view of which lineage they evolved in would be speculative. (This is one reason why work on the evolution of feathers based entirely on Archaeopteryx turned out to be so incomplete). Does this lack of complete understanding of the function of early feathers represent a problem for evolutionary biology? Obviously, we strive to create an increasingly complete and accurate description of the historical process of the origin of biodiversity, and we have made extraordinarily rapid progress in this specific area. Our scientific understanding is not complete, but it is wrong headed to imagine that rapid empirical and theoretical progresss is a failure because the story is incomplete. No one says the evolutionary biology is done. But this criterion cannot be used to critique the field evolutionary biology, since it is impossible for any field of science to be complete.

Harris, M. K., Fallon, J. F. and Prum, R. O. (2002). A Shh-Bmp2 Developmental Module and the Evolutionary Origin and Diversification of Feathers. Journal of Experimental Zoology (Molecular and Developmental Evolution) 294, 160-176.

Xu, X., Zhou, Z. and Prum, R. O. (2001). Branched integumental structures in Sinornithosaurus and the origin of feathers. Nature 410, 200-204.

Dr. Richard O. Prum
William Robertson Coe Professor of Ornithology, Ecology and Evolutionary Biology, Peabody Museum of Natural History

Note to DI:
If you're going to mine quotes, perhaps it's safest to mine those of safely dead authors.

Pasquale Vuoso (2004): As I've state in other posts, if you're dealing with a designer, then if you want to understand what's going on, you must in effect, "reverse engineer" the processes being studied. This leads to a whole set of "different questions", and different approaches to what nature exhibits. Steven Pinker, in How the Mind Works (1999): The rationale for reverse-engineering living things comes, of course, from Charles Darwin.

— Steve

Anyone vaguely familiar with biology knows that biologists have been using "reverse engineering" for a very long time in order to understand the function of biological structures. Afterall, there's not much more you can do, experimentally speaking, than take apart a complex structure in order to understand how it works. Knock-out experiments are as old as molecular biology itself. If this is ID's grand contribution to biology, then it's really missed the boat.

— Steve Reuland

Traditional neo-Darwinian approaches to the origin of feathers have focused on creating theoretical continuity with antecedent structures, and as a consequence, few of these theories have adequately appreciated the many novel aspects of feather morphology and feather development, and none have formulated adequately detailed hypotheses about the origin and evolution of these morphological and developmental novelties.(p. 265) . . . .Explicit attempts to reconstruct the evolutionary history of feathers based on natural selection for specific functions have failed to identify an unequivocal, plesiomorphic function of feathers or to accurately predict a transition series of ancestral feather morphologies. We submit that primarily functional approaches to reconstruct the evolutionary history of feathers have hindered rather than advanced our understanding of the origin of feathers. (p. 285)

Hey Pasquale, three quick questions 1) Is ID a scientific theory? 2) If so, what testable, novel predictions does it make? 3) Recently there have been several finds of dinosaurs with what appear to be protofeathers. Regardless of what evolution would say about this, would ID predict this? Or not?

— Steve

Hypothesized primitive feathers are frequently referred to as "protofeathers" (e.g., Brush 2000; Maderson and Alibardi 2000). Given the enormous structural diversity of extant feathers, it is arbitrary to attempt to distinguish "real" feathers from the various theoretically antecedent "protofeathers" on morphological grounds. In order to emphasize the fundamental importance of the cylindrical, tubular organization of the follicle as the inherent feather novelty, we think it is preferable to recognize all of the diverse structures that likely grow from feather follicles as feathers, and we recommend that the term "protofeather" be abandoned. Primitive structures that are entirely homologous with feathers should be called feathers.

In contrast to neo-Darwinian approaches, and in congruence with a macroevolutionary concept of novelty, the developmental theory of feather origins is focused specifically on reconstructing the transition of developmental novelties required for the origin and diversification of feathers (Prum 1999).

The tubular organization of the feather follicle and germ fostered the formation and proliferation of numerous hierarchically arranged developmental modules, such as the barb ridges within the entire feather germ and the barbules plates and ramus within the barb ridges. This hierarchical, modular organization apparently fosters the development of distinct, polarized molecular concentration gradients and asymmetries at multiple levels within different modules. The tubular epidermal feather tissue can be differentiated into barb ridges which themselves have the potential to differentiate along the peripheral-medial, lateral, and proximodistal axes into the ramus and a series of barbules. The evolution of the tubular epidermal feather germ provided a platform for the evolution of an array of subsequent developmental evolutionary novelties that has generated the diversity in feather morphology.(p.289)

The tubular feather follicle and feather germ led to subsequent evolution of numerous additional morphological and developmental novelties. This complexity appears to have exploited an inherent capacity of the innovative tubular form of the feather follicle and feather germ. Future research on the evolution of feather keratin and the molecular mechanisms of feather morphogenesis will provide additional insights into the innovative nature of feathers.

Pasquale says: "Prum and Brush, as the DIs pointed out, believe that natural selection, in the end, can explain the "evolutionary novelties" surrounding the development of the feather, but not in a "gradualistic" (my wording) way." Gradual change is change by small degrees or gradations, rather than by large ones. What is non-gradual here?

— Pete Dunkelberg

This view underscores why the traditional neo-Darwinian approaches to the origin of feathers . . . have failed. By emphasizing the reconstruction of a series of functionally and microevolutionarily plausible intermediate transitional states, neo-Darwinian approaches to the origin of feathers have failed to appropriately recognize the novel features of feather development and morphology, and have thus failed to adequately explain their origins.

— Prum and Brush

In conclusion, the model is testable, and has been corroborated by analyses from vastly different levels of analysis- paleontology and molecular development. I remain agnostic about the actual functions involved in the evolution and diversification of feathers because: (1) feathers actually evolved through a number of different stages each of which likely evolved for different of functional reasons, (2) because of the ambiguity in the fossil record (fossil feathers are rare!) we are not actually sure about the actual lineage in which feathers did originally evolve. So concluding WHY feathers evolved without having a clear view of which lineage they evolved in would be speculative.

— From the

As I understand ID and biologic reality, one would expect that all of the "information" for later development would already be present in the "initial" forms.

Why point out that you didn't answer question #2? You gave us something to have even more fun with:

— Steve

As I understand ID and biologic reality, one would expect that all of the "information" for later development would already be present in the "initial" forms.

