The DI Strikes Back

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True to their word, the DI staff has begun their rebuttal to Gishlick et al.’s PT critique of Meyer’s 2004 paper in PBSW. The DI reply is entitled “Neo-Darwinism’s Unsolved Problem of the Origin of Morphological Novelty.” For a history and (almost) comprehensive links, see The “Meyer 2004” Medley.

Rather than responding in this initial post, let me recommend a strategy for those of us that might wish to make a few counterpoints to the DI (after you’ve finished repairing your irony meters). Folks may follow these recommendations or not as this is something of an experiment.

If you are itching to comment on a particular point on the DI page, then give your comment a title (using bold tags: [bold]text[/bold] with “b” instead of “bold”) indicating what it is about. Then continue with your comment on that topic. If you comment on another topic, give it another title.

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.

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. If a fair number of people do this, we will end up with a point-by-point critique (that might end up as e.g. a talkorigins FAQ) much faster than one person can write something. I’ll post an example in the comments to start it off.

Like I said, this is an experiment, but hey, this is the blogosphere, right?

114 Comments

Unclear on the Concept 2

The semi-anonymous “Fellows of the Center for Science and Culture” do seem to have a problem with the concept of science.

In their “rebuttal” piece they write

FOTCFSAC Wrote:

“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. “

To paraphrase The Princess Bride; “That word, it doesn’t mean what you think it means.”

The hypothetico-deductive method is one of the core scientific methods (see Karl Popper, The Logic of Scientific Discovery). Ganfornina and Sánchez have just said they are going to study co-option scientifically, the exact opposite of what FOTCFSAC claim.

If FOTCFSAC don’t understand a core part of science, then why should we give any of their critique any credibility at all?

Ian, you need to provide the context of Ganfornina and Sánchez’s statement. They mean exactly what the DI quotes them to be saying, namely, ‘we [G & S] are going to assume common descent via natural causes (e.g., cooption) and will see what follows from that.’ G & S explicitly contrast their approach (i.e., method) with experimental approaches.

Here’s the context:

…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)

Maria D. Ganfornina and Diego Sánchez, “Generation of evolutionary novelty by functional shift,” BioEssays 21 (1999):432-439; p. 438.

The DI said the hypothetico-deductive method was “legitimate,” not unscientific. But 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.

Paul, far from me to go head-to-head with a philosopher of science about this, but it seems to me that G&S are clearly not saying, as claimed by FOTDICF(R)S&C, that “evolution by natural causes is assumed to be true, and inferences are then drawn from that assumption”. Rather, they are saying - true to the hypothetical-deductive method - that if evolution by natural selection etc. is true (hypothesis), then certain empirically verifiable predictions must hold (deduction).

Furthermore, it is also patently not true that

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.

On the contrary, the hypothetico-deductive method, by “working out the logical implications” of a hypothesis, goes to the core of its falsifiability.

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.

That’s a good idea, and I hope it’s successful.

Assuming that something is true, drawing inferences from the assumption, and then testing those inferences, is a core idea of science. An assumption, as it is being used by Ganfornina and Sanchez, is an hypothesis, which is the starting point of scientific investigation.

As with many words in this debate over ID (including the word “debate” - see here), there are two meaning of assumption being confused here (or less charitably, deliberately conflated.)

The first is the way I am describing here: a statement tentatively accepted as true in order to deduce testable inferences – “hence “hypothetico-deductive.” This is the scientific meaning of the word.

The second is the way the FOTCFSAC (pronounced “fotz-sack,” with a silent “p” in the middle?) are using the word: as a postulate which is assumed to be self-evidently true and from which, then, other statements can be declared also true. This is more the mathematical meaning of the word.

In his talks at various conferences (such as Design, Darwin and Democracy V in New Mexico recently), Paul Nelson commonly makes the argument that he does here:

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.

But common descent is a testable, and tested, assumption. It is not a dogmatically held postulate, as the IDists insist, but rather a conclusion the scientific world has come to after decades of investigation. Alternative assumptions about other means by which species might have come into existence have also been on the table for testing. In fact, special creation was the assumption (and for many remain a postulate) as scientists started exploring evolution, and scientists at this point have decided that the evidence supports common descent and not some form of biological discontinuity between species.

(My browser wouldn’t post this last night, but I too picked up on the hypothetico-deductive weirdness. So here are some comments following my proposed example.)

The Hypothetico-deductive method and cooption

In one of the many jaw-dropping statements contained in the DI staff’s reply to Meyer’s Hopeless monster, they write,

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.

