Nick Matzke posted Entry 559 on October 12, 2004 12:11 AM.
Trackback URL: http://degas.fdisk.net/cgi-bin/mt/mt-tb.cgi/558

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?

Comment #8682

Posted by Ian Musgrave on October 12, 2004 08:44 AM (e) (s)

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?

Comment #8683

Posted by Paul Nelson on October 12, 2004 09:11 AM (e) (s)

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.

Comment #8684

Posted by Andrea Bottaro on October 12, 2004 09:46 AM (e) (s)

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®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.

Comment #8685

Posted by steve on October 12, 2004 09:58 AM (e) (s)

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.

Comment #8686

Posted by Jack Krebs on October 12, 2004 09:59 AM (e) (s)

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.

Comment #8687

Posted by Nick (Matzke) on October 12, 2004 10:01 AM (e) (s)

(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:

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

In order,

  1. 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).

  2. 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.
  3. 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.

  4. 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/query.fcgi?cm…

Comment #8690

Posted by Hiero5ant on October 12, 2004 11:26 AM (e) (s)

“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?

Comment #8691

Posted by Nick on October 12, 2004 11:45 AM (e) (s)

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

Comment #8692

Posted by Andrea Bottaro on October 12, 2004 12:40 PM (e) (s)

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

Comment #8693

Posted by Andrea Bottaro on October 12, 2004 12:52 PM (e) (s)

That should have been MHM, not MOM.

Comment #8695

Posted by Dave Thomas on October 12, 2004 01:40 PM (e) (s)

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.

Comment #8696

Posted by PvM on October 12, 2004 01:44 PM (e) (s)

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.

Comment #8697

Posted by Steve on October 12, 2004 02:14 PM (e) (s)

“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.

Comment #8699

Posted by Les Lane on October 12, 2004 02:59 PM (e) (s)

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”.

Comment #8700

Posted by God Fearing Atheist on October 12, 2004 03:11 PM (e) (s)

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.

Comment #8701

Posted by Salvador T. Cordova on October 12, 2004 03:14 PM (e) (s)

Syntax Error: mismatched tag 'URL'

Comment #8702

Posted by PvM on October 12, 2004 03:58 PM (e) (s)

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.

[hr]
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

Comment #8703

Posted by a Creationist Troll, apparently on October 12, 2004 04:18 PM (e) (s)

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)?

Comment #8704

Posted by Steve on October 12, 2004 04:25 PM (e) (s)

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.

Comment #8706

Posted by a Creationist Troll, apparently on October 12, 2004 04:45 PM (e) (s)

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.

Comment #8707

Posted by a Creationist Troll, apparently on October 12, 2004 04:48 PM (e) (s)

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

Comment #8709

Posted by PvM on October 12, 2004 05:04 PM (e) (s)

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

Comment #8710

Posted by PvM on October 12, 2004 05:08 PM (e) (s)

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’

Comment #8711

Posted by PvM on October 12, 2004 05:15 PM (e) (s)

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.

Comment #8714

Posted by PvM on October 12, 2004 05:27 PM (e) (s)

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.

Comment #8717

Posted by Steve Reuland on October 12, 2004 06:04 PM (e) (s)

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.

Comment #8718

Posted by PvM on October 12, 2004 06:05 PM (e) (s)

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.

Comment #8720

Posted by PvM on October 12, 2004 06:14 PM (e) (s)

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?

Comment #8721

Posted by Admonitus on October 12, 2004 06:53 PM (e) (s)

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

Comment #8722

Posted by PvM on October 12, 2004 06:59 PM (e) (s)

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’..

Comment #8723

Posted by God Fearing Atheist on October 12, 2004 07:47 PM (e) (s)

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

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

Comment #8724

Posted by MJW on October 12, 2004 07:59 PM (e) (s)

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

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

Mike

Comment #8727

Posted by Russell on October 12, 2004 09:11 PM (e) (s)

Why did Meyer quote Valentine?

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

Strange, how the reviewers failed to catch that.

Comment #8728

Posted by PvM on October 12, 2004 10:14 PM (e) (s)

True and Carroll: Cooption

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.”

In context

What are True and Carroll doing?

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

Now to

Gene duplications and selective conflict

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

In other words, evidence for co-option are well documented but the importance of the various mechanisms requires additional studies

Conclusions

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

Quite a different tune…

Comment #8730

Posted by PvM on October 12, 2004 10:39 PM (e) (s)

Bill Dembski wrote:

“Ironically, though, by publishing and then repudiating the Meyer paper, the BSW has done the seemingly impossible. Not only has it given ID proponents a publication in a peer-reviewed biology journal, it has also handed a smoking gun to those ID proponents who argue that the peer-review process is unfairly stacked against them. Quite a feat for a single journal.”

http://www.arn.org/docs/wedge/mh_wedge_041012.ht…

How is the peer review unfairly stacked against ID? Because the BSW points out correctly that:

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

In addition BSW has done science a favor in that when given the opportunity to present its case, ID falters. Not only is the case against Neo-Darwinism poorly supported but the ID approach of appeal to ignorance is once again exemplified by the lack of any testable ID hypothesis. And yet Meyer did seem to argue that it may be time for a new causal theory… Ironic isn’t it, how ID comes up empty handed.

Come back to us when ID has a testable hypothesis until then, as you seem to have noticed, the real future of ID is in theology.

Comment #8731

Posted by PvM on October 12, 2004 10:42 PM (e) (s)

Thank you BSW by William Dembski

Bill Dembski wrote:

“Ironically, though, by publishing and then repudiating the Meyer paper, the BSW has done the seemingly impossible. Not only has it given ID proponents a publication in a peer-reviewed biology journal, it has also handed a smoking gun to those ID proponents who argue that the peer-review process is unfairly stacked against them. Quite a feat for a single journal.”

http://www.arn.org/docs/wedge/mh_wedge_041012.ht…

How is the peer review unfairly stacked against ID? Because the BSW points out correctly that:

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

In addition BSW has done science a favor in that when given the opportunity to present its case, ID falters. Not only is the case against Neo-Darwinism poorly supported but the ID approach of appeal to ignorance is once again exemplified by the lack of any testable ID hypothesis. And yet Meyer did seem to argue that it may be time for a new causal theory… Ironic isn’t it, how ID comes up empty handed.

Come back to us when ID has a testable hypothesis until then, as you seem to have noticed, the real future of ID is in theology.

Comment #8732

Posted by Pasquale Vuoso on October 13, 2004 02:42 AM (e) (s)

PvM wrote:

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.

Well, if we’re going to talk about ‘irony’, then here’s what Prum and Brush also wrote:

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

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

Comment #8733

Posted by Dave S. on October 13, 2004 08:00 AM (e) (s)

Pasquale wrote:

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

I must have missed the memo. Since when does ID address the question of a mechanism?

I thought they explictly claimed that ID is not a mechanistic theory.

“It must have been designed” is not a mechanism.

Comment #8734

Posted by Pasquale Vuoso on October 13, 2004 08:16 AM (e) (s)

Dave S wrote:

“It must have been designed” is not a mechanism.

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

Prum and Brush, as the DIs pointed out, believe that natural selection, in the end, can explain the “evolutionary novelties” surrounding the development of the feather, but not in a “gradualistic” (my wording) way. I consider this a step forward. Likewise, in the context of this board, I don’t think they’ve stated anything that undermines Meyer’s paper, and, in fact, perhaps its critique of “neo-Darwinian” mechanisms tends to support Meyer’s claims.

