Pharyngula

Wells lies. Again.

When I see Jonathan Wells’ name on anything, I know I’m in for some furious gnashing of the teeth because of the man’s infuriating tendency to blatantly lie with every sentence. That’s the case with his recent baseless criticisms of the peppered moth story; Mike Dunford takes care of him this time around.

Comments

  1. #1 David Marjanovi?
    September 6, 2007

    OK. It’s almost 1 at night over here. I’ll come back later. Just so much for now: I’m a paleontologist, and I can’t see what problems “Darwinism” is supposed to have with the Cambrian Explosion. Are you aware that it is full of intermediates between arthropods, tardigrades, and onychophores? Between trilobites, chelicerates, crustaceans, and the aforementioned intermediates? Between annelids and brachiopods? Are you furthermore aware that it took some 15 million years and had a prelude that lasted another 15? Furthermore, are you aware that the oldest known mollusk, Kimberella, is again ten million years older? (It’s a very simple mollusk as far as we can tell from its remains, but the radula is there, the creeping sole is there, and the tough dorsal covering is there.)

    Next, please suggest a definition of “species”. For your information, there are at least 25 species concepts out there (not all, but most of them, applicable to all of life), and the biologists can’t agree on one, even though the number of endemic bird species in Mexico (to pick one example) varies by a factor of over two depending on the species concept. Some, unsurprisingly, suggest that species don’t exist, that we can’t cut the tree of life into pieces unless those pieces are arbitrary. But if you can’t suggest a species concept, you can’t start from the assumption that a difference between “microevolution” and “macroevolution” has to exist. So, tell me one, and I’ll point out the holes in it.

    Unlike others here, I won’t doubt your IQ. It is, however, apparent that you have read very little about certain topics that you believe to have understood very well.

  2. #2 David Marjanovi?
    September 6, 2007

    Erm… as everyone will guess, my comment was directed at Jim (or for that matter any ID proponent). Good night, “see” you tomorrow.

  3. #3 David Marjanovi?
    September 8, 2007

    Sorry for the long post. This is one time-consuming thread!

    ——————

    This might get a little tough to follow. Jim, I’m going to use your convention of name followed by colon followed by comment in quotes. I’m putting all previous comments from either of us in italics. I’ve also separated things into artibrary numbered blocks. Let me know if this isn’t clear. -Josh

    I recommend HTML: start quotes with <blockquote> and end them with </blockquote>. That’s what I use, and why it says “you may use HTML tags for style” above the comment window.

    It is possible to nest any number of blockquote tags within each other. <blockquote><blockquote>a</blockquote>a<blockquote> produces

    a

    a

    (I put line breaks in. I don’t know if that’s necessary.)

    ————-

    Jim, you explained how to choose between necessity, random, and design. But you overlooked the fourth possibility: evolution.

    Obviously, evolution doesn’t apply to a deck of cards. Cards don’t reproduce, so they cannot evolve. So when you exclude necessity and random, it follows that design is the answer. But organisms aren’t cards. They reproduce, inherit, and mutate — and those which have certain mutations and lack others have more surviving fertile offspring than the rest.

    Hey, think of languages. Languages are inherited (even though not in the biological way), mutate, and spread. Give Latin 2000 years, and you arrive at French, which is a completely different language. That much is documented. So if you find a language, you can rule out necessity and random, but you don’t have the slightest reason to assume design.

    ——————-

    the chief prop of the theory (in the macro sense, and in its present form) is materialistic philosophy

    Is ToE open to the idea that an immaterial cause (intelligence) played a role – perhaps the key role – in life’s evolution? If not, then ToE is wedded to materialistic philosophy.

    What a bunch of nonsense. The theory of evolution is science, not philosophy.

    It seems you are thinking of methodological naturalism. All science is built on methodological naturalism, which is the assumption that miracles do not happen so often as to make the world wholly unpredictable. Perhaps ironically, but fortunately, that assumption is itself a scientific hypothesis, because it is testable — and it is tested in every single experiment and every single other observation! It still hasn’t been disproved, so it looks like a quite safe assumption.

    You know Popper and the concept of falsifiability. Fine. But how do we decide between two hypotheses that are both testable, tested, and unfalsified, and explain the same amount of evidence? We apply Ockham’s Razor, the principle of parsimony. Of such two hypotheses, the one must be preferred that requires the smallest number of ad hoc assumptions.

    So given the fact that it has been shown that a designer is not necessary (see below), we should, for the time being, not assume that one exists. After all, we simply don’t need to, and the assumption that a designer exists is “a huge, HUGE claim in and of itself” (Kseniya).

    As far as I know, the principle of parsimony is the only reason why the phlogiston theory of combustion was already universally considered disproven before it was possible to play with single molecules and atoms. It had to make more and more ad hoc assumptions (phlogiston has negative mass, yet still somehow doesn’t flee the Earth; oxygen is dephlogisticated air; and so on) that the oxygen theory of combustion simply didn’t need.