In a remarkably Wellsian fashion, here several subtle slants are imposed on the truth at once and mixed together into a toxic brew. These slants are:

  • The hypothetico-deductive method assumes “evolution by natural causes”
  • This is a scandalous insertion of naturalism into science by those dogmatic Darwinists
  • This assumption is then used to prop up the theory of evolution instead of evidence
  • In fact, all of this hypothetico-deductive stuff is “largely irrelevant” when determining the truth or falsity of the theory of evolution

In order,

  • In fact, the hypothetico-deductive method is better known as “the scientific method” and is more-or-less what gets taught in the introductory chapters of textbooks in many fields. To the extent that actual scientists frame their work self-consciously (a good bit of science is just puttering along, describing things and working out bugs), they usually frame it in terms of hypothesis-prediction-test. In the hypothetico-deductive method, one devises a hypothesis, preferably based on some data already available, and then one goes and gathers more data to test it, and then one evaluates the hypothesis and repeats. In the case of Ganfornina and Sánchez, the authors have two very specific hypotheses in mind, not just the vague “evolution by natural causes” that the DI implies. These hypotheses are based on their review of cooption (which happens in the six pages of their article before page 438), and they are (1) duplication followed by cooption, resulting in functional divergence of elements (genes or body parts) and (2) cooption followed by duplication, resulting in divergence of elements. Strangely, Meyer 2004, putatively a review and critique of evolutionary mechanisms, for some reason only briefly discusses duplication, and cooption is never discussed explicitly at all. When duplication is brought up (for genes only, even though structures often duplicate also), Meyer assumes duplication-first. Thus Meyer discusses hypothesis #1 only in a vague way and hypothesis #2 not at all, even though it is probably of equal importance. Among the important points brought forward by hypothesis #2 is that elements can be multifunctional, with only later divergence and specialization resulting in distinct functions. The discussion in Meyer (2004) throughout assumes a ludicrously oversimple one-element-one-function view of biology. This sort of biology-free view of the world is the kind of problem that is endemic in Meyer’s paper, and this is one of the reasons we cited Ganfornina and Sánchez’s paper. Another reason we cited Ganfornina and Sánchez’s paper is that they sketch the long scientific history of cooption, right back to Darwin himself, who gave several examples(see here).

  • There is nothing naturalistic about the hypothetico-deductive method. ID advocates could, if free from religio-political constraints, easily apply it to ID theory, if they could put forward an actual specific hypothesis about the ID “specifically causal theory” (Meyer 2004) and derive predictions about what we would expect to see in the natural world. Of course, essentially all prominent ID advocates think the “intelligent designer” is God, and apart from God being a notoriously difficult fellow to pin down and get biological predictions out of, ID advocates are too afraid of the Supreme Court and the First Amendment to say what they really think in their “scientific” publications. If they really had no interests in public schools they wouldn’t be worrying about this and could put whatever specific theological hypotheses they have forward. A much bolder approach has been taken by PT’s own Richard Hoppe, who has worked out Multiple Designer Theory in considerable detail based on a straightforward extrapolation of the fact that the obvious purpose of a biological design is usually the subversion or defeat of some other biological design.

  • The DI staff manages to dismiss the dozens of studies of cooption cited by Ganfornina and Sánchez as being merely “post hoc” and “comparative.” Apparently the DI thinks that unless all of evolution happens in modern times right in front of their eyes, they can dispense with any evidence that evolution happened with a dismissive wave. Why do the various genes mentioned by Ganfornina and Sánchez, such as the hox genes, share statistically significant similarity? Why do they fall into statistically neat phylogenies? Evolution explains statistically significant sequence similarity as being due to common ancestry from an ancestral gene. Intelligent Design basically doesn’t have an explanation for sequence similarity – neither Meyer 2004 nor the DI response provide an explanation. When pressed, IDists will sometimes speculate that the sequence similarity may have functional reasons, but they never deal with the massive counterevidence (such as the same function being carried out by analogous unrelated proteins, or closely related proteins carrying out drastically difference functions). As with so much of ID, they seem to mostly operate on the hope that no one will notice the gaping holes in their arguments.

    Furthermore, Meyer and his colleagues consistently ignore just how the hypothetico-deductive method can work with an evolutionary explanation such as cooption. For example, John Maynard Smith wrote in his book The Theory of Evolution (3rd edition 1993, and this passage probably occurs in the 1958 1st edition),

    It often seems that a perfected organ, although efficient at performing its function, is far too complex to have arisen by one or a few mutations, and yet is such that any intermediate stage between the absence of the organ and its full development would be incapable of performing this function. Thus it is inconceivable that the flight feathers of a bird could have arisen by a single mutation, but the intermediate stages between a scale and a feather would be useless for flight. In this case the difficulty disappears once it is realized that during the early stages of the evolution of feathers, the latter were probably of selective advantage because they conserved heat, and only later did they become functional in flight.