Comment #8735

Posted by Steve on October 13, 2004 09:09 AM (e) (s)

Hey Pasquale, three quick questions

1) Is ID a scientific theory?

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

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

Comment #8736

Posted by Steve Reuland on October 13, 2004 09:57 AM (e) (s)

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

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

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

Comment #8737

Posted by Jack Krebs on October 13, 2004 10:02 AM (e) (s)

Cheerleading here: Excellent post, Steve.

Comment #8738

Posted by Steve Reuland on October 13, 2004 10:20 AM (e) (s)

Pasquale Vuoso wrote:

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

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

At any rate, the pertinent question is how a structure originated, not just what its function is. Evolutionary theory gives us an approach to such understanding, using for example comparative biology and phylogenetics. What would ID’s approach be?

Comment #8739

Posted by 386sx on October 13, 2004 10:44 AM (e) (s)

Steve wrote:

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

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

Comment #8740

Posted by Hiero5ant on October 13, 2004 11:08 AM (e) (s)

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

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

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

HTH.

Comment #8741

Posted by Salvador T. Cordova on October 13, 2004 11:38 AM (e) (s)

Syntax Error: mismatched tag 'URL'

Comment #8742

Posted by steve on October 13, 2004 11:39 AM (e) (s)

Pasquale Vuoso (2004):

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

Steven Pinker, in How the Mind Works (1999):

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

Comment #8744

Posted by Pete Dunkelberg on October 13, 2004 12:04 PM (e) (s)

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

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

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

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

Pim says:
“Why would the DI quote this paper?”

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

Comment #8745

Posted by Great White Wonder on October 13, 2004 12:35 PM (e) (s)

Salvador writes

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

Sufficient for what, precisely??

And who claimed that those two mechanisms alone are sufficient to prevent extinction and sufficient to create new phyla??

Let’s see some answers, Salvador. You seem to have scraped the charcoal off since the last time you showed up here and pretended to be a scientist and an honest person. I highly doubt that you’ve changed one bit, but go ahead and prove me wrong. Please attempt to answer the obvious and simple questions that flow from your vague pronouncements if you are capable of being articulate and honest for five minutes.

Comment #8746

Posted by Steve Reuland on October 13, 2004 12:54 PM (e) (s)

Salvadore wrote:

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

Hi Salvadore. Whether or not gene duplication and cooption (and other mechanisms) are sufficient is worthy of discussion (another time) but irrelevant to the point of what I was getting at. If they are indeed insufficient, then Meyer is welcome to show how. But he did this neither in his original paper nor in his response. The original paper simply asserted the impossiblity of evolving novel morphology while failing to mention these rather crucial mechanisms. The response then retreats away from the “insufficient” criterion to an irrelevant and uncontroversial “incomplete” criterion. All of the DI’s criticisms of the papers cited by GME are, as far as I can tell, instances of saying that the evidence is less than air-tight, that the definitive experiment (which according to their standards, would require a time machine) has not yet been done, or that there are still unanswered questions. All that may be true, but it does not support the contention that evolutionary mechanisms could not, in principle, account for morphological evolution.

Comment #8747

Posted by PvM on October 13, 2004 01:45 PM (e) (s)

Pasquale wrote:

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

Remember that Meyer was arguing that neo-Darwinism could not explain but that’s not because neo-Darwinism is wrong but because it focuses on different aspects. Inclusion of developmental evolution is needed. But contrary to Meyer, Prum et al are NOT arguing neo-Darwinism is WRONG.
There is also no ‘logic’ behind ID that could be put to use as a guide to future research. All ID does is incompletely represent the data, revel in ignorance and fail continuously to present a scientifically relevant hypothesis.

DIS were suggesting that Prum was somehow relevant to what Meyer had argued. They could not have been wrong further….

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

Yes look at Valentine’s on the origin of phyla, just do not rely on the misunderstandings and misrepresentations of the Cambrian as references by Salvador. The pictures are strawmen, and misleading. That’s what happenes when one copies mindlessly from creationist resources Sal.
Let me ask you a question Sal, have you read any research on the Cambrian?

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.

Valentine On the Origin of Phyla 2004

Where is the scientifically relevant hypothesis of ID Sal? There is none…

Comment #8748

Posted by PvM on October 13, 2004 02:06 PM (e) (s)

It must have been designed” is not a mechanism.

Pasquale wrote:

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

Nothing in Pasquale’s argument suggests that we should take ID seriously. Meyer was attempting to argue that neo-Darwinism is unable to explain origin of novelty etc but as Prum shows and as has been the typical case with ID’s argument, ID fails to distinguish between neo-Darwinism needing to focus as well on development with neo-Darwinism being unable to explain. In other words when reading the resources ‘quoted’ by DIS and Meyer one gets a very different picture than painted by them. IF they would at least offer a better hypothesis but even there ID and DIS fails miserably since ID is not about science, it’s about focusing on our ignorance. (See for instance Meyer v Gilber or Meyer and Cambrian Explosion and CSI)
Reverse engineering is exactly what evolutionary science IS doing, and it is exactly what ID is NOT doing. Notice that ID fails to present ANY evidence for its designer. Compare this with science which proposes pathways, mechanisms and has a solid theoretical foundation. None of these apply to ID.

ID is a miserable failure scientifically and DIS, in their haste to read up on the research in the area supposedly reviewed by Meyer can do little better than use some ad hominem remarks and what I see as essentially quote mining of research to make their case. When actually reading the papers, time and time again, a very different picture emerges.
Could an ID proponent explain why ID has been such a scientific failure? If there were a foundation for scientific inquiry, how come that ID has failed to present it?

Del Ratzsch sees a role for ID but it is far less glamorous as ID pretend it to be

Del Ratzsch wrote:

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

Link

Pasquale wrote:

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

Indeed, ‘your wording’ and it would be a strained reading of their paper to find much support for your claims. Additionally Prum et al do not believe that natural selection played a role, they observe how they can make predictions and tests to that end.

Pasquale wrote:

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

Nice moving of goalposts. Meyer is not critiquing Neo-Darwinisn, he is trying to show that Neo-Darwinism is in principle unable to explain novelty and by eliminating a few competing ideas, Meyer hopes to make a case for ID. Of course Meyer fails on two fronts:

1. He fails to show that Neo-Darwinism is in principle unable to explain the data. All he shows is arguing for an evo-devo approach to evolution. Meyer would hardly be satisfied to reach the conclusion that evo-devo is the future of evolutionary theory, fully in line with (neo-)Darwinism. For the same reason that the discovery of DNA and genes ended up strongly supporting evolutionary theory, developmental biology has managed to resolve some very important paradoxes.

2. Meyer has failed to present ANY ID relevant hypotheses. Not surprisingly since ID cannot present a reliable theory without addressing issues of
2.

Comment #8756

Posted by PvM on October 13, 2004 06:07 PM (e) (s)

Syntax Error: mismatched tag 'kwickxml'

Comment #8757

Posted by Great White Wonder on October 13, 2004 06:44 PM (e) (s)

Thanks for the update, PvM!

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

Oy. Another “popular” writer steps into the pit of ignorance to share the putrid air with an ID apologist. Why????!?!!!!!!!!

Just for the record:

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

from http://www.wolfmanproductions.com/shermer.html

I wish Dr. Shermer luck. I’m not a fan of his “skeptic” label anymore than I am a fan of Dawkins ridiculously stupid “bright” label. I also hope he didn’t characterize himself using the silly shorthand “Darwinian evolutionist” but I wouldn’t be surprised if he did.