— Pasquale Vuoso

That is extraordinary. Is the DI building any software to extract that information (presumably) from the genetic code? Do you realize the magnitude of that? Why, we could learn the entire future of life on this planet. This would be, inarguably, the greatest accomplishment in science. Please, please, tell Dembski to stop wasting his time arguing with us, and writing books for laymen, when he could be extracting this CSI.

— Steve

This has fundamentally been, and continues to be, my argument in favor of ID: it can get us to what we want to know more quickly. The caveat is, of course, can ID help science do this (decrypt) with the genome? Maybe yes, maybe no. But if working biologists never stop to ask these kinds of questions, then I guess we'll never know.

Is the DI building any software to extract that information (presumably) from the genetic code?

Genentech is working to extract all the information for the development of future forms of an organism, from the current organism? Can you show me anything which suggests they believe that nonsense?

All of this seems to be friendly language for IDers.

Am I to assume from these responses that "neo-Darwinists" now accept the fact that when we're dealing with living biological systems that it is, in fact, "engineered" realities that we are dealing with?

— Pasquale

his has fundamentally been, and continues to be, my argument in favor of ID: it can get us to what we want to know more quickly. [/quote Why? It shows how natural mechanisms are at play and show little evidence supporting ID's thesis, whatever that one may be. Well, what does "a macroevolutionary concept of novelty" mean? Does it mean that things just "show up"? That's what it sounds like to me; and that is what one might expect if evolution is a (Designed) computer program: i.e., a new "routine" has been added; again, with "nested" "subroutines" inside of it.

— Pasquale

Yes. As I understand ID and biologic reality, one would expect that all of the "information" for later development would already be present in the "initial" forms. This is a subtle point, and I don't want to get bogged down with it, but, in a nutshell, when the first "tubular follicle" appeared, it had to appear in a form that would permit later layers of forms (barbs, barb ridges and barbules)to develop.

— Pasquale

The only point I was trying to make was that Prum and Brush's article did not provide a mechanism of origin that would have adequately countered Meyer's assertions (perhaps---despite their protestation, the opposite may "peer" through).

— Pasquale

The "pertinent question": Would ID predict this?

— Pasquale

This puts into question the forcefulness of GME's criticism about Meyer not including this article in his paper.

— Pasquale

While we sit before our computers, companies like Genentech are doing exactly that. I wouldn't be so smug.

— Pasquale

Seems Pasquale is unfamiliar with Darwinian and Neo-Darwinian theory. In fact that there is design in nature is not the question, rather the nature of the designer. Darwin succesfully addressed the issue in a scientific manner and his theory has withstood many attacks and is by now well supported in evidence.

— PvM

In fact that there is design in nature is not the question, rather the nature of the designer.

— PvM

This is a subtle point, and I don't want to get bogged down with it, but, in a nutshell, when the first "tubular follicle" appeared, it had to appear in a form that would permit later layers of forms (barbs, barb ridges and barbules)to develop.

— I

The idea that the genome of the original ancestor(s) was preloaded with the information is scientifically unsupportable. Of course there is really no need to require this front loading. New information in the genome can arise quite naturally, contrary to the flawed arguments by Dembski.

— PvM

The tubular feather follicle and feather germ led to subsequent evolution of numerous additional morphological and developmental novelties. This complexity appears to have exploited an inherent capacity of the innovative tubular form of the feather follicle and feather germ. Future research on the evolution of feather keratin and the molecular mechanisms of feather morphogenesis will provide additional insights into the innovative nature of feathers.

Feathers are composed of a suite of evolutionary novelties that evolved by duplication (they don't mean gene duplication, but morphological duplication; my note; see the underline.), heirarchical organization, interaction, dissociation, and differentiation of morphological modules. The unique capacity for modular subdivisons of the tubular feather follicle and germ has fostered the evolution of numerous innovations that characterize feathers.

New information in the genome can arise quite naturally, contrary to the flawed arguments by Dembski.

— PvM

Ganfornina and Sánchez argue that any approach to co-option "by definition, has to be hypothetico-deductive." (p. 438) In other words, evolution by natural causes is assumed to be true, and inferences are then drawn from that assumption. As we noted in the first installment of our response to GME, it is philosophically legitimate to presuppose a theory as a guide to research, but this is not the same as providing evidence for the theory.

Pasquale wrote: This puts into question the forcefulness of GME's criticism about Meyer not including this article in his paper. THat's just absurd. The paper shows how testable hypothesis exist to explain the origin of novelty.

— PvM

If ID want to become scientifically relevant I suggest it submits its hypothesis of design.

— PvM

Again showing how ID is meaningless scientifically. But of course that should be self evident given the Meyer paper, the DIS response and the lack of testable hypotheses of ID. It's that simple. . . "

As I understand ID and biologic reality, one would expect that all of the "information" for later development would already be present in the "initial" forms.

Is the DI building any software to extract that information (presumably) from the genetic code?

While we sit before our computers, companies like Genentech are doing exactly that. I wouldn't be so smug.

Genentech is working to extract all the information for the development of future forms of an organism, from the current organism? Can you show me anything which suggests they believe that nonsense?

(I bet scientists will say a bunch of things which comport with evolution, I don't understand that, and I will take them as evidence of ID)

Genentech is working to extract all the information for the development of future forms of an organism, from the current organism? Can you show me anything which suggests they believe that nonsense?

— Steve

Pasquale - thanks for your posts. You aren't the only person who thinks this way!

[qutoe=a Creationist Troll]Pasquale - thanks for your posts. You aren't the only person who thinks this way!

I've read some of your posts and have appreciated them as well. My hope here is, of course, that all of us can dialogue ourselves forward. Let's face it, it isn't easy to change our way of thinking--and maybe that's a good thing, because otherwise we'd flit about too much. But as long as we can dialogue in good faith, with an openness to the truth, good things will happen.

I stand ready to be corrected. But I need to be persuaded, and need to try and persuade. A knowledgeable endpoint, seems to me, is what we should aim for. Ciao!

As written, this is in error. The argument is not over the nature of the "designer." The argument is whether there IS a "designer" or not. Now, I know what you mean to say, but it would have been better if you had written: "In fact that there is design in nature is not the question, rather it is the "source" of this "apparent" design. Logically, it seems to me that if you say that "design in nature" is "not the question," then you are conceding the presence of "design", and hence a Designer/designer.

— Pasquale

New information in the genome can arise quite naturally, contrary to the flawed arguments by Dembski.