    This is a very common feature of evolution; a new structure evolves at first because it confers advantage by performing one function, but in time it reaches a threshold beyond which it can effectively perform a different function. […]

    (Maynard Smith, John (1993 [1958]). The Theory of Evolution. Third edition, Canto. pp. 303-304.)

    This was written long before any of the feathered dinosaurs were found. But in the late 1990’s a vertiable bestiary of nonflying, but feathered, dinosaurs have been discovered in China. Just last week a new article reported the discovery of protofeathers on a basal tyrannosaurid. Apart from the broad prediction that flying feathers were preceded by nonflying feathers, feathers on tyrannosaurids were specifically predicted based on their phylogenetic position.

  • Finally, the DI staff says, “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.” This is so obviously wrong it’s almost impossible to imagine why they said this. In the interests of thoroughness, however, the way one figures out the truth or falsity of a theory is by working out the logical implications and then testing them. As we’ve seen, cooption has been a major explanation for the origin of novelty ever since Darwin. It was cited prominently by Mayr and many other eminent 20th-century biologists. If one reads the work of developmental biologists that criticize the incompleteness of “neo-Darwinism” in the narrow sense (meaning basically just population genetics, but the IDists never clarify this for their readers) – and these are the authors that Meyer is so fond of citing – one finds that cooption is, if anything, a more important factor than in “neo-Darwinian” (broad sense) evolutionary theory. If Meyer really was serious about critiquing evolutionary theory’s explanations for the origin of morphological novelty, he should have spent a good chunk of his essay on cooption, rather than sideshows like punctuated equilibria or Kauffman’s complexity theory.

Unfortunately, this post shows that a paragraph of ID spin can take about a page to unravel. It is worth responding to at least the major claims, however it is much better for readers to look up the original papers themselves. Usually the pdfs are available on the web (follow the PubMed links) and/or through university subscriptions, and if you can’t get access via those routes you can often email the author who cited the paper for a copy.

Reference

Ganfornina MD, Sanchez D. (1999) “Generation of evolutionary novelty by functional shift.” Bioessays. 21(5):432-9. URL: http://www.ncbi.nlm.nih.gov/entrez/[…]ids=10376014

“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.

Valentine and the origin of phyla

From the DI Staff (DIS)

DIS Wrote:

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.”

I have recently bought Valentine’s book and the impression I get from reading it is quite a bit different.

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.

Leave it up to DIS to appeal to the typical argument from ignorance, namely that neo-Darwinism cannot explain the origin of phyla based on Valentine’s observation that no satisfactory accounts exist or that underlying causes remain uncertain. Valentine’s extensive book counts over 500 pages in which he discusses in great depth the fossil evidence, and the genetic evidence all of which seem to support evolutionary theory. More importantly DIS presents no competing hypothesis of ID to explain the Cambrian phyla. Using the common DIS ‘logic’ one could thus conclude that this lack of ID hypotheses to explain the Cambrian Explosion should be duly noted and can be seen as evidence that ID cannot explain Cambrian phyla.

I am beginning to understand why the DIS refers to the authors of the Meyer critique as members of the Militant Darwinist organization. Ad hominems may be the only way to save Meyer’s paper from scientific embarassment.

“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.”

Let’s ignore for a moment that this is stupid and wrong. I haven’t read Ganfornina and Sánchez’s article, but could it be that they were trying to study co-option? Not prove the truth of evolution? What scientists go around trying to prove evolution anymore? About as many as try to prove heliocentrism. If you were going to study perturbations in Mercury’s orbit, heliocentrism would rightfully be an assumption. G&S can’t be accused of assuming their conclusion, if ‘evolution is correct’ is not their conclusion.

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.

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

Meyer’s main question is:

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)

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 2) ID provides for a new and specifically causal theory which explains the origination of biological form.

Limited view: genetic v epigenetic

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.

If all Meyer argues that origin of body plans is not fully understood then his argument has little merrit other than to exemplify how ID relies on ignorance to draw its often hasty conclusion. If genes cannot generate this higher level information and structure, how does ID explain the origin of body plans? Is there information beyond that found in genes which is somehow relevant? What other variations does ID have in mind that would explain the origin of body plans?