Will Shermer pretend that Meyer that is interested in an honest debate about interpreting the facts scientists have deduced relating to mutations, the reproduction and fitness of living organisms and the fossil record? Or will he get right to the heart of the matter and call Meyer on his role in contributing to our country’s diseased public discourse, Meyer’s unconstitutional religious agenda, the litany of indisputable distortions of the truth in his recent paper, and the fact that the paper would not have been published but for the creationist leanings of a bariminologist crank on the editorial board?

My hunch is that Shermer will pretend, which begs the question of why he’s bothering unless it’s to generate a tablespoon of press which will allow him to move a few more copies of his choir-pleasing books.

Comment #8761

Posted by Pete Dunkelberg on October 13, 2004 07:34 PM (e) (s)

Two Fuzzies

Following Nick’s suggestion when he started this topic, I’m using a title for this comment.

Introduction

Prum and Brush 2002: THE EVOLUTIONARY ORIGIN AND DIVERSIFICATION OF FEATHERS:
The Quarterly Review of Biology Volume 77, No. 3 September 2002
review a strong advance in our understanding the evolution of feathers. Oddly, the DI, in defending DI Fellow Meyer, has made various comments hinting that this paper indicates that evolution is wrong. Several comments about the DI’s comments appear above; I hope to clear up a couple of questions that have arisen.

Fuzzy # 1: ‘neodarwinism’.

Prum and Brush emphasize repeatedly and in several ways that they find it best to investigate the actual pattern of events in the evolution of feathers before proposing a specific ‘selection for’ type scenario, or process as they call it. Fine - Darwin first noted patterns among organisms, extant and extinct, before proposing the explanatory process known as natural selection. Prum and Brush refer obliquely to premature speculations on process as ‘neodarwinism’, which they consequently criticize. This is less clear than simply referring to and explaining the ‘pattern vs process’ issue directly, and also provides the DI with individual sentences which they present as supporting their antievolution cause.

A smaller fuzzy of this type is Prum & Brush’s use of the term ‘macroevolution’. The evidently mean the evolution of morphological characters, or character evolution for short. Their usage of the term ‘macroevolution’ is probably the best, if one takes the attitude that since the term is floating around, it might as well be used for something. But again, referring directly to character evolution, which is central to the process they present, is clearer.

By the way the term ‘neodarwinism’ has along history of being used in straw man fashion. Bulletin to Prum & Brush: the non-strawman meaning of the term is just current evolutionary biology, which your paper exemplifies. Bulletin to the DI: This clear statement from the abstract:

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

is quite Darwinian enough for reasonable persons.

Fuzzy # 2: Is evolutionary theory a necessary and or sufficient explanation for specific details of evolution?

It is not necessary, as one could suppose that a purposeful agent has caused evolution, or even that the earth was created last week and there was no evolution.

Is it sufficient, and if so in what sense? It is a general rule that general theories don’t predict specifics, except with the aid of a great deal of auxiliary data, aka initial conditions or boundary conditions. For instance, mechanics does not predict that there will be a planet earth at all, and certainly does not predict the time and details of the formation of our solar system. However, mechanics together with the assumption that there is a universe like this one in the first place, is sufficient to show that our planet and solar system are possible and understandable in general.

Similarly, evolutionary theory does not predict the timing and details of feather evolution, the Cambrian or the extinction of the dinosaurs. Just as in other branches of science the particulars are contingent. But the details are consistent with the theory, and understandable thanks to it.

Getting back to Prum & Brush, we find, after mentioning pertinent facts about diverse feathers in living birds, this:

p 275

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

This is soon followed by an extensive section on paleontological data. They of course can’t predict all the fossil discoveries from their hypothesis. However, the data are all quite possible given their hypothesis, illustrating my point and theirs.

At the DNA level, mutations including duplications of beta keratin genes, and sundry developmental mutations and probably other mutations that have not yet been noticed are obviously sufficient to produce feathers, or there wouldn’t be any feathers.

Comment #8764

Posted by God Fearing Atheist on October 13, 2004 10:23 PM (e) (s)

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

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

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

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

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

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

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

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

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

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

Comment #8776

Posted by Russell on October 14, 2004 11:28 AM (e) (s)

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

Comment #8788

Posted by Pasquale Vuoso on October 14, 2004 07:12 PM (e) (s)

Syntax Error: mismatched tag 'quote'

Comment #8789

Posted by Steve on October 14, 2004 07:41 PM (e) (s)

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

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

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

Comment #8792

Posted by Pasquale Vuoso on October 14, 2004 08:36 PM (e) (s)

Steve wrote:

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

Where’s your answer to #2? My answer to #2 is incorporated in my response to #3. Is it too subtle?

Pasquale Vuoso wrote:

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

This is, in true, general. In the specific case of the evolution of the “feather”, the “discrete”, “heirarchichal” nature of what is observed—both extinct and extanct—conforms to this “hypothesis.”

Steve wrote:

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

Now, this is what I wrote. It would be a courtesy if you would read the whole post, not just parts.

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

As to:

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

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

Comment #8793

Posted by Steve on October 14, 2004 08:50 PM (e) (s)

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

Comment #8794

Posted by Great White Wonder on October 14, 2004 08:56 PM (e) (s)

Pasquale writes

All of this seems to be friendly language for IDers.

Maybe it seems that way to you, Pasquale. But somehow you’ve managed to shut down the part of your brain that would allow you to recognize that the authors of that seemingly “friendly language” consider you and other ID apologists to be dishonest charlatans with nothing to offer science (read post 8764 again including the last few sentences which you omitted from your obnoxiously dissembling post 8788 above).

It’s a neat trick, Pasquale. I’m confident that you are capable of maintaining all sorts of strange beliefs inside the ugliest part of your body. I’m also confident you’ll not hesitate to share them with us.

Comment #8796

Posted by Pim van Meurs on October 14, 2004 09:20 PM (e) (s)

Syntax Error: mismatched tag 'kwickxml'

Comment #8825

Posted by Pasquale Vuoso on October 16, 2004 09:35 PM (e) (s)

PvM wrote:

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

I think I’m more familiar with Darwinism and neo-Darwinism than a lot of biologists. That’s precisely why I’m critical of Darwinism. It doesn’t add up. ‘Punctuated Equilibrium’ (Equilibria, for the blue-bloods) is a retrenchment from strict neo-Darwinism in the face of the Cambrian explosion. Kimura’s Neutral Theory is a retrenchment from strict neo-Darwinism based on the results of protein gel-electrophoresis. ‘Neutral drift’ is a retrenchment from the elevated requirements of strict neo-Darwinism’s gene fixation in large populations. The bulk of neo-Darwinism hinges on Ronald A. Fisher’s work on population genetics and his mathematical “hypothesis” that “positive” mutations can—eventually—be “fixed;” however, Sewell Wright disagrees with Fisher’s interpretation of this fundamental equation. As well, Sir Fred Hoyle has punched gigantic holes in Fisher’s mathematical work in his (Hoyle’s) The Mathematics of Evolution. And, then, of course, there is Charles Darwin himself who tells us, “species will give rise to genera, genera to families, families to orders, and orders to classes.” Well, where did the “species” that started all this come from? A “genera”. Where did that “genera” come from? A “family”. Where did the “family” come from …. and so forth. So, in sum, “classes” give rise to “classes.” Doesn’t that seem circular? Now, how about Darwin’s initial motivation for “natural selection.” Well, it comes from the “artificial selection”, which was on the rise in his day. And now, well….evolutionary biologists will tell you that the EXPLANATION for “artificial selection” is…………………… “natural selection”. Isn’t that the greatest circular argument in human history?