    Now, be careful not to confuse methodological naturalism with metaphysical naturalism. Metaphysical naturalism is the assumption that nothing supernatural such as miracles –no matter how little it meddles with observable nature — exists. As its name says, it is metaphysics, it is philosophy. That is not what science is built on.

    This is why not every scientist is an atheist: science doesn’t require it. Even dogmatic Catholicism, according to which every single saint has (by definition) worked at the very minimum one miracle, is (barely, but still) compatible with methodological naturalism and therefore with science. Result: the Papal Academy of Sciences.

    I have no quarrel with what the fossil record tells us about the existence, structure, and age of the organisms you mention, but I suspect that the “intermediates” among them are identified by reference to the needs of Darwinian theory, which makes their identification self-referential (or circular), a kind of reasoning that confirms nothing. If you didn’t view those “intermediates” through the lens of Darwinian theory, is there something about them that cries out “We are intermediate, transitional forms”?

    Oh yes.

    Ignore all fossils and look around yourself. Every species and subspecies is, in many features, intermediate between others. And indeed, the botanist Jussieu thought in the 18th century that nature is a continuum: everything is intermediate, and all lines we draw are arbitrary.

    Now, the interesting thing is that we find intermediates between some groups, but not between others (contrary to what Jussieu had assumed). We have the platypus and echidna, but we don’t have an intermediate between mammals and butterflies. Why is that?

    Common descent is an easy explanation. It’s also a testable explanation, because it makes testable predictions. It predicts intermediates between placentals and marsupials, and between those two together and the monotremes, as well as between those three together and the “reptiles”. Lo and behold, we have plenty of fossils of just such animals.

    Don’t you first have to assume unguided (or Darwinian) evolution before you can label an organism an intermediate, transitional form? Wouldn’t it be senseless to label an organism an intermediate, transitional form without first assuming unguided evolution?

    No, as explained above.

    Let me ask you this, David: Is the platypus an intermediate, transitional form?

    In many respects, yes.

    If so, is it on its way to becoming fully reptilian, or fully mammalian?

    Like everything else, it’s on its way to become ever more unique.

    In many respects, we are intermediate between the chimps + bonobos on the one hand and the gorillas on the other.

    The problem Darwinism has with the Cambrian explosion is that its primary mechanism (random mutations acted on by natural selection) has not been shown to be capable of producing such an explosion of new, complex life forms in such a short (geologically speaking) period of time. In fact, that mechanism has not been shown to be capable of producing new life forms if it is given hundreds of millions of years to operate.

    How would you do that? What would such a test look like?

    What we see confirms to the predictions. We see a wild bush in the fossil record and in today’s world that grows in all directions. That’s what we expect from evolution by mutation, selection, and drift. It’s not what we expect from anything that leads towards progress or suchlike.

    David: “For your information, there are at least 25 species concepts out there (not all, but most of them, applicable to all of life), and the biologists can’t agree on one…”

    I know. That’s what makes claims that speciation has been observed so unenlightening. If you define species down far enough, you’re bound to observe speciation and find that Darwinian mechanisms can produce it.

    How would you define it, then?

    David: “…you can’t start from the assumption that a difference between ‘microevolution’ and ‘macroevolution’ has to exist. So, tell me one, and I’ll point out the holes in it.”

    OK. Adaptive changes that leave organisms essentially unchanged (such as adaptive changes in the coloration of peppered moths, or in the size of finches’ beaks, or in the resistance of bacteria to antibiotics) are microevolutionary changes. Creative changes that cause organisms to evolve from one kind (say, fish) to another kind (say, amphibians) – or creative changes that introduce biological novelty (i.e., new organisms, new organs, new structures, new processes, new systems) – are macroevolutionary changes.

    I regret to say that this is exactly the non-answer I would have expected from a creationist.

    Let’s start with your seventh word: “essentially”. Can you define that?

    Then please tell me which changes are “creative” and which aren’t. To get from Tiktaalik to Acanthostega you need to do very little: modify the way the ends of the paired fins grow (that could be just a small change in the amount of expression of a single gene, though I’m admittedly guessing here), switch off the production of fin rays at their ends (that might even be a result of the same mutation, and if not, a small change in the area of expression of another gene is necessary), and mess a little — just a little — with the proportions of… mainly the skull. That’s it. Why are such changes “creative” while a color change in a moth is not?

    Lastly, you use the term “kind”. As several others have mentioned above, only creationists do that.

    I am not quibbling over the fact that you didn’t use terms like “class”, “order” or “family”. The ranks traditionally used in classification are undefined, and you will not find anyone who denies that they are subjective. The groups are real; the ranks that their names get are not. There is no way to define “class”, and there is no way to define “kind”. Moreover, the term “kind” carries the assumption that there are no intermediates between “kinds”, which is simply not the case.

    If we confirm the ability of Darwinian mechanisms to accomplish the former, we haven’t confirmed the abilities of those mechanisms to accomplish the latter.

    Eh, no. But you have yet to show me that we need to assume that “creative changes” exist in the first place. If you can’t do that, I’ll bring Ockham’s Razor.

    If changes that leave the organisms “essentially unchanged” are demonstrated to occur now, the principle of parsimony says we have to consider them demonstrated at all times. Show me there are “creative changes”, or give up.