— PvM

If this were so obvious, we'd probably not be having this discussion, but, per my discussion above, neo-Darwinism is not established as an "innovator", only as an "adaptor."

— Pasquale

THat's just absurd. The paper shows how testable hypothesis exist to explain the origin of novelty.

— PvM

IMHO, it does no such thing. It simply takes "one developmental novelty", and breaks it down to "five developmental novelties." Aren't "five times" MORE information now needed, i.e., how Stages I thru V came about? It is true that "five times fewer" intermediate forms are now needed; however, we likewise now need "five times as many" functions---one for each stage.

— Pasquale

The words "inherent capacity" imply, to my ear at least, an almost 'innate predisposition' to 'future devolopment': as if it could already "see" what was coming. That is what "designers" do. So, you can see why I think this "suggestive"

— Pasquale

Is this valuable work and information? Of course. But can this work be done more efficiently, more quickly? Yes, it can.

— Pasquale

Pasquale trying to show that he understands evolutionary theory writes: And, then, of course, there is Charles Darwin himself who tells us, "species will give rise to genera, genera to families, families to orders, and orders to classes." Well, where did the "species" that started all this come from? A "genera". Where did that "genera" come from? A "family". Where did the "family" come from . . . . and so forth. So, in sum, "classes" give rise to "classes." Doesn't that seem circular. It's your argument, please explain why decided to represent Darwin's work as such. I am looking forward to some references to Darwin's original work since your argument seems to be what is commonly known a strawman. I thought you understood Darwinian theory?

— PvM

(p.103, Origins of Species, "Oxford World Classics" [follows 2nd Edition]) I see no reason to limit the process of modification, as now explained, to the formation of genera alone. If, in the diagram, we suppose the amount of change, represented by each successive group of diverging lines to be great, the forms marked a14 to p14, those marked b14 and f14, and those marked o14 to m14, will form three very distinct genera. We shall also have two very distinct genera descended from (I), differing widely from the descendants of (A). These two groups of genera will thus form two distinct families, or orders, according to the amount of divergent modification supposed to be represented in the diagram. And the two new families, or orders, are descended from two species of the original genus, and these are supposed to be descended from some still more ancient and unknown form. (Elsewhere in the same Chapter) I shall have to return to this subject in the chapter on Classification, but I may add that as, according to this view, extremely few of the more ancient species have transmitted descendants to the present day, and, as all the descendants of the same species form a class, we can understand how it is that there exist so few classes in each main division of the animal and vegetable kingdoms.

— Charles Darwin

Although few of the most ancient species have left modified descendants' yet, at remote geological periods, the earth may have been almost as well peopled with species of many genera, families, orders, and classes, as at the present time.

— Darwin

I think he's explained it quite adequately, but I'll elaborate anyway. If common descent is true, there is only one correct phylogenetic tree for all living organisms. That tree represents the true genealogy of life. According to modern systematics, the correct way to construct taxonomic groups is to choose monophyletic groups, which means groups that consist of an ancestor and all of its descendents. Think of a monophlyetic group as a branch and all of the daughter branches and twigs that come off of it. If you leave off some of those daughter branches, then the group is no longer monophyletic, it's now paraphyletic. That's exactly what would happen to phylum Chordata if we declared Mammalia to be its own phylum. Suddenly, phylum Chordata would not include an ancestor and all of its descendents, because the mammals would be in their own phylum. And that's a big no-no. The problem in systematics is, when you have a large number of branches (every speciation creates a new branch point), then you have a massive number of possible monophyletic groups. So we have thousands (if not millions) of monophyletic groups when tracing any one lineage back to the earliest time. That raises a big question: which monophyletic groups should we recognize and give a name to? We can't do it for all of them, because they're way too many. The answer is that it doesn't matter -- the particular taxonomic groups that we've chosen, along with the names that we've given them, are completely arbitrary. We therefore choose them based on our communication needs, as well as tradition and history. We still recognize most of the groups invented by Linneaus, because those are the ones we're familiar with. Taxonomy is plagued, however, by what are known as "spitters and lumpers", people who keep creating new taxonomic categories in order to emphasize well-resolved groups above or below the more common taxonomic ranks. Those new groups aren't wrong, just as long they're monophyletic, but they're often needlessly confusing. So I hope you can see now that taxonomic groups are "real", in the sense of being monophyletic, but the particular group you choose to call "phylum" or "class" or whatever is itself entirely arbitrary. The problem we've been having is with your insistance that those groupings represent something beyond a mere convenience of communication, so that the specific rank they're in denotes some sort of actual quality about the group itself. The name means nothing. In reality, all taxonomic groups originated in the same way: speciation. It's only after long periods of evolution have passed, and many groups have diverged and become separate thanks to extinction, that we invent larger categories to denote a split that happened way back when. Grape Ape on ARN

— Grape Ape

Indeed. And science has identified the 'designer'. For the same reason teleology in nature is not really the issue. As Ayala and Ruse have argued, teleology is what is to be expected from mechanisms such as natural selection.

— PvM

I am not sure then why we are having this conversation since the new information in the genome can arise under well understood and natural circumstances such as variation and selection.

— PvM

It simply takes "one developmental novelty", and breaks it down to "five developmental novelties." Aren't "five times" MORE information now needed, i.e., how Stages I thru V came about? It is true that "five times fewer" intermediate forms are now needed; however, we likewise now need "five times as many" functions---one for each stage.

— Pasquale

Does Pasquale understand how ridiculous these assertions are? To claim that breaking down one giant step into five steps which can be tested somehow is less of an explanation. Mind boggling.

— PvM

To suggest that this teleology/design cannot be explained by evolutionary processes is one thing, to suggest that 'thus there is evidence of an intelligent design' remains totally unfounded in any mechanism, pathway, means, motive etc.

— PvM

In the last decade while ID has been claiming that the Cambrian explosion remains unexplicable under regularity and chance processes, real science has uncovered new cambrian and pre-cambrian fossiles, has uncovered fascinating evidence that links the developmental hox genes to the Cambrian explosion, has uncovered phylogenetic evidence that shows how the Cambrian explosion was preceeded by fascinating ground work.

— PvM

Although few of the most ancient species have left modified descendants' yet, at remote geological periods, the earth may have been almost as well peopled with species of many genera, families, orders, and classes, as at the present time.