Now, if we can just move on.

PvM wrote:

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

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

I wrote:

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

PvM wrote:

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

You’ll notice I didn’t use the words “original ancestors”. Now, if you mean that all the information for “future” “avian” feathers was all there when the “original ancestors,” to use your terminology, first developed their “feathers”, then it might indeed be the case, scientifically, that this is not so. It’s possible there is some kind of mechanism by which this additional “information” is “added” to the genome at each level of “novelty” (per Prum and Brush), and it is precisely these kinds of “mechanisms” that biologists should be interested in. My hunch is, though, that the “mechanism” won’t be found at the the “lower” classification levels, but “higher” ones. We’ll just have to wait and see.

However, Prum and Brush’s article, despite the fact that they don’t “see” it that way, seems almost to imply that when they write:

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

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

And, again, from their abstract:

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

My feeling is, as I say, that likely everything will be in place right from the beginning.

PvM wrote:

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

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

So this is really just presuming what, in the end, needs to be demonstrated. Here’s what the DIs said”

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.

PvM wrote:

Pasquale wrote:

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

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

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

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

PvM wrote:

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

And, in answer to my comment:
“While we sit before our computers, companies like Genentech are doing exactly that. I wouldn’t be so smug.” He also wrote:

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

It’s that simple… “

It also shows how ID doesn’t get in the way of science. My point was that this kind of analysis is being done already. And they will come up with results because they’re not driven by ideology, but by market forces. They can’t afford ideology.

What do I expect? I expect the biotech firms to find “layers” of complexity in the genetic code. As they do their searches, they will hone their search engines. And, let me make this prediction: they will find that the genetic code is full of “heirarchichal” routines and subroutines. They will end up saying something like: “We have found startling complexity in the mammalian genome. It has all the appearances of having been programmed. It’s almost as if it were designed.” Let me also predict that when the scientists say this, I doubt that you will change your point of view.

And to point out what I mean, note that Paul Davies (editor of New Scientist magazine) has recently suggested that the newly discovered, “highly conserved” junk DNA, in, I believe, the mouse genome, is a “message” from ETs. Yes, a message from space. He suggests that it is more efficient to send this kind of bio-message than to beam out high-energy EM (electro-magnetic)waves. Isn’t the presupposition behind such a suggestion that this junk DNA has been “designed”?

As I said before, I guess we’ll just have to wait and see. But I don’t think it will take very long.

Comment #8828

Posted by Steve on October 16, 2004 10:26 PM (e) (s)

Review Post For Busy People

Pasquale:

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

Steve:

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

Pasquale:

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

Steve:

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

Pasquale paraphrased:

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

Comment #8830

Posted by Pasquale Vuoso on October 16, 2004 11:00 PM (e) (s)

Steve wrote:

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

What does this mean?

Comment #8834

Posted by a Creationist Troll, apparently on October 17, 2004 10:12 AM (e) (s)

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

Comment #8835

Posted by Pasquale Vuoso on October 17, 2004 10:30 AM (e) (s)

Syntax Error: mismatched tag 'quote'

Comment #8837

Posted by Pim van Meurs on October 17, 2004 12:02 PM (e) (s)

Pasquale wrote:

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

Indeed. And science has identified the ‘designer’. For the same reason teleology in nature is not really the issue. As Ayala and Ruse have argued, teleology is what is to be expected from mechanisms such as natural selection. So what is the issue then? The issue is what hypothesis best explains the data. And since ID refuses/is unable to present their hypotheses of design and since science hsa proposed very well supported hypotheses, ID remains scientifically irrelevant.

PvM wrote:

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

Pasquale wrote:

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

I am not sure then why we are having this conversation since the new information in the genome can arise under well understood and natural circumstances such as variation and selection. That neo-Darwinism can be both an innovator and adaptor may not have been established to YOUR satisfaction but then you have to accept the simple fact that the evidence for your ‘designer’ is even more lacking in supporting evidence.
However, much research exists which indicates that evolutionary theory can explain new information in the genome, as well as the origin of novelty. It is through equivocation between Neo-Darwinism cannot explain novelty and Neo-Darwinism needs to include the knowledge from developmentary biology to explain how variation and selection explain novelty in nature.
Since Dembksi is arguing that new (complex specified) information cannot increase naturally under processes of regularity and chance, the fact that his arguments are theoretically flawed and empirically disproven, it surely seems a relevant aspect namely that the foundation of ID is fundamentally and theoretically flawed. The explanatory filter has been shown to be unreliable, unable to eliminate natural selection as the intelligent designer, based on flawed concepts (No Free Lunch theorems, law of conservation of information) and so on. On a practical level ID has been unable to apply its ideas to anything but the trivial. In the mean time science has shown why most of the fundamentals of ID are quite flawed and that ID remains without any scientific hypotheses. Worse, science has shown how new information and novelty can arise under evolutionary processes.

PvM wrote:

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

Pasquale wrote:

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

My goodness, it provides for testable hypotheses and now Pasquale uses the ‘transitional fossil’-like fallacy of complaining that these steps reduce the information since there are five steps. No wonder ID never wants to go beyond the massive gap of knowledge aka as ‘the designer did it’. Does Pasquale understand how ridiculous these assertions are? To claim that breaking down one giant step into five steps which can be tested somehow is less of an explanation. Mind boggling.

Pasquale wrote:

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

Yes, I understand how someone desperate for any hints of a designer can take such a word out of context to come to a conclusion of teleology. But teleology or function is hardly surprising from the perspective of a process of variation and selection. To suggest that this teleology/design cannot be explained by evolutionary processes is one thing, to suggest that ‘thus there is evidence of an intelligent design’ remains totally unfounded in any mechanism, pathway, means, motive etc.

Anything…. Does that not bother you? That ID’s argument is reduced to cherry picking of quotes and comments from papers to make their case NOT in favor of ID but against a particular aspect of evolutionary theory. Look for instance at the Cambrian explosion, long touted by creationists alike as evidence against evolutionary theory and somehow evidence in favor of an intelligent designer although noone will explain really why… Details are to be shunned when it comes to ID. In the last decade while ID has been claiming that the Cambrian explosion remains unexplicable under regularity and chance processes, real science has uncovered new cambrian and pre-cambrian fossiles, has uncovered fascinating evidence that links the developmental hox genes to the Cambrian explosion, has uncovered phylogenetic evidence that shows how the Cambrian explosion was preceeded by fascinating ground work. And while the DIS and Meyer inexplicably quote from Valentine’s 2004 work on the “origin of phyla”, Valentine lays out a fascinating description of the Camrbrian and shows how it vindicates Darwin. All ID seems to be able to do is to cherry pick from old research, or reference recent research which actually contradicts their claims.

Pasquale wrote:

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

Then let someone do this and show that ID can make a difference in science beyond arguing from ignorance. But so far ID papers, even when they make it into peer reviewed literature show why peer reviewed examples of ID scientific work are hard to find. It’s because little science is being performed to promote the case of ID beyond appeal to ignorance.