A new ‘causal theory’? Nope, ID presents nothing relevant that could be construed as a causal theory, let alone a hypothesis.

Meyer does not seem to believe that genetics or epigenetics resolve the issue

Origin of information

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

If the argument is that evolutionary mechanisms cannot genereate information (another negative argument, contradicted by fact) then it should be once again noted that ID does not present ANY hypothesis to explain the origin of information.


Scientific resources to information/complexity and the genome

Evolution of complex information T. Schneider Nucleic Acids Res 28(14) 2000 2794-2799

Adami and biological complexity

The evolutionary origin of complex features. Lenski, R. E., C. Ofria, R. T. Pennock, and C. Adami. 2003. Nature 423:139-144

Steve and others: At issue was the fact that G&S was cited by GME as a paper that demonstrated that evolution can produce new morphologies, viz:

(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

The point that the DI response makes is that G&S in their paper are assuming that evolution produces new morphologies - and indeed, are proposing future research to establish the validity of these assumptions:

(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.

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

So to me that looks like one point to DI. How about we lay that sidetrack to rest and look for a better one (to mix metaphors)?

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.

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.

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

Also, the Meyer paper does mention areas of epigenetic information:

(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

Your final objection is that

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.

“Well, … it was unlikely he died of flu, but he didn’t die of smallpox either, so he must have died from flu.” Sorry.

Prum and Brush: THE EVOLUTIONARY ORIGIN AND DIVERSIFICATION OF FEATHERS

DIS claims that Prum and Brush argue against Neo-Darwinism, when in fact they are arguing against Neo-darwinian approaches to resolve the evolutionary history of the feather

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.

The Quote Mine

The puzzle of feathers is unsolved, they argue, because of “conceptual problems faced by macroevolutionary biology.” (p. 262)

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.

* Neo-Darwinism (their term) tries to dissolve all morphological novelties into a microevolutionary continuum from some earlier structure. But “genuine evolutionary novelties are distinct from simple microevolutionary changes in that they are qualitatively or categorically different from any antecedent… structure.” (p. 265)

Followed by

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).

Are DIS arguing for a synthesis ala evo-devo? They are a bit late.…

“This failure reveals an inherent weakness of neo-Darwinian attempts to synthesize micro and macroevolution.” (p. 289)

Indeed, functional approaches are considered circular by Prum and Brush but they continue to present an independent hypothesis which they consequently use to support functional hypotheses

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.

For Prum and Brush, change-of-function is an inherently weak approach: “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) Clearly, Prum and Brush do not think that the origin of feathers can be explained by change-of-function.

A misunderstanding of the argument. Prum and Brush argue that change of function has so far been a circular argument, their approach however resolves this complication. It’s not that they do not believe that change of function did not happen but rather that the neo-darwinian approach is unable to support such pathways.

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.

It seems obvious that Prum et al are not objecting to change of function perse but are arguing that such evidence may be tricky to obtain.

Of course, Prum and Brush do go on to assert that natural selection was responsible for the origin of feathers. But they offer no evidence in support of this assertion, only a sketch of the kind of events that “must have” happened in order for feathers to have arisen.

So in other words Prum and Brush do propose a causal theory to explain the origin of feathers. That Prum et al refuse to speculate as to the details of selective pressures given the historical intractability should not be seen as a rejection of their ideas. Let’s compare Prum and Brush’s hypothesis with ID’s hypothesis… Oops I forgot, there is none. But let’s see what Brush et al really did:

A causal theory of origins of feathers

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.

In other words Prum and Brush have formulated a hypothesis of feather evolution which is independent of phylogenetic and functional assumptions. The next step is to test the hypothesis. Of course ID has to object to such scientific approaches since it fails to have any testable hypotheses of its own.

Supporting evidence

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.

Not bad…

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).

even better…

And then

Functional Explanations Reconsidered

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?

One functional hypothesis bites the dust

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

Another one survives

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

Selective advantages

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.

Congruency

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.

Functional theories again

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.

Evolution of novelty and feathers

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…

Duplications and alterations of processes

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.

Duplication and divergence

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.

Conclusions

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).

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.