— Charles Darwin

If you understood Darwinian theory you would realize that whenever a species arises, in order to name it as a species in the Linnaean tradition you have to specify its genus, family, order, class, phylum etc? In other words, above the species level, this hierarchy becomes quite artificial. Which is why Darwin focused on species which is the most relevant evolutionary concept anyway. It's this confusion between Linnaean ranking and phylogenetic trees or 'Tree of life' which leads creationsts to make claims about the Cambrian period and Darwinian so called 'predictions' which are fallacious.

— PvM

The concept of species is the only biologically real concept, the other concepts are merely categorizations on our part, sometimes leading to confusions of confusing these two concepts. For instance ID proponents have argued that phyla arrive before the lower classes, since a Linnaean hierarchy starts with a species and has to name its genus, family, class, phylum etc, a phylum will have to be automatically assigned to a species. It's not surprising that the branches arise before the leafs. But a Linnaean hierarchy should not be confused with a phylogeny.

— PvM

When "feathers" represented ONE "novelty", "neo-Darwinism" suggested that there was some "functional advantage" to having feathers; namely, "flight." It was because of the "selective pressure" for "flight", "neo-Darwinsism" would assert, that "feathers" developed. Alas, "neo-Darwinism" couldn't find a proper explanation for all of the "feather's" features. So, "neo-Darwinism" was abandoned, and a new "guiding paradigm" was chosen, namely, "developmentalism". Developmentalism enabled the "isolation" of five FUNDAMENTAL "novelties", the tubular follicle, the feather germ, the barb, etc. Now, if "neo-Darwinism" is to succeed, FIVE "new", and "different" functions have to be identified. This could be construed as an "advance" save for this uncomfortable problem: "neo-Darwinism" couldn't find any "intermediate forms" to provide a "pathway" from 'non-feathered' to 'feathered' forms, nor has it found 'intermediate forms' between the final 'form' of feathers used in flight, or, to be sure, these 'intermediate forms' would have been ballyhoed all over the article (By the way, I would have considered that a true advancement). So, if I'm not mistaken, without any kinds of 'intermediate forms', natural selection now has to explain how all FIVE of these "novelties" came about.

Normally when someone has your understanding of evolution, I recommend an introductory book on the subject, such as the excellent What Evolution Is:

(http://www.amazon.com/exec/obidos/tg/detail/-/0465044255/102-7995667-4756108?v=glance)

But in your case I have to add another book.

http://www.amazon.com/exec/obidos/tg/detail/-/020530902X/102-7995667-4756108?v=glance

I think a "mathematical argument" contra Darwin's thinking can be constructed. So, give me some time, and I'll get back to you.

— Pasquale Vuoso

Isn't this really what the argument is about? You feel that "novelty" is established through RM&NS, and I don't. I've investigated "proposed mechanisms", and can't find one that is convincing. This is really an independent "problem", if you will, than arguing ID.

— Pasquele

Although few of the most ancient species have left modified descendants' yet, at remote geological periods, the earth may have been almost as well peopled with species of many genera, families, orders, and classes, as at the present time.

— Darwin

Alas, this is not what the pre-Cambrian and post-Cambrian show. We see a build up of more "primitive" forms, and then an "explosion" of phyla, followed by "stasis." All of this is completely at odds with what Darwin would have "predicted." But nobody reads Origin of Species, and if they do, they just glide over these troubling aspects of his theory.

— Pasquale

Let's do a "mind experiment" (That's how Einstein worked) If you were a colleague of Einstein back in 1910, and he told you of some of his ideas, would you have said, "Oh, that's nonsense!" Twenty years ago, ID didn't exist. The only reason it "exists" nowadays is the discoveries that microbiologists have made, as well as the "information revolution", meaning computers and the rise of ways to "systematize" information, not to mention what is being learned about the genome itself.

— Pasquale

But it is precisely Darwin who has introduced "confusion." There's a logical fallacy present in this thinking. Darwin stands the "Linnaean System" on its head when he says that a "variety" is an "incipient species", and that "species" are really "varieties." Given what we know about Mendelian genetics (and unknown to Darwin), doesn't this seem wrong-headed? If one believes in "typology", then you don't have this "confusion" when it comes to the "Linnaean system."

— Pasquale

This is neither an "advance" nor an "explanation"; rather, it is a "concession" that "neo-Darwinism" is not up to the task of explaining the "origin" of the avian feather using "flight" as that which is being "selected for". The authors say as much in the article. They say using "neo-Darwinsim" has "failed", that it has "hindered" the discovery of the searched for explanation.

— Pasquale

I think a "mathematical argument" contra Darwin's thinking can be constructed.

he fully expected the same "number" of species then, as we "peeked" back in time, as we do now

— Pasquale

This is wrong when it comes to Darwin. Darwin explains common descent through modification. Common descent implies 1, or just a few, original life forms. Thus Darwin did not believe in an "eternal earth" but believes in a beginning. Also he did not believe that at any point of time in the past you should find the same number of species as you do today.

— Wayne Francis

The uniformitarians were, on the whole, disinclined to countenance the intrusion of strange or unknown forces into the universe. They eschewed final causes and all aspects of world creation, feeling like their master Hutton that such problems were confusing and beyond human reach. The uniformitarian school, in other words, is essentially a revolt against the Christian conception of time as limited and containing historic direction (interesting!), with supernatural intervention constantly immanent. Rather this philosophy involves the idea of the Newtonian machine, self-sustaining and forever operating on the same principles.

The world is made by nature to decay but it is also made to renew itself eternally.

— Eiseley

While I'm all for new ways of looking at things I can not apply this to ID because ID is basically just promoting the god of the gaps to fill in unknowns. The problem here is they don't explain anything.

— Wayne Francis

Here they started with a system that couldn't move without falling through a number of generations that evolved into the system walking.

— Wayne Francis

Strangely this is what I would classify God as. An entity that set up some basic rules and set the universe in motion to see what came about. I don't see the need for a designer to be creating genetic material.

— Wayne Francis

Normally when someone has your understanding of evolution, I recommend an introductory book on the subject, such as the excellent What Evolution Is:

— Steve

"Pasquale", "Let" us KNOW 'as' soon 'as' "you' get that MATHEMATICAL "disproof" of 'Darwinism'.

I feel that based upon the evidence it is too soon to claim that (neo)Darwinian theory which includes RM&NS is unable to explain novelty. In fact, evolutionary theory has presented much evidence to the contrary. Thus the ID enthusiast, lacking much of any scientific hypothesis of its own has to be argue in favor of insufficiency of regularity and chance processes.