    ————

    Suppose that we define species in terms of reproductive isolation. Suppose, also, that we experimentally produce the reproductive isolation of a new strain of bacteria

    What, don’t you know that bacteria don’t do sexual reproduction?

    They do engage in activities termed “parasexual” or “conjugation” — and that is the (one- or two-sided) exchange of DNA with anything. Absolutely anything. It probably doesn’t matter statistically, but you are not isolated against conjugation from any of the bacterial “species” in your gut.

    Ernst Mayr, the most famous proponent of the reproductive isolation criterion as a species concept, said outright that “bacteria do not form species”. (I don’t know if that’s an exact quote.)

    —————

    would no doubt say: “But they’re still bacteria. I thought Darwinian mechanisms were supposed to be capable of generating descendants that are quite different from their ancestors – amphibians from fish, for example. How in the world does this new species of bacteria you’ve produced confirm that claim?”

    If you really believe a frog and a trout are more different than an Oscillatoria cyanobacterium and a Rickettsia alpha-proteobacterium, you have a lot to learn…

    ——————-

    Those advances are posing increasing problems for Darwinism. Darwin thought the cell was a simple blob of protoplasm. I wonder if he would have proposed his theory if he knew what we know today about the cell – that it’s an enormously complex “factory” containing an elaborate network of interlocking “assembly lines” – that it’s jam-packed with power plants, automated workshops, recycling units, miniature monorails, sensors, gates, pumps, identification markers, and (in some cases) rotary outboard motors – that a single cell contains (as Richard Dawkins has observed) more information than a complete set of the Encyclopedia Britannica. I wonder how seriously he would have taken the notion that the complex machinery of the cell arose by way of unintelligent material mechanisms.

    Aaaah… that talking point again. It’s an argument from ignorance. Take the microtubuli in your cells, composed of alpha-tubulin and beta-tubulin. These two proteins are very similar, except that the beta one functions as a GTPase, while the alpha one is a defunct GTPase — it has a pointless inbuilt GTP, so to speak, and can’t destroy it. It is very easy to figure out which mutations — and there are few — were necessary to derive both from a common ancestor that was a functioning GTPase. Then the next step. Behold FtsZ, a protein with an important function in the cell division (it pinches the cell together in the middle) of bacteria (including chloroplasts and many mitochondria) and archaea. It, too, is a globular GTPase that forms long chains which change their curvature and become less stable when the FtsZ hydrolyzes its GTP. Not only that, its precise shape is very similar to that of the two tubulins of eukaryotes. Why should that be?

    —————

    Now the biggie. I mentioned alpha-tubulin with its inbuilt GTP above, a GTP that has to be produced using energy. What a waste of energy. That’s my last question: How does ID “theory” explain stupid design?

    I bet it doesn’t.

    By “stupid design”, I mean things that a halfway reasonable designer would not have done. Our eyes correct for chromatic aberration only in having a very small number of blue receptors — the error is still there, but we don’t see it, at the price of seeing blue very badly. Then there’s the fact that the retina and all is inside-out: light traveling through the eyeball has to traverse a layer of blood vessels and nerves and then the whole retina to strike the light receptors at the back end. The trachea and the oesophagus join in the pharyngeal cavity; as a result, we can die from choking. (The whales have solved this problem: their trachea grows through the pharyngeal cavity all the way up to the nasal cavity. This limits the size of the prey they can eat; after all they don’t chew. A stupid solution to a stupid problem.) Our kidneys first let everything pass that’s water-soluble and then frantically work to transport the valuable stuff from the primary urine back into the blood, using a lot of energy. Our urogenital system… the word says it all. Our knees and intervertebral discs can barely stand the usual stresses of life. And it’s not just us humans, mammals, or tetrapods who’s botched up: about 800 amino acides occurred in living organisms last time I checked, yet only 20 (OK… 22) occur in proteins and are coded for in the DNA. Why this restriction? More amino acids could make a lot more versatile proteins. Then there’s DNA itself. It slowly but steadily falls apart when you keep it in water. What a stupid idea to use that as the carrier of heredity! You spend most of your energy constantly repairing your DNA, especially (but not only) replacing bases that have fallen off. It doesn’t have to be that way: for biochemical experiments that DNA wouldn’t survive, the so-called PNA was developed. It has a protein backbone, and it does not react with water to a noticeable extent. But no, we are stuck with the stupid solution.

    Evolution can explain all of these cases of stupid design, and it can explain why we use DNA and not the even more unstable RNA. (Ask, and I’ll explain them; this post is really long enough.) ID runs into a contradiction at worst and is silent at best, right?

    —————————

    Josh again:

    I think Spriggina is a very credible possibility as a trilobite precursor.

    I disagree. (See? Those evilutionists can’t agree on anything! Obviously they’re all wrong! ;-) ) First, trilobites are arthropods, so when we look for a trilobite precursor, we must look within the arthropods. (Indeed we have found plenty of animals that look very closely related to trilobites, and others that are closely related to both trilobites and chelicerates.) Spriggina has indeed been interpreted by some as an arthropod relative, but it’s probably a vendobiont. The closest known relatives of the arthropods — anomalocaridids and water bears especially — are quite different. Jim, note that the anomalocaridids are part of the Cambrian explosion, and that they are only preserved as fossils under very rare circumstances.