THE EVOLUTIONARY ORIGIN AND DIVERSIFICATION OF FEATHERS Prum and Brush, The Quarterly Review of Biology Volume 77, No. 3 September 2002

Shifting goalposts

Creationist troll Wrote:

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

versus

GME Wrote:

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

Note the subtle difference between ‘evolution cannot produce new morphologies’ versus ‘evolution produces new morphologies’

In other words, the DIS has changed the argument to a strawman arguing that GME stated that

DIS Wrote:

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

arguing

(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

(I) is irrelevant, that it is unresolved does not mean that neo-Darwinism cannot explain new forms and body plans or that a new causal theory is needed. What is needed is a synthesis between evolutionary theory and development (evo-devo) to unravel the evolutionary history. In their eagerness, DIS confuses the failure of Neo-Darwinism’s approaches with a failure of Neo-Darwinism (see for instance the feathers paper)

(II) is a strawman of the original claim by 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:”

(III) is irrelevant, as it seems to ignore those papers which do propose Neo-Darwinian/evolutionary explanations.

Of course none of the DIS’s objections really addresses the obvious lack of any causal theory of ID, let alone any ID relevant hypotheses.

Creationist troll Wrote:

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.

But it is a sound argument. First of all there ARE explanations for the origin of novelty, etc. DIS seems to be arguing that these explanations are non-Neo-Darwinian, and even if we were to accept their misinterpretation of the statements made by scientists arguing that neo-Darwinian approaches failed not the theory itself, we have conclude that there do exist evolutionary explanations. As such, the typical ID approach of arguments from ignorance fail to support either the eliminative approach as well as the best explanation approach. The latter fails because ID has failed to present ANY ID releveant hypothesis for comparisson

Creationist troll Wrote:

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

If it were a review paper then it did miss some relevant papers in its review, focusing mainly on the negative argument. Compare Meyer’s so called review paper with Prum and Brush’s paper in “The Quarterly review of Biology”.

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.

An unsupported assertion that seems to indicate a retreat. It’s those evil evolutionists who caused the what I see as a poor quality review paper in that it does NOT present a complete review.

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.”

I am glad you realize that ID’s approach is fallacious and no I am not arguing your strawman.

Creationist troll Wrote:

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.

It is obvious that Meyer did NOT make his case that Darwinian/evolutionary theory cannot explain the origination of biological form. In fact, as I have shown, the DIS response serves to strengthen my conclusions since they are now spinning their own strawman.

And remember it was Meyer who asked “Is a new and specifically causal theory needed to explain the origination of biological form?”. Certainly he may think so but he fails to present any and does a poor job at arguing that a ‘new theory’ is needed, especially a new theory which is non-Darwinian.

Creationist Troll Wrote:

“Well, … it was unlikely he died of flu, but he didn’t die of smallpox either, so he must have died from flu.” Sorry.

Good lord, do you have any idea how ironic this statement is? Meyer’s entire argument comes down to this: “The accepted theory is that he died of the flu, but there are a few oddities that the flu theory can’t explain. Therefore, he died of smallpox. Even though we have no evidence that smallpox was present in this particular death, we’ve seen smallpox kill people before, so we know the smallpox theory is causally adequate.” I don’t think anyone needs to be a logician to see what’s wrong with this reasoning. One can take issue either with 1) the premise which states that the flu theory can’t explain the death, or 2) the illogical jump to the smallpox theory, the proclaimed evidence for which consists of nothing more than arguments against the flu theory. Clearly, both criticisms are sound.

Valentine and the origin of phyla (2)

From the DI Staff (DIS) (remember that they are arguing that origin of phyla etc is at odds with (Neo-)Darwinian theory:

DIS Wrote:

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.”

From the Preface of “On the origin of Phyla”, Valentine 2004

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.

Valentine and CSI

Unresolved issue

Meyer2004 Wrote:

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.)

From the paper

Valentine 1995 Wrote:

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 Wrote:

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

Compare this with

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

Why did Meyer quote Valentine?

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

Co-option hypothesis

DIS Wrote:

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

I thought the argument was that neo-Darwinian theory cannot explain novelty, now the objection is that it is hypothetical. Does the DIS even understand the meaning of science?

True and Carroll on co-option

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).)

DIS Wrote:

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.”

I wish I had the paper since this sounds like another wishful interpretation by DIS.

Where is that ID hypothesis again, you know this ‘new causal theory’? Or was it ‘casual’..

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.

Wayne Francis Wrote:

“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.

I don’t have time to be posting night and day, so I’m going to just point out a couple of things and get back to some serious reading.

Having said that, while I agree with you that it is unclear–we just don’t know enough yet–if ALL the “information” needed for the avian feathers is there from the beginning–nonetheless, what is suggestive is that the feather continues to be a “tubular” structure, meaning that the germs, barbs, barbules, etc, are ALL “tubular” in nature. Of course, this would be needed for “flight.” Now in Aristotlean philosophy, the “final cause” is apparent ‘from the beginning.’ That is, no one starts out to build a house and ends up skating rink–the “goal” is present throughout. This is “suggested” by what Prum and Brush write–though not intended that way by them. I’m not going to press it any further than that.