— PvM

Various problems with Pasquale's arguments include: 1. Darwin's may become a 'must' 2. An oversimplified picture of pre- and post-Cambrian explosion. While stasis was definitely a feature in fossils, characterizing the Post-Cambrian as 'stasis' does not represent well the actual fossil record. 3. Pasquale argues that people do not read the Origin of Species. I encourage people to read and re-read this fascinating work since it is well reasoned ard argued and often quite a bit different for the stereotypical picture painted of Darwin.

— PvM

(Pasquale's numbering) 1) None of the discoveries that microbiologists have made nor the misnomer of 'information revolution' has given any support to ID as a scientifically viable contributor to science. 2) If your argument is that it needs another 10 years, fine, lets see if the second decade become more fruitful than the first. 3) Remember however that ID has proposed many ideas (NFL, CSI, LCI, IC) which have all shown to be fundamentally flawed. In addition ID has shown no interest to present its own hypothesis.

— PvM

(Pasquale's numbering) (1) The Linnaean hierarchy is a human invention, ad hoc and thus really unsuitable for the purposes it is being abused. (2) I am not sure what your comments about incipient species, varieties etc refer to but these are common concepts in taxonomy in which animals (subspecies) and plants (variety, form) are subdivided beyond the species level. (3) Since I fail to understand what Pasquale's argument or objection is to Darwin's incipient species/varieties argument, it is hard to address it but reading Darwin, his comments seem quite logical. How are his comments in conflict with Mendelian genetics?

— PvM

(p. 109) The fact of varieties of one species, when they range into the zone of habitation of other species, often acquiring in a very slight degree some of the characters of such species, accords with our view that species of all kinds are only well-marked and permanent varieties. (p.138)In these remarks we have referred to special parts or organs being still variable, because they have recently varied and thus come to differ; but we have also seen in the second chapter that the same principle applies to the whole individual; for in a district where many species of a genus are found- that is, where there has been much former variation and differentiation, or where the manufactory of new specific forms has been actively at work- in that district and amongst these species, we now find, on an average, most varieties or incipient species. (p. 333) In the second and fourth chapters, on Variation and on Natural Selection, I have attempted to show that within each country it is the widely ranging, the much diffused and common, that is the dominant species, belonging to the larger genera in each class, which vary most. The varieties, or incipient species, thus produced, ultimately become converted into new and distinct species; and these, on the principle of inheritance, tend to produce other new and dominant species.

(1) They also note why they consider neo-Darwinism as having failed. It's not that the explanation is at odds with neo-Darwinism, in fact they seem to argue that it is quite in line with neo-Darwinian theory but rather they argue that the Darwinian approach was unsuitable to unravel these issues and find the explanations. (2) Rather than rejecting Darwinism, the authors extend it with new tools. (3) I have seen some confusion among ID proponents when it comes to the realization that the argument is not against Neo-Darwinism but rather that Neo-Darwinism has focused on the wrong tools in some cases.

— PvM

The remarks at the end of my last post were not intended, nor directed towards PvM. Rather, they were directed to other posts that are out there, some responded to, others not.

My apologies to PvM that I didn't make this clear in my last post. It was quite late and I was a little tired.

what amounts to "hints" that he sees an almost "eternal" world.

— Pasquale

Darwin also believed (but this can be seen only implicitly in his writings) in an "eternal" earth

— Pasquale

self-sustaining and forever operating on the same principles.

The world is made by nature to decay but it is also made to renew itself eternally.

But if you don't "believe" in NS, as I don't, then you see the "problem" grow. "Believers" see the "gap" narrowed; but I see more "gaps" developing. Why? Because NS has never been able to demonstrate "intermediate forms." It's as simple as that. There will always be gaps in your view. If I showed you a human with 6 fingers next to a human with 5 fingers you'd probably ask where they human with 5.5 fingers are then say "AH HA! now you have to find a human with both 5.25 and 5.75 fingers if you find one with 5.5 fingers" What Prum and Brush also seem to be saying is that the "tubular" follicle that first emerges, i.e., Stage I, has already in place, i.e., an INHERENT CAPACITY, to "develop" ALL the "stages" that follow.

— Pasquale

Let me ask you: Based on what I just finished writing, who's invoking the "god of the gaps"? I'm saying that something happens to the genome via a mechanism which is not now apparent, but from which "development" flows. You say, "Oh, Natural Selection (notice I capitalized it in juxtaposition to the lower case "god"), little bit by little bit, got us from "here" to "there". How? What are the steps? Where are the forms demonstrating it? Let me predict: they'll never be found.

— Pasquale

Be careful. This was all done with the aid of "intelligence" via the "programmers" who "directed" the "program" towards a 'walking system.' This is right out of Chapter 3 of Blind Watchmaker where Dawkins would be happy to admit, we're not dealing with NS, but with Artificial Selection.

— Pasquale

If you've read Eisely's quote above, you'll see that this is right out of late 18th Century/early 19th Century scientific thought. Isn't it time to move on?

— Pasquale

I don't consider myself an ID enthusiast. Aren't you being a bit patronizing. I'm familiar with ID and agree with what I've become familiar with. But I've had problems with Darwinism ever since I read the Origins for the first time, back in 1985. Despite my studies, I find no published "mechanism" that I find satisfying. Let's remember, "peppered moths" are still "moths"; they're not "ants". And Darwins' "finches" never stopped being "finches." Where's "macroevolution"?

— Pasquale

As to #1, Michael Behe is a microbiologist and has argued, persuasively, that microbiological discoveries have made known a level of complexity heretofore completely unanticipated. (We've moved far beyond the "cytoplasm-is-nothing-but-gook" thinking that marked the time of the Origins )

— Pasquale

As to #2, yes, the complexity of the genome is immense, and only at such time as we begin to understand it better (remember how 98.5% of the genome was considered "junk"), nothing definitive can really be adduced. It could be five years; it could be 10; it could be longer. But I would start with an ID premise, rather than a NS one.

— Pasquale

As to #3, I recognize CSI, but can't decipher the rest. So, please help me out with those.

As to (3): It seems clear that what Darwin is saying is that a "variety" is some "middle-ground" between the "old" species and the "new" (incipient) species. Do you think that Mendelian genetics supports such a view? Is that what modern biology teaches? I think the answer to both questions is "no." (Remember, he's talking about age-old, documented VARIETIES.)