    Trilobites do appear suddenly (in a geological sense) with already pretty well developed eyes. There isn’t any direct evidence for trilobites right now (that I know of) as to earlier stages of those eyes.

    The chelicerates have simpler eyes than the trilobites (and, independently, the insects).

    the trilobite record overall is a rather striking example of increasing complexity through time, with gradually increasingly complex forms appearing as one goes up from the Lower Cambrian into increasingly younger rocks…

    Nope. What increases through time is the range of complexity. :-)

    ——————

    Like you (apparently), I think all the other pre-trilobite organisms don’t recommend themselves as credible evolutionary precursors of trilobites. So we have one credible precursor (why is Spriggina credible?) and – what, thousands? millions? – of non-credible precursors. To me that sounds like the pre-trilobite fossil record contains few, if any, credible trilobite precursors (which is the claim I made).

    Jim, you seem to have rather odd ideas about the Precambrian fossil record and our knowledge of it. There aren’t millions, there aren’t thousands, there are probably not even 100.

    And why should the Precambrian record be full of trilobite precursors? One (or, rather, an arthropod-tardigrade-onychophore precursor) should suffice, shouldn’t it?

  4. #4 David Marjanovi?
    September 8, 2007

    Based on statements like that made by Darwinist Richard Dawkins, who claimed that the Cambrian phyla appear to have been “planted” without any evolutionary history, I inferred that paleontologists had found little in the fossil record in the way of likely precursors to the Cambrian phyla (otherwise, why would Dawkins, who would love to see a plethora of precursors, say such a thing?).

    He’s exaggerating. Perhaps for dramatic effect, probably out of ignorance (not everyone has read the necessary papers, and he’s not a paleontologist, let alone one who works on the Cambrian).

    Hm… I wrote the above before I read comment 203. Looks like I was right. :-)

    Or should we expect to see in the fossil record a clear lineage before we make such a claim with the air of certainty displayed by Stanton?

    No.

    Imagine a very bushy bush — not really a bush because all branches have the same (and very small) thickness. Take a few cross-sections at not too small intervals. Throw away on average 99.99 % of each cross-section, less from the higher ones and more from the lower ones, roughly. (And that not at random; introduce a complicated bias.) Then compare any two successive cross-sections. What is the probability that you will find any particular branch in both? What is the probability that we should find a direct ancestor of anything we know in the fossil record?

    I haven’t commented the brontothere example yet. I don’t know the details of that particular one, but, if taken literally as an ancestor-descendant sequence, it’s almost certainly wrong. Most supposed ancestors in the… terrestrial vertebrate record before the Pliocene anyway have turned out to have innovations of their own, which makes it an unparsimonious assumption that they are direct ancestors of anything known. That includes, for example, Archaeopteryx.

    If taken less literally, the brontothere example is still a nice illustration: it is what we expect to find.

    Edward Reed, among others, has argued that natural selection may be a law of nature.

    I don’t know who that is, but I don’t need to know that to see that the claim is not very intelligent. Natural selection is already inescapable, based on what we already know. It’s almost a tautology: after a while, most will be descendants of those who have had the most surviving fertile offspring; those have had the most surviving fertile offspring who were best equipped to do so. If reproduction, inheritance, and mutation exist, natural selection is impossible to avoid.

  5. #5 David Marjanovi?
    September 8, 2007

    …aha… comment 203 is now 204…

  6. #6 David Marjanovi?
    September 9, 2007

    Graculus: “‘Meaning’ is entirely subjective, and not measurable, even in biology.”

    In that case, why bother doing science? If all science can deliver is subjective meaning, what’s the point of it?

    I don’t understand that.

    Science is not about meaning. Or what do you mean by “meaning”?

    —————–

    I disagree. First, trilobites are arthropods, so when we look for a trilobite precursor, we must look within the arthropods.

    That’s not true at all.

    Oh, so you’re just saying you aren’t looking for an immediate trilobite precursor? In that case, of course, I agree.

    I was trying to keep things as ‘stratigraphic’ as possible.

    That only works when the fossil record is very good, and in the Cambrian, let alone before that, it isn’t. However, here is an article that should give an impression on how many and how close relatives of the trilobites and chelicerates are known from the Cambrian.

    BTW, how old is the oldest known trilobite?

  7. #7 David Marjanovi?
    September 9, 2007

    To answer my own question… Comment 79 contains the link to a nice table. So apparently the oldest trilobites are from the Tommotian-Atdabanian boundary according to the Siberian scale, and not even 530 million years old, which leaves plenty of time within the Cambrian before their first appearance in the fossil record.

    Also, I don’t have access to the article I posted the link to, only the first page. It’s enough for an impression, however. I got it from googling for Olenellida.