Pasquale trying to show that he understands evolutionary theory writes

And, then, of course, there is Charles Darwin himself who tells us, “species will give rise to genera, genera to families, families to orders, and orders to classes.” Well, where did the “species” that started all this come from? A “genera”. Where did that “genera” come from? A “family”. Where did the “family” come from … . and so forth. So, in sum, “classes” give rise to “classes.” Doesn’t that seem circular
It’s your argument, please explain why decided to represent Darwin’s work as such. I am looking forward to some references to Darwin’s original work since your argument seems to be what is commonly known a strawman.
I thought you understood Darwinian theory?
If you understood Darwinian theory you would realize that whenever a species arises, in order to name it as a species in the Linnaean tradition you have to specify its genus, family, order, class, phylum etc? In other words, above the species level, this hierarchy becomes quite artificial. Which is why Darwin focused on species which is the most relevant evolutionary concept anyway.
It’s this confusion between Linnaean ranking and phylogenetic trees or ‘Tree of life’ which leads creationsts to make claims about the Cambrian period and Darwinian so called ‘predictions’ which are fallacious. I am presently working on a contributions which explores in more detail the many fallacies.

Comment #8840

Posted by Pasquale Vuoso on October 17, 2004 04:36 PM (e) (s)

Syntax Error: mismatched tag 'i'

Comment #8844

Posted by Pim van Meurs on October 17, 2004 07:45 PM (e) (s)

Pasquale, I fail to see how Darwin’s explanation has much relevance to your original claim. Remember that the main concept of Darwin is species, anything else is a somewhat arbitrary naming. You cannot confuse phylogeny and Linnean hierarchy to suggest support for your claim. The concept of species is the only biologically real concept, the other concepts are merely categorizations on our part, sometimes leading to confusions of confusing these two concepts. For instance ID proponents have argued that phyla arrive before the lower classes, since a Linnaean hierarchy starts with a species and has to name its genus, family, class, phylum etc, a phylum will have to be automatically assigned to a species. It’s not surprising that the branches arise before the leafs. But a Linnaean hierarchy should not be confused with a phylogeny. There are many differences, one which is quite relevant is that the Linnaean hierarchy assumes equal distance for genera, families etc. Another one is that while a phylogenetic tree is monophyletic, a Linnean hierarchy can be polyphenetic
In fact Darwin’s explanation shows that the typical ID strawman of an upside down pyramid is fallacious and based on the confusion of phylogenetic trees and Linnean hierarchies. I am writing a quite extensive posting on this and other ID misconceptions.

Darwin’s last statement is an interesting one. But I fail to see the relevance of this statement.

Grape Ape wrote:

I think he’s explained it quite adequately, but I’ll elaborate anyway. If common descent is true, there is only one correct phylogenetic tree for all living organisms. That tree represents the true genealogy of life. According to modern systematics, the correct way to construct taxonomic groups is to choose monophyletic groups, which means groups that consist of an ancestor and all of its descendents. Think of a monophlyetic group as a branch and all of the daughter branches and twigs that come off of it. If you leave off some of those daughter branches, then the group is no longer monophyletic, it’s now paraphyletic. That’s exactly what would happen to phylum Chordata if we declared Mammalia to be its own phylum. Suddenly, phylum Chordata would not include an ancestor and all of its descendents, because the mammals would be in their own phylum. And that’s a big no-no.

The problem in systematics is, when you have a large number of branches (every speciation creates a new branch point), then you have a massive number of possible monophyletic groups. So we have thousands (if not millions) of monophyletic groups when tracing any one lineage back to the earliest time. That raises a big question: which monophyletic groups should we recognize and give a name to? We can’t do it for all of them, because they’re way too many. The answer is that it doesn’t matter — the particular taxonomic groups that we’ve chosen, along with the names that we’ve given them, are completely arbitrary. We therefore choose them based on our communication needs, as well as tradition and history. We still recognize most of the groups invented by Linneaus, because those are the ones we’re familiar with. Taxonomy is plagued, however, by what are known as “spitters and lumpers”, people who keep creating new taxonomic categories in order to emphasize well-resolved groups above or below the more common taxonomic ranks. Those new groups aren’t wrong, just as long they’re monophyletic, but they’re often needlessly confusing.

So I hope you can see now that taxonomic groups are “real”, in the sense of being monophyletic, but the particular group you choose to call “phylum” or “class” or whatever is itself entirely arbitrary. The problem we’ve been having is with your insistance that those groupings represent something beyond a mere convenience of communication, so that the specific rank they’re in denotes some sort of actual quality about the group itself. The name means nothing. In reality, all taxonomic groups originated in the same way: speciation. It’s only after long periods of evolution have passed, and many groups have diverged and become separate thanks to extinction, that we invent larger categories to denote a split that happened way back when.

(Grape Ape on ARN)

Comment #8862

Posted by Pasquale Vuoso on October 18, 2004 06:01 PM (e) (s)

PvM wrote:

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

To me this is just circular reasoning. So maybe we just agree to disagree on this point.

PvM wrote:

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

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

Thomas Huxley, “Darwin’s Bulldog”, wrote in 1891, or thereabouts, that he found it troubling that there still had been no successful attempt to “breed” a new species. This is what they fully expected to happen when Darwin first published. When science can take a ‘dog’ and turn it into a ‘cat’, I’ll be the first to ‘sign-on’ to Natural Selection. I’m not adverse to NS. If it were proven to my satisfaction—then no problem. I accept the “evolution” of life. We’re arguing mechanisms. Logically, ID makes sense and NS—as argued by Darwin—does not.

You ask for evidence. Einstein intellectually “conceived” of his “general relativity” well before he could provide “evidence” for it. To him, “general relativity” made sense. Then he had to work out his theory. Based on the mathematical form that his theory took, he then was able to make predictions. ID will have to work itself out little by little as more and more science is done. In this regard, it is at the mercy of current science. But it seems likely—IF it is, indeed, correct (we should get a sense of its rightness or wrongness as we go along)—that as more microbiological discoveries are made, a reasonable “mechanism” will be identified, and, hopefully, used to make predictions.

Let’s do a “mind experiment” (That’s how Einstein worked) If you were a colleague of Einstein back in 1910, and he told you of some of his ideas, would you have said, “Oh, that’s nonsense!” Twenty years ago, ID didn’t exist. The only reason it “exists” nowadays is the discoveries that microbiologists have made, as well as the “information revolution”, meaning computers and the rise of ways to “systematize” information, not to mention what is being learned about the genome itself. Just two years ago, no one would have argued much about “junk DNA”, yet there is a complete “reappraisal” of that going on right now, with that “junk DNA” being described as exhibiting “embedded networking”. So, time will tell.

Pasquale wrote:

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

PvM wrote:

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

I’ll take it slowly. Here’s the explanation:

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

So, it would seem, to truly provide “evidence” that an explanation for the development of avian feathers has been discovered, and not to merely assert it, instead of ONE “function” and ONE “set” of “intermediate functions”, you now need to “identify” FOUR new “functions” (the last developmental “novelty” can be presumed to have made “flight” possible) and FIVE new “sets of intermediate forms”. This is neither an “advance” nor an “explanation”; rather, it is a “concession” that “neo-Darwinism” is not up to the task of explaining the “origin” of the avian feather using “flight” as that which is being “selected for”.

The authors say as much in the article. They say using “neo-Darwinsim” has “failed”, that it has “hindered” the discovery of the searched for explanation.

PvM wrote:

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

For the time being. See above.