I wouldn't consider the Linnaean System "ad hoc". I don't know what your position is versus "cladistics", but the very systematized cladistics system, as far as I understand it, jives fairly well with the Linnaean. But, as you've stated, you'll get into that more on another post.

— Pasquale

For example, birds are now known to be the direct evolutionary descendents of small, predatory dinosaurs. The skeletal similarities between Mesozoic birds and coelurosaurian dinosaurs are remarkable, yet birds are not classified as reptiles because they have feathers. Feathers are the evolutionary novelty that define birds apart from reptiles. So, because dinosaurs lack feathers, they are grouped with crocodiles as reptiles, even though they are much more distantly related to crocodiles than they are to birds. Another example are the so called "mammal-like reptiles" a group of extinct animals that are defined on their lack of several key traits possessed by modern mammals. These animals are classified as reptiles because they appear to be at a reptilian grade of evolution (lacking inner ear bones, sprawling stance) even though they have only a distant evolutionary relationship to reptiles. In a sense, this is equivalent to taking a roomfull of people and determining which have the same last name based on how similar they appear. In some cases this will work just fine - appearance is related to familial descent - but it would also tend to result in all small children being grouped together (they are the same size and at a similar stage of development) and in some family members who happen to look different being assigned to separate groups. Another problem with a phenetic classification is that it imposes a hierarchy of discrete categories on an evolutionary history that is continuous. For example, an Order might contain twenty different Families. Assigning all twenty families to an order indicates that all twenty families are related by common descent, but it says nothing about the detailed relationships of descent among the twenty families. If ten of the families are very closely related such that they share a common ancestor, then to indicate this we have to make a new category between Order and Family, such as Superfamily or Suborder. Then, if we decide that five of the ten families are also related by a common ancestor, then we need yet another category. The terminology of classification quickly becomes cumbersome.

For what it's worth, I don't think that various people understand the problem that some of us have with evolution as a process. Going back to feathers, it is asserted that they have appeared by a ND process - and yet we don't see species with "partly formed" feathers or proto-feathers. It was accepted in the paper given above that no hopeful monster could statistically expect to go from no feathers to feathers in one generation - so the functionality of feathers was broken down into five steps. However, not only do we have no intermediates for each of the five steps, I don't believe we actually have species in which we see each of the five steps. Hence the proliferation of gaps. And yes, I agree with Pasquale, this has become an issue of faith. "We don't have any evidence of these gaps being filled - either in terms of intermediate species, or fossils, or possible genetic intermediate steps. But we believe that NS did it." Why? This is just as arbitrary as believing that God did it!

By the way, evolutionists really need to avoid going down the line of ad hominem arguments when the going gets tough - just keep on arguing persuasively and scientifically. You may be unhappy with the stylistic presentation of an argument, but considering the attempts at reformatting it were attempts to get you to understand what the issues are, I think it's a bit rich for you to grumble about the style when you consistently refuse to engage with the content. This isn't argument.

In the meantine .......

Are there any more subtantive deconstructions of the DI's paper responding to "Meyer's Hopeless Monster"? Or are DI basically right in their challenges thus far?

For what it's worth, I don't think that various people understand the problem that some of us have with evolution as a process. Going back to feathers, it is asserted that they have appeared by a ND process - and yet we don't see species with "partly formed" feathers or proto-feathers. It was accepted in the paper given above that no hopeful monster could statistically expect to go from no feathers to feathers in one generation - so the functionality of feathers was broken down into five steps. However, not only do we have no intermediates for each of the five steps, I don't believe we actually have species in which we see each of the five steps. Hence the proliferation of gaps. And yes, I agree with Pasquale, this has become an issue of faith. "We don't have any evidence of these gaps being filled - either in terms of intermediate species, or fossils, or possible genetic intermediate steps. But we believe that NS did it." Why? This is just as arbitrary as believing that God did it!

By the way, evolutionists really need to avoid going down the line of ad hominem arguments when the going gets tough - just keep on arguing persuasively and scientifically. You may be unhappy with the stylistic presentation of an argument, but considering the attempts at reformatting it were attempts to get you to understand what the issues are, I think it's a bit rich for you to grumble about the style when you consistently refuse to engage with the content. This isn't argument.

In the meantine .......

Are there any more subtantive deconstructions of the DI's paper responding to "Meyer's Hopeless Monster"? Or are DI basically right in their challenges thus far?

Are there any more subtantive deconstructions of the DI's paper responding to "Meyer's Hopeless Monster"? Or are DI basically right in their challenges thus far?

— Creationist Troll

For what it's worth, I don't think that various people understand the problem that some of us have with evolution as a process. Going back to feathers, it is asserted that they have appeared by a ND process - and yet we don't see species with "partly formed" feathers or proto-feathers.

Important support for the plausibility of the developmental model of the evolutionary history of feathers comes from extant feather diversity (Prum 1999). All the primitive feather morphologies proposed by the model exist among extant avian feathers.

— Prum

aCTa, Not only do we have a number of fossil specimens with feathers not cappable of flight we are, with every passing day, learning more and more about feathers at the cellular and molecular levels.

We've identified the gene, WNT, that causes feather, scales, hair, and other appendages forming from the epidermal epithelia layer. Scientist can cause scales on the feet of birds to be expressed as feathers. I.e. the genetic material responsible for growning scales is the same material for growing feathers. The difference is a slight change in how the genes are expressed. This all, not surprisingly, meshes well with NS, CD, RM, & GD. All ID can say is "The designer made the 2 genetic materials seperately and could not possibly allowed this to happen via NS, CD, RM, & GD" We might never know the cause of the mutation but we can reproduce the change and see the effects quite clearly.

Try reading
Molecular Biology of Feather Morphogenesis: A Testable Model for Evo-Devo Research
JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL) 298B:109--122 (2003)
to get a insight on the development and evolution of feathers.

Creationist Troll wrote:

Are there any more subtantive deconstructions of the DI's paper responding to "Meyer's Hopeless Monster"? Or are DI basically right in their challenges thus far?

Geez! How much more substantive do you want? If you're waiting for the DIS to concede they've ever been wrong on this (or anything else, for that matter) it ain't gonna happen.

"INHERENT CAPACITY"? you seem to have a problem with this. If someone is born with 6 fingers that person has "Inherent Capacity" to do things You can not. For instance they can play pieces on the piano that you physically can not. The "Inherent Capacity" for flight from primitive feathers is that at first the feathers where not used or even capable of use for flight but with further genetic modification the feathers could be adapted to be useful for flight. There is nothing saying that the genetic info used to create those primitive feathers had the information needed for feathers useful in flight. What we see are emergent properties. ie a function arising from a number of separate changes that isn't always directly apparent from the original functions.