  8. #8 David Marjanovi?
    September 9, 2007

    The 550 figure must be outdated — the Cambrian only began 542 million years ago. http://www.stratigraphy.org/gssp.html

    Given their calcified armor, we should expect the trilobites to turn up in the fossil record long before their relatives. However, what definition of the base of the Cambrian was used in Morocco?

  9. #9 David Marjanovi?
    September 9, 2007

    Scholar.google.com finds this Geological Society of America meeting abstract for Fallotaspis which shows that Fallotaspis is Atdabanian in age, at least in North America. The next pages of results seem to show that, in North America anyway, the base of the Cambrian was put at the base of the Fallotaspis zone in the 1960s and 70s.

    Figure 2 (on p. 6) of this Google Scholar result shows that there is a “pre-trilobite” part of the Cambrian underneath the Fallotaspis zone, which begins in the Atdabanian. Warning: if you click on that link, you start downloading a pdf that has over 5 MB.

  10. #10 David Marjanovi?
    September 9, 2007

    Thanks for that link, Stanton. So the oldest known trilobites are 525 to 530 Ma old, but their tracks “extend right down to the earliest Cambrian beds”, and there’s biogeographic evidence for an even earlier origin which would mean the trilobites aren’t part of the Cambrian explosion.

    Two clicks away is this page, which depicts the closest known relatives of the trilobites.

  11. #11 David Marjanovi?
    September 9, 2007

    OK, Parvancorina it is then. :-)
    GSA abstract
    explanation

  12. #12 Torbjörn Larsson, OM
    September 9, 2007

    FWIW, if Jim comes back, here is my favorites (not the “best of thread”, but what I liked):


    I imagine he’d say that “interlocking complexity” and “irreducible complexity” are not the same thing. He’d likely also say that no one actually knows that “interlocking complexity” arose through unguided evolutionary processes.

    I know you retracted this later, as Behe’s original IC is identical to interlocking complexity. As some noted, what Behe did was dropping his original definition without a trace and replaced it with the current brand of creationist probability arguments on strawmen of evolution. (Situations or proposed mechanisms that aren’t observed.)


    I don’t know who wrote “Good Math Bad Math”, but the author evidently failed to understand Dembski’s explanation of specified complexity (or its subset, complex specified information).

    As Dembski explains it, you can’t just read specified complexity off of a pattern after the fact; in addition to reading the pattern, it must be shown that the pattern conforms to an independently given specification (i.e., a specification that exists independently of the event that produced the pattern).

    The blogger of GMBM is Mark Chu-Carroll, a computer scientist who enjoys debunking bad math, especially from denialists of different kinds.

    David Marjanovi? cuts to the chase in his answer, specification will not yield a parsimonious explanation in the face of the existing theory.

    But there are specific problems too.

    First, coupled to the discussion of information and complexity, there is no one information or complexity measure that can describe all possible patterns. So you really have to specify and test a relevant one. Which as we know ID proponents doesn’t want to do. Your examples doesn’t describe an ID mechanism for that specification or even an ad hoc specification that applies to all of biology.

    Second, either a mechanism or ad hoc specification is provided which then is indistinguishable from causation from natural processes, or ID is forced to look at “rarefied design”, that which remains when chance or necessity is excluded. But we can’t reliably detect rarefied design due to its low likelihood when all else should be excluded first. [Linking didn't work, but see the article "The Advantages of Theft over Toil: The Design Inference and Arguing from Ignorance" by Wilkins and Elsberry in Biology and Philosophy, Volume 16, Number 5, November 2001 , pp. 709-722(14).]

  13. #13 Torbjörn Larsson, OM
    September 9, 2007

    [The missing ingress in the previous comment:]

    I read this thread with gratification, great comments from David Marjanovi?, windy, Stanton, et cetera. And who will forget JimV’s new theory: “The Murphy Method, or, The Theory of Intelligent Failure”?

    We are getting used to creationists who claims IQ’s “to the north of 150″ and still are ignorant. I’m reminded of that genius bartender who suggested that he had explained nature and science by philosophy…

    [Cont.]


    With regard to biological systems, however, the only relevant information is that which is meaningful (i.e., the information that shapes matter into biological forms).

    [Later:] “Meaning” and “information” aren’t synonymous, but some information is meaningful and some isn’t. ID theory isn’t concerned with meaningless information.

    Information isn’t an especially useful characteristic or concern for biology. Also, as for “specification”, information needs models (are semantic) to be useful. And genetic or phenotypic information is contingent on the environment.

    But FWIW we can measure information in some cases. In its technical sense it is slightly related to complexity as for example in Kolmogorov complexity. And as no one complexity measure can characterize all possible structures, Kolmogorov complexity is not well defined. In practice you can pick a specific compression scheme to compare information content, but you can’t do much else with that type of information.

    Specifically, we can identify both Shannon and Kolmogorov information associated with genomes. It isn’t practically useful I think, but doable. Instead of giving references I will give another example.

    Apparently a model for allele frequencies in asexual populations look like Bayes theorem. [See http://golem.ph.utexas.edu/category/2006/12/back_from_nips_2006.html#c006690. And Bayes theorem is a model for trial and error inferences, where it decides which hypotheses should be weakened or strengthened. By this model we could call the populations alleles hypotheses and the population frequencies its current theory of the environment.