Now, in a later post:

Wayne Francis Wrote:

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.

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”?

Here’s what Stephen J. Gould has to say about “Equus” in Full House:

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.

Maybe you can find a better chart.

PvM Wrote:

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).

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.

PvM Wrote:

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.

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. Alleles move around, but there’s a “conservation” law: alleles neither increase, nor decrease in a population from one generation to another. We know “varieties” are blends, and that the “true” species is not the variety. We know that rather well. After all, we still don’t have a “blue” rose. But Darwin saw it otherwise.

Now, it’s easy to read him quickly, and to correct his thinking as you go along; but his thinking is just plain wrong based on what we now know about genetics.

To buttress my point, notice that Darwin “firmly” argued AGAINST “infertility.” Infertility is an argument–per Darwin–that goes against his Theory. It is an argument against his theory because if, as naturalists of his day (and to this day) believed, “varieties” become “infertile,” then “varieties” can’t be the “progenitors” of “future species.” Likewise, “infertility” is something that is not “beneficial to the organism” (since, from Darwin’s point of view, “vigor” is the true sign of “true” species.) And, so, Darwin, with an argument that is really weak (but necessary for this theory to survive), says that, basically, “infertility” is an ‘illusion.’ It’s not really like that. We don’t know enough. There are these funny things that happen, and when we really study it, we’ll find that “infertility” is due to something else (for Darwin, it had something to do with “reproductive organs.”)

Does anyone today seriously say that “infertility” amongst “varieties” doesn’t exist?

Thanks, by the way, for the “deciphering.” I was familiar with all of them–once decoded–except for NFL. Now I’ve read something about it–a sentence or two, here or there, but will have to go see what Dembski means by that. Doesn’t he have a book coming out, or recently published, with that title? He gives you a headache when you read him!

By the way, I’m off the “boards/posts”, and onto some serious reading. Adieu.

Pasquale Wrote:

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”?

Why are you using the common horse as the base line? Their common anscestor is where you need to go from and we can trace the changes that this line has undergone.

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. You might not like the idea but thats about the difference between humans and chimps. Humans had 2 chromosome fuse where chimps did not. Chromosomal painting shows this picture clear as day.…if you don’t want to look at the picture thats fine but its still there. Back to the Equid line.

I’ll just pull one paper that goes into this .… there are more

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) Wrote:

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.

Stephen J. Gould comments on this does not, in ANY way, conflict with evolution. Gould is just refering to PE. If you look at the horse development you can see different changes going on at the same time. Adaptations like changes in teeth to deal with eating tougher grasses in a new open terrian from the woodland areas they inhabited before. Along with this change in teeth other mutations occured and helped member survive longer thus breeding more such as longer legs and adaptation to the feet for faster running.

The chart I provide doesn’t contradict what Gould says. The “Bushieness” is there. The chart gets updated as new information come forth such as finding a fossil that date younger or older then the points that species was thought to lived. Cross breeding will also cause some interesting developments but I imagine you wouldn’t be happy until you had a chart showing every single equid that ever lived and their relationships to others.

If you look at the article you would read this.

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.

So I’m left once agian wondering what you are reading in between the lines because the words are not actually in conflict. I love it when IDers try to use Gould as a scientist agianst evolution.

pasquale Wrote:

Likewise, “infertility” is something that is not “beneficial to the organism”

Yes and being homosexual is not beneficial to an organism when it comes to reproduction. So if tendancy to homosexuallity was a genetic trait you might think that it would kill itself out wouldn’t you. But many conservative Christians, and others, think it just some individual being perverse etc. Low and behold with genetic studies we’ve found a genes linked to homosexuality in men. How can this be! Surely they would not propergate that gene and thus it would die out. Well well further study shows the genes are passed down through the maternal line. I.e. if your a gay male it might be your moms fault. The genes seem to increase an individuals attraction to males. In women this is expressed via a hyper-heterosexuality. Studies show that mothers of gay men have on average 2.7 children compaired to the those without gay sons at 2.3 So we have a complex situation here where a genetic trait seems to be detrimental to a member but still survives just fine. Hmmm JUST what natural selection would predict when you get the whole picture.

This might be painful for you .… If you question your sexuality ask your mom if she’s a nympho. If she is there might be a genetic cause to your sexual confusion.