— Wayne Francis

The 5 modern day equids are 5 different species. Via random mutation and genetic drift over the last 4 million years they have changed their genome a considerable amount. So much so that these 5 species can interbreed with different levels of viability. Lets look at just the chromosome level Grevy's have 46 chromosomes Plains Zebra's have 44 chromosomes Mountain Zebra's have 32 chromosomes Horses have 64 chromosomes donkeys have 62 chromosomes. all these species can interbreed with varying levels of success with almost all offspring being infertile. Just what Natural selection predicts. These 5 species isolated from one another built up numerous genetic changes over the last 4 million years. Some of these changes more of a problem, breeding wise, then others.

— Wayne Francis

First, the two genera can be sharply distinguished by features of the footbones, previously undiscovered. Mesohippus does not grade insensibly into Miohippus. . . . Second, Mesohippus does not evolve to Miohippus by insensible degrees of gradual transition. Rather, Miohippus arises by branching from a Mesohippus stock that continues to survive long afterward. . . Third, each genus is itself a bush of several related species, not a rung on a ladder. . . Fourth, the species of these bushes tend to arise with geological suddenness, and then to persist with little change for long periods. Evolutionary change occurs at the branch points themselves, and trends are not continous marches up ladders, but concatenations of increments achieved at nodes of branching on evolutionary bushes. Prothero and Shubin write, This is contray to the widely held myth about horse species as gradualistically varying parts of a continuum, with no real distinction between species. Throughout the history of horses, the species are well-marked and static over millions of years. At high resolution, the gradualistic picture of horse evolution becomes a complex bush of overlapping, closely related species. In other words, bushiness now pervades the entire phylogeny of horses.

Certainly Behe's 'findings' are hardly a shock to many. But Behe tried to argue, not very convincingly that this complexity showed a characteristic which he called IC which he argued was reliable evidence against Darwinian pathways (and thus in favor of ID).

— PvM

Darwin is explaining how variation in species is the foundation for sub-species/varieties to arise which can diverge and become new species. I am not sure why you believe this is against Mendelian genetics. Species evolve.

— PvM

Now all of these animals are in the Genus "Equus". Tell me, how did "one" species go from having 64 chromosomes (horses) to having 44 chromosomes (zebras)? Was it by "point mutations"?

— Pasquale

HSA 4 hybridized to horse 2q and 3q and to a single metacentric chromosome in both the donkey and the zebra. HSA 8 weakly hybridized along the length of horse chromosome 9 and to narrow pericentromeric regions on two metacentric zebra chromosomes. HSA 9 hybridized to horse chromosomes 23 and 25, to the p arm of a metacentric chromosome and to an acrocentric chromosome in the donkey, and to the pericentromeric regions of two metacentric zebra chromosomes. HSA 16 identified segments on horse chromosomes 3p and 13q, two acrocentric chromosomes in the donkey and two small regions on the p arms of two metacentric zebra chromosomes. HSA 21 hybridized to horse chromosome 28 and to a narrow distal region on the q arm of a metacentric zebra chromosome. From this preliminary data, these studies could provide data clarifying the types of complex rearrangements which have occurred during the rapid chromosomal evolution of the Equidae.

— CHROMOSOME EVOLUTION IN EQUIDS: ZOO-FISH STUDIES OF THE HORSE, DONKEY AND HARTMANN'S ZEBRA USING HUMAN, WHOLE CHROMOSOME PAINTS (Plant & Animal Genome V Conference P318)

And here's the tree...note that the timescale is a bit weird (e.g. the Oligocene is compressed almost to nothing) to keep it from being too long. All the names on the tree are genus names, so recall that each genus encompasses a cluster of closely related species.

Likewise, "infertility" is something that is not "beneficial to the organism"

— pasquale

I'm not an ID "enthusiast", but I agree completely with Behe and irreducible complexity. And I agree with ID. And I think that ID will have the "best" final answer. And . . . I hope someone takes it seriously and that it becomes a way to learn more about life.

— pasquale

And I think that ID will have the "best" final answer.

I think a "mathematical argument" contra Darwin's thinking can be constructed. So, give me some time, and I'll get back to you.

Pasquale: I think a "mathematical argument" contra Darwin's thinking can be constructed. So, give me some time, and I'll get back to you.

There are delusions of grandeur in this view of life. Is it likely that after a century and a half of the some of the best minds in science thinking - hard - about it, you're going to discover the mathematical argument that shows evolution impossible?

(Besides - Bill Dembski beat you to it!)

Russel: Shhhh!

I want to see what he comes up with.

Wait! I got it:

2 + 2 = evolution is a lie because I said so!

Sure 2+2=4. That's micro-addition. But nobody has ever added a trillion objects to a trillion objects to get 2 trillion objects! Macro-addition is a damned lie. Look, there's not enough time to add up a trillion objects because the universe is 6000 years old. 1 object per second, 3600 per hour, 28800 per workday, 7.5 million per year, equals 45 billion objects in 6000 years. So there's just not enough time. Anyway, macro-addition is really a religion. And satanic. And christianity has the best math theories. And also christianity is science, not religion. Also they explain every result in math. Math teachers suppress this in their journals. That's proof of censorship. They should Teach The Controversy.

I don't think you understand what he is saying. He's saying that what we consider a "species", he considers a "variety", and what we consider a "variety", he considers a "species." It's upside down "taxonomy." This is not in accord with Mendelian genetics because it doesn't jive with the Hardy-Weinberg Law of stasis.

— Pasquale

Hardy-Weinberg law of stasis? What Darwin is arguing that the dominant species will show natural varation which generates sub-species or varieties, eventually these varieties may become separate species.

— PvM

I understood that ID was *already* the best final answer. It is impervious to evidence, can't be disproved, is most wonderfully flattering to those whose beliefs require it, and provides nothing tangible to be grasped by anyone doing potentially hostile research. Who could ask for more?

— Flint

equids have gone through rapid chromosomal evolution during their speciation in the last 4 million years. Their common anscestor gave rise to more then the 5 existing species we see today but lets focus on them. The difference in chromosome count can occur through processes of fusion and duplication.

— Wayne Francis

As I see it, in the end there will be an explanation. The most "sensible" one will be something along ID.