PvM wrote:

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

But nonetheless, this doesn’t conform with what Darwin envisioned. So, as I’ve stated in an earlier post, Darwin fully expected that in each age—he believed, a la the Hutton-influenced University of Edinburgh school of thought, that the earth was “eternal,” (which forms the basis of Darwin’s and Lyell’s “gradualism”)—and he fully expected the same “number” of species then, as we “peeked” back in time, as we do now. That’s why I included this quote:

Charles Darwin wrote:

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

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

As to James Valentine’s Origin of Phyla, I can’t get my hands on a copy. So I can’t comment.

PvM wrote:

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

But it is precisely Darwin who has introduced “confusion.” There’s a logical fallacy present in this thinking. Darwin stands the “Linnaean System” on its head when he says that a “variety” is an “incipient species”, and that “species” are really “varieties.” Given what we know about Mendelian genetics (and unknown to Darwin), doesn’t this seem wrong-headed?

If one believes in “typology”, then you don’t have this “confusion” when it comes to the “Linnaean system.”

In a later post,

PvM wrote:

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

Referring to the italicized portion, to me, this is the only logically consistent position one can take; maybe that’s why I favor ID.

Nevertheless, I agree: there is tremendous confusion here, and I believe that it stems from Darwin’s theorizing, not from actual nature—nature is not confused, just us. I’m going to do some more thinking on this. I think a “mathematical argument” contra Darwin’s thinking can be constructed. So, give me some time, and I’ll get back to you.

In the meantime, I guess I’ll await the extensive post you’ve promised. Adieu!

Comment #8865

Posted by Steve on October 18, 2004 06:42 PM (e) (s)

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

That’s among the worst writing I’ve seen in my entire life.

Comment #8867

Posted by Steve on October 18, 2004 06:47 PM (e) (s)

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

(http://www.amazon.com/exec/obidos/tg/detail/-/04…)

But in your case I have to add another book.

http://www.amazon.com/exec/obidos/tg/detail/-/02…

Comment #8868

Posted by Wesley R. Elsberry on October 18, 2004 08:07 PM (e) (s)

Pasquale Vuoso wrote:

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

So far, I haven’t seen anything that indicates that Pasquale understands “Darwin’s thinking”, far less that he is going to serve up a competent and novel criticism.

One more ID promissory note, noted. I have little doubt it will prove as valuable as the rest of them have so far.

Comment #8870

Posted by Pim van Meurs on October 18, 2004 08:31 PM (e) (s)

Pasquele wrote:

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

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

Darwin wrote:

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

Pasquale wrote:

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

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

Pasquale wrote:

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

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

Pasquale wrote:

But it is precisely Darwin who has introduced “confusion.” There’s a logical fallacy present in this thinking. Darwin stands the “Linnaean System” on its head when he says that a “variety” is an “incipient species”, and that “species” are really “varieties.” Given what we know about Mendelian genetics (and unknown to Darwin), doesn’t this seem wrong-headed?

If one believes in “typology”, then you don’t have this “confusion” when it comes to the “Linnaean system.”

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

Pasquale wrote:

This is neither an “advance” nor an “explanation”; rather, it is a “concession” that “neo-Darwinism” is not up to the task of explaining the “origin” of the avian feather using “flight” as that which is being “selected for”.

The authors say as much in the article. They say using “neo-Darwinsim” has “failed”, that it has “hindered” the discovery of the searched for explanation.

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

Comment #8872

Posted by Steve on October 18, 2004 08:48 PM (e) (s)

Pasquale wrote:

I think a “mathematical argument” contra Darwin’s thinking can be constructed.

I have a feeling this is going to be entertaining.

Comment #8875

Posted by Wayne Francis on October 18, 2004 09:11 PM (e) (s)

Pasquale you keep harping on about

Pasquale wrote:

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

I think you don’t understand what he meant. We know he doesn’t mean what you are saying which is, basically,
If there are x number of species today then we can expect ~x number of species at any point in time during the past.

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

What I view is the fact that he acknowledges that species evolve and go extinct. Remember that a species to him was a population of interbreeding organisms. You could have many different species around the world that could interbreed but because of isolation they do not. Just as we see with the equines today.

As far as the feathers go I laugh. You make it sound that breaking a problem down n number of smaller parts makes the job n times more difficult. And you make it sound like you need n times more information. This simply is not true. The only thing required in the development of feathers is that you need n genetic modifications that get propagated through the species. These modifications of themselves don’t have to show a functional advantage if they occur within the same members that have some other trait that makes them better breeders thus spreading the genetic information through the population faster.

There might be 5 well define steps in the evolution of the feather but you don’t need a distinct reason why each step occurred. Having not really studied this particular issue let me throw up some possibilities.

The first feathers may have served a roll in breeding. Functionally they wouldn’t do anything but attracted the opposite sex of that species. Miss species x might just like the look of the feathers and decide to breed with Mr species x with primitive feathers.

Offspring species x (with feathers) might have hit a threshold where the genetic mutation of scales into feathers covered much of their body. This mutation may have developed further into multiple branches. Some of these branches going extinct simply because of chance others surviving because of chance while other mutations may have survived because they provide an advantage. This could be insulation helping the species move into environments that where not accessible before.

Any number of the feather could have occurred. At some point these feathers along with genetic changes that cause the forelimbs to slowly change gave species y (a descendant of species x) an advantage by allowing them to move with greater ease or with greater speed. This trait would, over time, prove more and more advantage to species y now becoming species z.

The key is that a species only needs a member with a mutation to be successful at breeding for that mutation to be, for a lack of a better term, successful within the linage of said species.

Lastly you keep saying that ID will provide answers, while Natural Selection can not, is a laugh. To this date ID has produced any answers and Natural Selection has produced vast amounts of answers. While I’m all for new ways of looking at things I can not apply this to ID because ID is basically just promoting the god of the gaps to fill in unknowns. The problem here is they don’t explain anything.

I also would love some references to all this information you have that DNA is like a computer program blah blah blah. While I can see some analogy between the 2 I don’t see the 1 to 1 correlation you seem to be trying to preach. The best I can equate it to is the genetic programming techniques that are coming out where they have programs are developed by introducing random mutations into the code testing the whole generation of programs then picking the best few programs and doing the whole process over again. I’ve seen many programs that use this technique. You should know that major aerospace manufactures develop new wing designs this way with little to no human intervention with greater results then a human can produce. NS is just the rules. There is no design of the wing here just the random code changes. Now you might say “well the wing had to be there to begin with it.” Ok with the wing I admit they start with an existing wing but I’ve seen this same technique used to evolve a program to simulate bipedal walking. Here they started with a system that couldn’t move without falling through a number of generations that evolved into the system walking. It was interesting to see some of the solutions the program came up with to include a summersault type of mobility. But this is far from what you mean because these program evolve independent of the “designer”

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

Comment #8879

Posted by Pasquale Vuoso on October 18, 2004 11:14 PM (e) (s)

Syntax Error: mismatched tag 'u'

Comment #8880

Posted by Pasquale Vuoso on October 18, 2004 11:19 PM (e) (s)

Steve wrote:

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

I was in a Discount Book Store about a year-and-a-half ago, and they had the book—just out if I remember. I perused the book, looked at pertinent sections, and thought it wasn’t worth the $7.00 they were asking. But thanks anyway.

Comment #8882

Posted by Steve on October 19, 2004 12:57 AM (e) (s)

“Pasquale”, “Let” us KNOW ‘as’ soon ‘as’ “you’ get that MATHEMATICAL “disproof” of ‘Darwinism’.