    This is information that the population picks up in its genome at selection by the environment. It is contingent as we noted earlier. Changing environment will lose the meaning of the information. Over time it will make the population forget the old environment and learn about the new one.

    Again, not an especially exciting observation except for the analogies we can make. But we can see that even if genomes doesn’t exhibit static and communicable information, it has definable and measurable information.

    But note:
    We can’t point to a specific feature of a system and say “this is the information”. What we can say is that we can observe information change. (In the Kolmogorov complexity case, differences in compression, by some scheme, before and after. In the Shannon information case, data loss over a channel.) In the analogy above it is by observing allele frequencies change.

    Information is a relative, not absolute, measure. It is not an object or a specific feature, nor necessarily static and communicable.

  14. #14 Torbjörn Larsson, OM
    September 9, 2007

    [Cont. And now the link script works...]


    and (in some cases) rotary outboard motors

    I would think that a retired flight captain would be more careful with technical details – the flagellum is an inboard engine embedded in the different membranes of different cells.


    Edward Reed, among others, has argued that natural selection may be a law of nature.

    But laws can be statistic. In fact, quantum mechanics is famous for combining deterministic state propagation with statistic outcomes of measurements.

    Similarly selection picks the most fit alleles in a certain situation, but which selection pressures are present is unpredictable, which population and frequency of alleles are present is unpredictable, and AFAIK the fixation process is also statistical. (I.e. with some probability it can fail.)

    Not that evolution is a solid observation among biological life. It is also observed to be robust.

    An early onset is observed in lieu of extinction risks or possible early total extinction. And it has survived other near total extinctions.

    Also, viruses and cells from different extant and extinct domains could have crossed the Darwinian threshold several times from a progenotic state. These crossings seems to be initiated by diverse selfish elements, and shows the competitive [sic!] nature of evolution.

    So evolution is a competitive and robust process which we should expect to be common elsewhere. Maybe we will meet singular existences, biological or mechanical, that aren’t described thusly. But I believe the way to bet is that they are rare and bound on an extinction path.

    So a law could be attempted, even warranted. For simplicity, I suggest “biological systems shows local common descent”. (Global common descent would be another observation. It seems difficult to ascertain if there was one or several progenotic communities which coalesced before passing the Darwinian threshold. Similarly it is wrong if we expect to apply the law elsewhere in the universe.)

  15. #15 David Marjanovi?
    September 10, 2007

    Congratulations for catching the “outboard motor” mistake!

    ————–

    Of course I wasn’t discussing an immediate precursor. Look back through Jim’s comments over the last few days…a basal arthropod wasn’t what he was asking for.

    Looking back through those comments, I don’t get the impression Jim knows what an arthropod is. In other words, I don’t think he himself knew and understood what he was asking for.

    —————–

    Respondents who continue to toss around the word “ignorant” (or other not-so-subtle insults) can expect to be ignored.

    “Ignorant” is not an insult. It is a statement that your claim to be widely read in the Theory of Evolution is mistaken. If correct (…and you have quite clearly shown that said claim is mistaken), you can do something against it by simply reading more.

    “Stupid” is an insult, because it implies that you can’t do anything against that condition, that you are beyond hope and best ignored.

    Whether the scarcity of fossils “from periods before about 600 million years ago” is a problem with the fossils or a problem with the theory, it is – notwithstanding Dawkins’s “explanation” of it – an unresolved problem for Darwinism (ToE).

    No, it is a problem of the fossil record. Older strata don’t contain different fossils, you see — they contain almost nothing. That’s because only the mineralized parts of organisms usually have any reasonable chance of becoming fossils — and before the Cambrian Explosion, few animals had mineralized parts.

    Also keep in mind that The Blind Watchmaker was written when of the few Early and Middle Cambrian sites that preserve soft-bodied organisms only the Burgess Shale was known. Now we have the Orsten in Sweden, Sirius Passet on the north coast of Greenland (first you need the idea of looking for fossils on the north coast of Greenland!), Chengjiang in southern China, and one in Australia. Now we can say a lot of things about the Cambrian Explosion that Dawkins had no idea of when he wrote The Blind Watchmaker.

    As PZ has also pointed out recently, it’s not quite clear why you try to cast doubt on evolution by a quote by, of all people, Dawkins.

    Oh, BTW, you can see when The Blind Watchmaker was written by its hopelessly outdated dating of the beginning of the Cambrian as 600 million years ago. That date hasn’t been advocated by geologists for decades.

    I was referring to the three explanatory modes: necessity, chance, and design. Evolution, as it is conceived by Darwinism, is not a fourth explanatory mode; it instead relies on chance (random variations) and necessity (natural selection) to produce life’s diversity and complexity. To say that something – life, languages, automobiles, civilization, or whatever – evolved is to describe, not explain. Descriptions can be informative, but they’re not explanatory. That’s why I say that if we “prove” beyond the shadow of a doubt that life evolved, we haven’t explained life’s origin and development. All we’ve done is describe it. To explain life’s diversity and complexity, we need to find the causes that produced them.