If a genetic trait is detrimental to an individual doesn’t mean that same trait doesn’t have a overall positive effect on the genetic line.

pasquale Wrote:

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.

And IDers like Behe don’t claim to be creationist but when they belong to institutions that mandate you must take a literal interpretation of the scripture you can add 1 and 1 together and get 2

Until ID get an asnwer they can’t get a “best” final answer.

Pasquale, I’m still confused why you think companies like Genentech don’t believe in evolutionary biology. Genentech actively promotes these mainstream theories.

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

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?

Pasquale said:

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

Done with that yet Pasquale?

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.

Pasquale Wrote:

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.

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 Wrote:

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.

Pim, you’re simply “correcting” Darwin. (Which is natural since he takes a position that is so contrary to what we consider natural.) It’s quite clear that the “dominant” species you’re talking about is what Darwin considers a “variety.” This is seen only if you read him closely. But that is what he is saying. As to Hardy-Weinberg Law, that’s in standard population genetics books.

Flint Wrote:

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?

As I see it, in the end there will be an explanation. The most “sensible” one will be something along ID. However, since we will still be dealing with “gaps”, if one is so inclined, one might choose to cling to NS. All of this is ALREADY apparent in the discussion that took place about Prum and Brush’s article. And, if Paul Davies can explain “extremely highly conserved” junk-DNA as something sent from aliens, then what hope is there that there will ever be a consensus. The mind’s ability to rationalize, to think what it wants, is enormous.

And, the cute remarks about the “mathematical” demonstration: the “mathematical demonstration” had to do with the problem of “geneology”, of the “phylogenetic tree.” The purpose is to get away from the inherent “relativity” that, per force, accompanies such a discussion. It’s easier to talk about it in “quantitative” terms, rather than “qualitative” ones. As I’ve looked over the Origins of Species due to our discussion, I see more “nuance” in Darwin’s thinking than the first time. I still think his thinking is wrong-headed; but there are subtleties requiring time and thought to work through. (But, just in passing, in a “sketchy” sort of way, Darwin is convinced that “species” will “morphologically”, as we would say, endlessly move farther and farther apart. Is that what the Cambrian Explosion tells us? Not really. Therein lies the problem.) As my discussion above points out: people tend to believe what they want to believe.

In fact, per Paul Davies argument, I’ve now come to the realization that, for the first time in my life, I believe in ETs. Yes, I believe in God the Father, God the Son, and God the Holy Spirit. I believe in the Saints. All of these, to the best of my thinking, are “out of this world.”

Wayne Francis Wrote:

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.

As is becoming abundantly clear to me, none of you know the difference between “Darwinism” and “neo-Darwinism.” That’s why you bridle at the use of the term “neo-Darwinism.” Historicaly, at the turn of the 20th century, Darwinism was as good as dead because of the criticisms, principally, of Bateson. Roughly, through the work of Fisher and Dobzhansky, Darwinism was “rescued.” 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. My argument concerning the difference of 20 chromosomes is devastating to “point-mutation”, as is the recent experiment wherein a million (or was it a billion) nucleotide bases were eliminated without harm to the organim, i.e., they reproduced normally.

I really must read. Ciao!

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

Sigh. ID, once the smoke and mirrors are factored out, is a simple definition: God did it. One can accept this definition or reject it for reasons of their own. But since it is not based on evidence, it cannot be either supported by or falsified using evidence. Evidence is not relevant to definitions. Definitions are right by definition. If the definition sounds sensible to you, then it will probably always sound sensible. But ID is not an “explanation” of anything. It is a statement of faith. You believe it or you do not.

As for there being an explanation “in the end”, the end is always with us. There is always a “best fit” explanation. As evidence accumulates, sometimes a different explanation (or an enhanced version) fits better. This process continues indefinitely; there is either no end, or the end is continuous with the process, however you want to look at it.

I’m always amused here, that some people make claims based on preference, and others attempt to show that reality as best we understand it fails to ratify those preferences. Claiming that life was intelligently designed by some anthropomorphized designer is like saying that blue is the prettiest of all colors. And like clockwork, we get genuine experts on the electromagnetic spectrum explaining (and perhaps the cones of the eye?) explaining color in full 4-part harmony. As though all this erudition could somehow overturn a preference for blue.

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.

Pasquale … why do you get biology advice from Davies…he’s a physicist. The closest he comes to biology is being a professor of natural philosophy at the Austrialian centre for Astrobiology

While he is good at explaining Cosmology, I still like Sir Martin Rees better, quotes from him like

Paul Davies Wrote:

“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.”

is some what of a “Holier than thou” mentality.