Comment #8884

Posted by Pasquale Vuoso on October 19, 2004 02:28 AM (e) (s)

PvM wrote:

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

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

PvM wrote:

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

As to #1, in my answer to Wayne Francis ( a couple of posts ago) I indicate that Darwin’s “tentative” may is in reality almost a “must.” Darwin just wasn’t that sure. He wasn’t willing to go out that far on his “Tree of Life” limb.

As to #2, Darwin thought that “vigorous” (let us say) species have a predisposition to change (where it comes from, he doesn’t know. I suspect this is no more than what’s called “heterosis”, something still not understood by geneticists.), and so the kind of “stasis” that is seen in the fossil record doesn’t accord well with his thinking.

As to #3, I don’t think it is logical, nor do I think it well-reasoned—and it was criticized as such at the time it came out. Is it brilliant? Yes. That it is. Was Darwin a phenomenol “observer” of nature and a great experimentalist? Yes. Did he reason things through adequately enough? No, I don’t think so. But my hat is off to him nonetheless. He was a great Naturalist; that no one can dispute.

But that doesn’t make him right.

PvM wrote:

(Pasquale’s numbering)
1) None of the discoveries that microbiologists have made nor the misnomer of ‘information revolution’ has given any support to ID as a scientifically viable contributor to science.

2) If your argument is that it needs another 10 years, fine, lets see if the second decade become more fruitful than the first.

3) Remember however that ID has proposed many ideas (NFL, CSI, LCI, IC) which have all shown to be fundamentally flawed. In addition ID has shown no interest to present its own hypothesis.

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

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

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

PvM wrote:

(Pasquale’s numbering)
(1) The Linnaean hierarchy is a human invention, ad hoc and thus really unsuitable for the purposes it is being abused.

(2) I am not sure what your comments about incipient species, varieties etc refer to but these are common concepts in taxonomy in which animals (subspecies) and plants (variety, form) are subdivided beyond the species level.

(3) Since I fail to understand what Pasquale’s argument or objection is to Darwin’s incipient species/varieties argument, it is hard to address it but reading Darwin, his comments seem quite logical. How are his comments in conflict with Mendelian genetics?

As to (1): I wouldn’t consider the Linnaean System “ad hoc”. I don’t know what your position is versus “cladistics”, but the very systematized cladistics system, as far as I understand it, jives fairly well with the Linnaean. But, as you’ve stated, you’ll get into that more on another post. So I’ll be interested in getting your fuller view then. I’ve read Henry Gee’s “In Search of Deep Time,” and understand he’s critical of NS to a degree. So maybe it cuts both ways.

As to (2): If it doesn’t make sense, then you need to blame Darwin, not me. Here are some quotes from the Origins:

(p. 109) The fact of varieties of one species, when they range into the zone of habitation of other species, often acquiring in a very slight degree some of the characters of such species, accords with our view that species of all kinds are only well-marked and permanent varieties.

(p.138)In these remarks we have referred to special parts or organs being still variable, because they have recently varied and thus come to differ; but we have also seen in the second chapter that the same principle applies to the whole individual; for in a district where many species of a genus are found- that is, where there has been much former variation and differentiation, or where the manufactory of new specific forms has been actively at work- in that district and amongst these species, we now find, on an average, most varieties or incipient species.

(p. 333) In the second and fourth chapters, on Variation and on Natural Selection, I have attempted to show that within each country it is the widely ranging, the much diffused and common, that is the dominant species, belonging to the larger genera in each class, which vary most. The varieties, or incipient species, thus produced, ultimately become converted into new and distinct species; and these, on the principle of inheritance, tend to produce other new and dominant species.

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

PvM wrote:

(1) They also note why they consider neo-Darwinism as having failed. It’s not that the explanation is at odds with neo-Darwinism, in fact they seem to argue that it is quite in line with neo-Darwinian theory but rather they argue that the Darwinian approach was unsuitable to unravel these issues and find the explanations.

(2) Rather than rejecting Darwinism, the authors extend it with new tools.

(3) I have seen some confusion among ID proponents when it comes to the realization that the argument is not against Neo-Darwinism but rather that Neo-Darwinism has focused on the wrong tools in some cases.

As to (1): I fail to see any distinction here. “Neo-Darwinism” failed to provide an “explanatory filter” for what scientists found. (Pun intended.) There’s no way around that.

As to (2): To me, this is simply being unable, or unwilling (probably more the former, than the latter) to allow this “failure” to change their way of thinking.

As to (3): This is said with all due respect: I think you’re having the same difficulty as they are.

Finally, let me make it perfectly clear, as Nixon used to say, that I understand perfectly what Prum and Brush are trying to say. I understand their results; I understand perfectly their analysis. I understand the “hope” they have for future research. I understand all of that—it’s not that complicated really. I just think they can’t see the “forest” for the “trees.” So, please, no more lectures!

Comment #8885

Posted by Pasquale Vuoso on October 19, 2004 03:12 AM (e) (s)

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

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

Comment #8886

Posted by Wayne Francis on October 19, 2004 03:13 AM (e) (s)

Syntax Error: mismatched tag 'kwickxml'

Comment #8887

Posted by Wayne Francis on October 19, 2004 03:46 AM (e) (s)

Pasquale wrote:

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

Do you consider Grevy Zebra, Mountain Zebra, Plains Zebra, Common Horse, and Donkey all different species?

What do you define as a “Species” All the above are individual species. They all evolved from a common descendant. These last 5 remaining species of Equine. I’ll borrow the tree of Equid family as we know it from

Horse Evolution

I’ve modified the top bit

 
 
        Grevy  Mountain  Plains  Common  Donkey  
        Zebra   Zebra    Zebra   Horse     | 
           |      |        |       |       | 
2My        --------------------------------- 
                    |  
                    |  
4My   Hippidion  Equus                                           Stylohipparion 
         |        |                   Neohipparion   Hipparion   Cormohipparion 
         |        |    Astrohippus         |           |             | 
         |        |    Pliohippus          --------------------------- 
12My     Dinohippus    Calippus                     \  |  / 
             |          |         Pseudhipparion     \ | / 
             |          |              |               | 
             -------------------------------------------     Sinohippus 
15My                  \  |  /                                 | 
                       \ | /                     Megahippus   | 
17My                Merychippus                      |        | 
                         |           Anchitherium    Hypohippus 
                         |                 |           | 
23My                Parahippus             Anchitherium             Archeohippus 
                         |                       |                       | 
                  (Kalobatippus?)----------------------------------------- 
25My                              \  |  / 
                                   \ | / 
                                     | 
35My                                 | 
                                Miohippus  Mesohippus 
                                      |        | 
40My                                  Mesohippus 
                                          | 
                                          | 
                                          | 
45My                      Paleotherium    | 
                              |          Epihippus 
                              |              | 
                       Propalaeotherium      |       Haplohippus 
                              |              |       | 
50My         Pachynolophus    |              Orohippus 
                   |          |                 | 
                   |          |                 | 
                   ------------------------------ 
                                    \  |  / 
                                     \ | / 
55My                             Hyracotherium 

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.

So while I agree you’ll never see a cat give birth to a dog you will see over the long term a species come to the point where if you could bring back its ancestor species that it would not be able to interbreed.

So we not only have fossil evidence of equids evolving new species but we also have the present day species showing their divergence from a common ancestor and how 2-4 million years of random mutations and genetic drift cause the species to move further and further apart.