    There we have it: the causes are mutation (random), selection (not random), and to a small extent drift (random). Isn’t it obvious that the results of such a process will look neither like those of random alone nor like those of necessity nor like those of design?

    Common descent is essentially the starting point for everything else in Darwinism.

    That is not true. Darwin himself envisaged descent from “one form or a few”. The actual evidence for common descent of all known life is without exception biochemical (e. g. the universal genetic code) and was only discovered late in the 20th century.

    If necessity, chance, and design are all ruled out, then there is no explation for the evolution (or development) of languages. If we can’t say that languages arose by necessity (i.e., the nature of the universe compels the existence of languages), or if we can’t say that languages arose by chance (i.e., by linguistic “accidents”), or if we can’t say that languages arose by design (i.e., by conscious, deliberate choices made by human beings), then what CAN we say about the evolution of languages?

    I think it’s obvious. It’s mutation (random — sound changes, reinterpretations of grammar, and the like) plus selection (changes that make a language too ambiguous to understand are selected against) plus drift (neutral changes can become fixed within a population of speakers by chance). Evolution. The nature of the universe doesn’t compel the existence of languages; random cries will not become a language; conscious decisions are very rare and always have very little impact (see for example how prescriptivists have for centuries been trying to stop their fellow English speakers from ending sentences with prepositions the way Shakespeare and the King James Bible did, and it didn’t work, even though plenty of languages that have prepositions never end sentences with them). Not necessity, not random, not design — evolution.

    Behe made a big mistake when he tried to decide between three modes of explanation and didn’t notice there was a fourth. You have repeated his mistake.

    Most people intuitively sense that the gap between humans and, say, oak trees, is an unbridgeable gap.

    The gap between a choanoflagellate and a glaucophyte, on the other hand… Google for “Choanoflagellata” and “Glaucophyta” if you don’t know what I mean.

    You will also have noticed that both people and oaks are eukaryotes. That means a long, long, long list of commonalities just with respect to bacteria.

    As you may know, French biologist Georges Cuvier (the “father” of vertebrate paleontology and comparative anatomy) thought that the divisions in nature are grounded in necessity and that true intermediates cannot exist because such forms would likely be non-functional.

    Yep. His view quite soon turned out to be an exaggeration. (And that was still in the 19th century. Acting as if science had stopped back then won’t earn you any brownie points.)

    the fact remains that the fossil record is as discontinuous today as it was in Darwin’s day.

    Acting as if the science of paleontology had stopped in 1859 will not earn you any brownie points either. For crying out loud, in 1859 we had the living birds, the living crocodiles, perhaps two or three Mesozoic crocodiles, Archaeopteryx, Megalosaurus, Iguanodon, Hylaeosaurus, and that was it. Now we have hundreds on the dinosaur side as well as dozens on the crocodile side. Just last week… click here. In 1859, we had the living amphibians and amniotes, the living bony fishes, a few fossil lungfish (the extant lungfishes weren’t even recognized as such yet, I think), and that was it. Then we got swamped in temnospondyls, lepospondyls, embolomeres and whatnots on the one side and “osteolepiforms”, porolepiforms, and whatnots on the other, then in 1934 came Ichthyostega, and today Ichthyostega is just a little weirdo on a whole tree of ancient limbed and almost limbed vertebrates, the latest addition being Tiktaalik (don’t tell me you didn’t read about that one).

    As Denton wrote: “Whatever view one wants to take of the evidence of paleontology, it does not provide convincing grounds for believing that the phenomenon of life conforms to a continuous pattern. The gaps have not been explained away.”

    Then Denton is wrong, unless maybe (!) if I’ve misunderstood what he means by “continuous pattern”. Could you provide a little context instead of quote-mining?

    What you explained was that if we assume (or posit) common descent, then we should expect to find intermediates.

    No. I said we find intermediates (an observation made long before Darwin or even Lamarck; that’s why I mentioned Jussieu), and that common descent provides a nice after-the-fact explanation of why we find certain intermediates (like monotremes) but (contra Jussieu) not others (like mammal-hymenoptere intermediates).

    Quite so. If life’s history conformed to the predictions of Darwinism (ToE), it should resemble a “wild bush,” or Darwin’s “tree of life.” The phyla, then, should be greater in the branches of the tree than towards the base of the tree. But that’s not the case with the Cambrian phyla. They appear towards the base of the tree, not in the branches, and the number of phyla – rather than increasing since the Cambrian era as Darwinism predicts – has actually decreased. The Cambrian phyla look more like blades of grass on a lawn than branches in a tree. They are at odds with the expectations of Darwinism.

    Wow. You have misunderstood Gould about his misunderstanding of the Linnaean hierarchy.

    So, firstly, remember that all those terms like “genus”, “family”, “order”, “class”, “phylum”, “kingdom” are undefined and entirely subjective. Anyone can make up a classification giving any rank to any name, and as long as the ranks are nested within each other according to the agreed-upon pattern, nobody can say it’s right or wrong. It happens all the time; compare any two classifications of the same group, and you’ll never find them completely agreeing.