The long war between science and religion.

http://cscs.umich.edu/~crshalizi/White/

Steve,
I hope you are being facetious with the Andrew Dickson White link. White's conflict thesis is widely acknowledged by modern historians of science to be simply wrong (see Science and Religion: A Historical Introduction, edited by Gary Ferngren, as a good place to start). White's A History of the Warfare of Science with Theology in Christendom helped to perpetuate many of the widespread myths about science and religion, like the idea that Columbus had to search far and wide for patrons free of the religious flat earth doctrine, as well as popular (but incorrect) ideas about the persecution of Galileo.

You can count on me not to provide 100-year-old analysis when modern scholarship is so much better. (And White wasn't considered particularly insightful among academics even back then) When I link to something like that, it's largely out of historical interest. I suppose I should have been more specific, and titled my post something like "An out of date look at the long, and very real, historical conflict between science and religion."
In the same way, I might link to something about Denis Gabor, or Mark Twain. But you can trust that I don't mean to suggest that Alpha Centauri is really only 25 trillion miles away, as Twain believed.
I like to see how ideas evolve. It's less satisfying to get all your info from precise, modern, up-to-date textbooks. You miss seeing the brutal struggle with the blurry and contradictory facts on the ground.

"My personal belief is that biologists tend to be uncompromising and reductionistic because they're still feeling somewhat insecure with their basic dogma, whereas physicists have three hundred years of secure foundation for their subject, so they can afford to be a bit more freewheeling in their speculation about these complex systems."

— Paul Davies

As is becoming abundantly clear to me, none of you know the difference between "Darwinism" and "neo-Darwinism."

— Pasquale

The "rescue" was based on theories concerning "point-mutations." Argue all you want about "chromosomal" this, and "chromosomal" that, but that's not what "neo-Darwinsim" (and, by extension, "Darwinism") hangs on.

— Pasquale

I think some unhelpful semantics that I tried to clear up way back is still here.
What does neo - darwinism mean? Nothing in particular. The term has been around since the 1890's I believe. The term is often used to contrast some portion of current evolutionary biology with the whole. Then one may triumphantly conclude "This portion is not the whole!" and make it sound impressive. No cigar from me. If your meaning is anything other than present evolutionary biology, without qualification, you are strawmaning.

Some here seem to think chromosomal evolution is newer than new, or something like that. I don't quite get the point, but there was enough material for M J D White to write a book on it in the 60's.

Flint still calls assumptions definitions, and says definitions are true by definition. Huh? By which definition? It is much healthier, not to mention correct, to say 'assumption' and 'assumed to be true' when these are what you mean. One important class of definition, the rule for usage of a new term using existing terms, is counted true by convention. Many other 'definitions' are descriptions, and are subject to being wrong in the ordinary way.

GWW, way back, displays atrocious manners toward Pasquale and ought to apologize. GW, surely you can restrain such outbursts.
TIA.

Pete:

I'll take a crack at this again. We may be close. I distinguish a definition from an assumption in a way that I consider essential. A definition is something true because we SAY it is true, and for no other reason. In my terminology, we define it as true. Perhaps a better word is an axiom; something taken as a given and not subject to question or investigation. An assumption as I conceptualize it is something subject to investigation and alteration. There can be false assumptions, there can NOT be false definitions. So assumptions can be corrected or improved; definitions can be accepted or rejected, depending on whether they are considered useful or not.

Perhaps your phrase "true by convention" matches my notion of a definition? So one adopts the convention or not. Conventions (definitions) lie outside the boundaries of observation, evidence, or investigation. They are arbitrary. The entire mindset behind Intelligent Design is conventional in this sense - life was designed because WE SAY it was designed. This claim is not subject to the scientific method or to the weight of evidence. ID was not derived from evidence in any way, and cannot be "disproved."

A description is most emphatically not a definition, as I understand it. Descriptions are observations, the very antithesis of definitions. A definition becomes true because we have decided to define it as true. Definitions are circular by nature. What's tricky (and I think confusing you, due to my inability to express myself well enough) is that SOME definitions sound like factual statements, subject to empirical methods. Indeed, two people can make identical statements, yet one is a definition and the other is a hypothesis. One way to tell the difference is to ask, "Under what hypothetical circumstances would you agree that you were wrong?" If the statement is a definition (a convention?), there are no such circumstances.

GWW, way back, displays atrocious manners toward Pasquale and ought to apologize. GW, surely you can restrain such outbursts.

Perhaps a better word [for what I mean by 'definition'] is an axiom....

— Flint

Pete:

OK, It's harder than it looks to straighten these things out. As I hope I've communicated, I've been talking about statements based on preference rather than evidence, which cannot be argued against on the basis of any amount of evidence, and which must be changed (if possible) only by appeal to a change in the preferences of whoever finds the statement useful.

And I hope also that I've communicated that people making the same statement can nonetheless have made it on entirely different bases - one because he prefers to believe it's true, and the other because he considers it best supported by evidence. And so the statement's validity can be altered (in the mind of who made it) in the first instance by changing someone's preferences, and in the second instance by presenting new evidence or a new interpretation of existing evidence.

And so there is a qualitative difference between the two syntactically identical statements, depending on WHY those positions are adopted. "Macroevolution" to one person does not happen because his interpretation of religious doctrine tells him it does not happen. What it MEANS doesn't really have much to do with the degree to which life forms have diverged from a common ancestor over time, etc. Instead, its meaning is more in the nature of a switch or litmus test -- those who "believe in" macroevolution belong to the atheistic humanism religion (a false faith), those who know better are "true Christians." Another way of putting it is, if someone regards their personal interpretation of scripture as Absolute Truth, and their visualization of reality cannot tolerate certain doubts, "macroevolution" becomes something in conflict with a commitment to a given interpretation of scripture, and which must therefore be rejected. In my shorthand, I think of them as having defined macroevolution as wrong.

Intelligent Design isn't an explanation of the origin of anything, nor is it based on any kind of methodological exploration of the objective universe. It is a statement of preference. It becomes true in the minds of those who for some reason need it to be true, and will be considered unimpeachable until those needs change. Perhaps I've been using the wrong semantics in saying that such people define it as true? For them, it is true a priori.

I appreciate your feedback on this, because I consider it worth addressing. A great deal of effort is expended here attempting to correct statements which are wrong in fact, but true by preference for those who make them. And as we've all been seeing for a long time, no amount of factual correction changes strong preferences. Preferences are not based on facts.