There is no clear point where equus became one of the 5 species we see today. There are only gradual changes. My guess is if we could clone a equus that it would probably be able to interbreed with the current 5 species much like the hybrids we get today. The offspring would probably be infertile like the hybrids of these 5 species are normally infertile. But that is just a sign of their common descent and the modifications they’ve under gone.

Will humans ever evolve into a new species? Depends on what you mean. If you look at humans now and in 4 millions years from now descent with modification will predict that the 2 would probably not be able to interbreed very successfully. What would ID’s prediction be? Humans will only branch into 2, or more, species if we isolate them for long periods of time such as interstellar space travel. This is because humans on earth constantly interbreed sharing their genetic changes. But again in 4 million years the human genome will be different then it is today.

Comment #8890

Posted by PvM on October 19, 2004 09:27 AM (e) (s)

Pasquale wrote:

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

If that is all you argue Behe has done then there is little we disagree on. As is the case with any science, our increased knowledge and abilities to study details have uncovered many complexities.
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).
Behe’s arguments were on shaky fundamentals.

Pasquale wrote:

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

What is the ID perspective other than a negative one? Your comments on Junk DNA are also misleading since Junk DNA may suggest that it has no function when all it means it that is is not expressed as protein. I am working on a contribution on evolvability (the ability of evolution itself to evolve under selective pressures) which help us understand issues of neutrality, Junk DNA, hypermutations etc. An ID premise is not going to help us establish scientific pathways or increase our understanding in any positive manner. Calling something ID merely reflects our ignorance and gives no guidance as to how to resolve this. In fact ID has to object to any attempts to resolve these manner (Prum’s paper comes to mind) as any resolution will undermine the ID gap argument.

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

NFL: No Free Lunch
LCI: Law of conservation of information
IC: Irreducible complexity

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

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.

Comment #8894

Posted by PvM on October 19, 2004 09:43 AM (e) (s)

Pasquale wrote:

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

Cladistics and Linnaean hierarchies are moving close in many cases where previous paraphyletic groups become monophyletic. However a major difference of Linnaean hierarchies wrt cladistics is that the various taxa genus, family etc are all at the same distance.
Linnaean hierarchy serves a purpose of having common names for species but at a higher level, what makes a genus, family all the way to phylum is quite ad hoc.

For example, birds are now known to be the direct evolutionary descendents of small, predatory dinosaurs. The skeletal similarities between Mesozoic birds and coelurosaurian dinosaurs are remarkable, yet birds are not classified as reptiles because they have feathers. Feathers are the evolutionary novelty that define birds apart from reptiles. So, because dinosaurs lack feathers, they are grouped with crocodiles as reptiles, even though they are much more distantly related to crocodiles than they are to birds. Another example are the so called “mammal-like reptiles” a group of extinct animals that are defined on their lack of several key traits possessed by modern mammals. These animals are classified as reptiles because they appear to be at a reptilian grade of evolution (lacking inner ear bones, sprawling stance) even though they have only a distant evolutionary relationship to reptiles. In a sense, this is equivalent to taking a roomfull of people and determining which have the same last name based on how similar they appear. In some cases this will work just fine - appearance is related to familial descent - but it would also tend to result in all small children being grouped together (they are the same size and at a similar stage of development) and in some family members who happen to look different being assigned to separate groups.

Another problem with a phenetic classification is that it imposes a hierarchy of discrete categories on an evolutionary history that is continuous. For example, an Order might contain twenty different Families. Assigning all twenty families to an order indicates that all twenty families are related by common descent, but it says nothing about the detailed relationships of descent among the twenty families. If ten of the families are very closely related such that they share a common ancestor, then to indicate this we have to make a new category between Order and Family, such as Superfamily or Suborder. Then, if we decide that five of the ten families are also related by a common ancestor, then we need yet another category. The terminology of classification quickly becomes cumbersome.

Source

Comment #8895

Posted by a Creationist Troll, apparently on October 19, 2004 09:43 AM (e) (s)

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

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

In the meantine …….

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

Comment #8896

Posted by a Creationist Troll, apparently on October 19, 2004 09:46 AM (e) (s)

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

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

In the meantine …….

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

Comment #8899

Posted by PvM on October 19, 2004 10:20 AM (e) (s)

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?

ROTFL. As has been shown by various contributors here, DIS’s challenges do not hold water when looking at the papers. Remember that they have to support Meyer’s position that Neo-Darwinism (and/or other evolutionary mechanisms) cannot explain the origin of novelty. DIS’s appeal to various papers totally misses the point, fails to address why Meyer missed these papers which seem to undermine his viewpoint, fails to address why Meyer appeals to various papers which do not seem to support his assertions (Dilbert, Valentine come to mind).

Has the DIS proposed a scientific hypothesis to explain the origin of novelties? Thought so…

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

An interesting strawman. Should we expect such partly formed feathers or proto feathers right now? Or are you asking for fossilized evidence? And are you sure that recent fossil finds do not show exactly this?

Prum wrote:

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.

Comment #8902

Posted by Wayne Francis on October 19, 2004 10:28 AM (e) (s)

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.

Comment #8905

Posted by Russell on October 19, 2004 10:36 AM (e) (s)

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.

Comment #8938

Posted by Pasquale Vuoso on October 19, 2004 09:40 PM (e) (s)

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.

Comment #8939

Posted by Pasquale Vuoso on October 19, 2004 10:09 PM (e) (s)

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.

Comment #8945

Posted by Wayne Francis on October 20, 2004 01:04 AM (e) (s)

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.

Comment #8951

Posted by Flint on October 20, 2004 11:03 AM (e) (s)

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?

Comment #8952

Posted by steve on October 20, 2004 11:17 AM (e) (s)

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?

Comment #8954

Posted by Russell on October 20, 2004 11:34 AM (e) (s)

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!)

Comment #8955

Posted by steve on October 20, 2004 11:38 AM (e) (s)

Russel: Shhhh!

I want to see what he comes up with.

Comment #8957

Posted by Neil Johnson on October 20, 2004 11:48 AM (e) (s)

Wait! I got it:

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

Comment #8958

Posted by steve on October 20, 2004 12:06 PM (e) (s)

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.

Comment #8962

Posted by Pim van Meurs on October 20, 2004 01:17 PM (e) (s)

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.

Comment #8978

Posted by Pasquale Vuoso on October 20, 2004 07:04 PM (e) (s)

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.”

Comment #8980

Posted by Pasquale Vuoso on October 20, 2004 07:18 PM (e) (s)

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!

Comment #8983

Posted by Flint on October 20, 2004 08:52 PM (e) (s)

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.

Comment #8985

Posted by Steve on October 20, 2004 09:09 PM (e) (s)

The long war between science and religion.

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

Comment #8986

Posted by Sage Ross on October 20, 2004 10:48 PM (e) (s)

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.

Comment #8987

Posted by Steve on October 21, 2004 12:01 AM (e) (s)

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.

Comment #8991

Posted by Wayne Francis on October 21, 2004 02:32 AM (e) (s)

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.

Comment #9002

Posted by Pete Dunkelberg on October 21, 2004 10:30 AM (e) (s)

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.

Comment #9003

Posted by Flint on October 21, 2004 11:03 AM (e) (s)

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.

Comment #9007

Posted by Great White Wonder on October 21, 2004 12:47 PM (e) (s)

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).

Comment #9011

Posted by Pete Dunkelberg on October 21, 2004 02:47 PM (e) (s)

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.

Comment #9013

Posted by Flint on October 21, 2004 03:40 PM (e) (s)

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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