When I want to talk about time loops etc I’ll talk to people like Davies and Penrose and Rees. When I want to talk about psychology I’ll talk to Pinker. When I want to talk about Biology I’ll talk to people like Dawkins and Goodwin. While I love how all of these men, and I don’t limit myself to listening to men, are big thinkers that are not scared to talk outside of their field of expertise.

Pasquale Wrote:

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

Hmm Darwinism a theory of organic evolution saying new species arise from the process of natural selection Hmmm Neo-Darwinism a modern darwinian theory that explains new species in terms of genetic mutations.

Darwin didn’t know about genes. All neo-darwinism has done is identified the causes of mutations. It still relies on the process of natural selection to take hold. Darwin’s theory still holds true. It is just we can explain what changes in the organism causes the mutation.

Pasquale Wrote:

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.

Darwinism is a generally. If organism x has trait y and breeds alot its offspring will carry trait y on thus causing trait y to be more abundant in a population

Neo-Darwinism extends this to say “trait y” is cause by mutation of genetic code z.

the two do not conflict. What they both hang on is that a trait will be passed on if its carrier successfully breeds.

Its a SIMPLE concept that you seem not not grasp.

If you have a wife and you are white, she is white and both your families are white and she has a baby that is black…well its not your traits that that baby is carrying.

Take enough mutations to the genetic code and you have a new species. Since they don’t all happen at the same time, ie with a small number of generations, the species can continue to successfully breed. But with more changes adding up they have less and less viable offspring if they where to breed with the original species

Like I said if you travel 2 million years into the future you’d probably find that you would not be able to produce viable offspring with the humans of that time because of the accumulated difference in genetic code. Miss Smith born in 2,002,004 woiuld be just fine having sex with Mr Jones born in 2,002,004. They would still call themselves human. But now you have 2 humans that are of different species.

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.

You mean when Pasquale lied through his rotten teeth and I busted him point blank? You think Pasquale is the type of person whose honest opinions can be compelled by “gentlemanly” behavior? If you want to play patty-cake with Pasquale and humor him, be my guest. Frankly, I find his intellect disgusting and it was that part of his body (his mind) which I was referring to in my earlier post (a tribute to the late great Frank Zappa who also knew better than to waste time trying to “edumcate” dissembling evangelicals).

Flint Wrote:

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

Well, it has the advantage of being correct. Most of the definitions we encounter are dictionary definitions. These are inductively based claims about how words are used, and clearly may be mistaken.

What about definitions of concrete things? Establishing a concept of a thing and establishing (defining) a corresponding term is done at first by ostension - by pointing at several rock samples, for instance, and saying “This is flint” (and perhaps by pointing at other rocks and saying “This is not flint”). Since one can’t carry around samples of all the things one wants to talk about, verbal descriptions, called definitions in dictionaries and textbooks, are created. “Flint is of mineral”. There is no rule or convention that can prevent your textbook or dictionary from making an error.

How about mathematical definitions? This is where the ‘true by definition’ idea comes from. New terms are essentially abbreviations for longer expressions involving known terms. “By a triangle I mean a plain figure with three sides, each side being a straight line segment”. Later, if it is shown that some X is a plain figure with three sides, each side being a straight line segment, then X is a triangle by definition. The notion of ‘true by definition’ is misguided in other contexts.

In reality, Flint, I think you know all the above even though you haven’t been sounding like it.

Finally the troublesome category: terms that are used as if they point to real things, without the thing existing first or without any agreement about what the thing itself is. Two examples in this set of comments are ‘neodarwinism’ and ‘macroevolution’. These are just floating terms. It is not automatically bad to use them in a particular book or article provided one makes his own usage clear. But all to often people start positing implicitly or explicitly a definition of the term, then going on as if there exists an external thing that the term thus defined points to, and which has some great significance that a mere definition does not have.

I have mentioned neodarwinism earlier in this thread. ‘Macroevolution’ is another term that floats around and gets used this way and that way. What seems to be the best (most useful) usage in biology is, oversimplifying: macroevolution refers to the evolution of morphological characters. As I mentioned in some other topic where it came up, a very good place to learn about it is Levinton’s book _Genetics, Paleontology and Macroevolution_. But to get righteous about it, and argue that there is an actual thing to which the term refers, and any other usage is ‘wrong by definition’ is misguided. ‘Macroevolution’ doesn’t truly mean anything. It is just a term which is sometimes useful. And sometimes not.

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.

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This page contains a single entry by Nick Matzke published on October 12, 2004 12:11 AM.

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