    Secondly, Gould didn’t notice that. He thought that if we call something a phylum, there has to be something that makes us call a phylum. But there isn’t. Instead, it’s based upon vague considerations of diversity, size, and distinctness (in terms of entirely subjectively chosen “important” features). Many of these depend (loosely) on the age of the group in question. And this is why many “phyla” are Cambrian in age — not the other way around. As Dawkins aptly observed, Gould was like someone who thought it eminently notable that on an old tree all the thickest branches are near the ground, and that no new thick branches have grown in 100 years. Gould got suckered by the Linnaean hierarchy.

    Next, “a wild bush that grows in all directions” is exactly what we expect from mutation + selection + drift. If anything else were involved, such as a metaphysical drive towards progress, we’d expect something different — less branching, fewer directions, something closer to a straight line. What we see in the fossil record (and in extant nature as well) is positive evidence that all those late-19th- and early-20th-century theses about “orthogenesis” or “aristogenesis” were wrong. There is no progress, natural selection guides towards better adaptation to the present environment, not to any future one. As expected — from Darwin, not from Lamarck, not from Osborn, not from Schindewolf, not from Lysenko.

    I don’t require that you read The Structure of Evolutionary Theory. (I haven’t read it myself, for starters.) But I do think you should not have made your claim to be “widely read” in the theory of evolution. You have once again demonstrated that you aren’t.

    Note that I’m not calling you a liar or stupid. I think you haven’t noticed how much there is to read on evolution and have jumped to the false conclusion that you’ve read most of it.

    If that’s the case, how can bacteria be used to show that Darwinism explains the origin of species?

    I didn’t say they can be. I said the notion of “species” is itself very vague. Some say outright that “species” is nothing but yet another arbitrary Linnaean rank, just like “genus” or “phylum”. They have a fair number of points.

    Intelligent agents can produce lousy designs (witness the Edsel).

    So you explain stupid design by saying the designer was stupid?

    (BTW, not that it matters, but Behe has another explanation in The Edge of Evolution. You know the old atheist joke, “omniscient, omnipotent, omnibenevolent — pick two”? He has picked two — the first two. He is a dystheist. He states outright that the malaria parasites have been designed in order to harm and kill us.)

    If natural selection is “inescapable,” then it operates like other natural laws, whose effects cannot be escaped. You’re supporting Reed’s argument while calling him unintelligent for making it.

    Sorry for not being clearer. I only have a stricter definition of “natural law”. Take the law of the conservation of mass in chemistry. Is that a natural law? No, it’s only a special case of the law of the conservation of energy. No separate law of nature is necessary to explain natural selection; we already understand it. That’s what I’m saying.

    I’ve found that Darwinian true-believers often take great umbrage when a skeptic refers to natural selection as a tautology, and I didn’t see any point in fanning the flames. But since you’ve brought it up, I’ll simply say that I agree.

    Wait, wait. I wrote “almost a tautology”. Please explain why you disagree with the “almost” part. :-)

    Unless science can deliver explanations that have meaning (i.e., understandable content that the explanations are intended to convey), science has no purpose.

    Fine, but what does that have to do with finding meaning in nature? Or what have I misunderstood?

    I didn’t say that there is “no trace of a Precambrian trilobite precursor.” I said there is no trace of any LIKELY precursors to trilobites among the pre-Cambrian fossils. A possible precursor – like Spriggina – is not necessarily a likely precursor. It shouldn’t be necessary for me to explain the difference between a possibility and a probability.

    Ah. And why isn’t Parvancorina a likely precursor? How would you decide if it’s “likely” or merely “possible”? And, most importantly, why isn’t “possible” enough? If we only had impossible precursors (…in spite of a good fossil record, which we don’t have for that time…), that would be a problem for the idea that there were Precambrian animals that were more closely related to the trilobites than the spiders are.

  16. #16 David Marjanovi?
    September 11, 2007

    If Jim really doesn’t come back, he’d be the first to act out his threat to himself that he would stop learning…

    It ought to be obvious that it’s senseless to label an organism an “intermediate, transitional form” unless gradual evolution (either guided or unguided) is assumed to have occurred.

    Nope, we simply aren’t using the same concept of “intermediate”. I am not talking about phylogenetically intermediate, I’m talking about morphologically intermediate. I’m talking about the pattern, not the process. Where exactly is north on the IQ scale?

    I was not even talking about fossils. Just in today’s living world we find intermediates galore — and while we find some intermediates, we don’t find others. I went on to explain that exactly this is what the ToE predicts.

    ID, on the other hand, expects nothing in particular. We could live in the real world, we could live in Jussieu’s imagination where nature is a flat plate rather than a tree, we could live in a world where each species is totally, fundamentally different from each other species (as in, one using DNA, the next using different sugars, another using different bases, another using who knows what) — all would be equally compatible with ID. Tell me again how ID explains anything by explaining everything and their brother.

    And if this isn’t enough of an explanation for you, Anton has handled it admirably.

    Central to the problem of identifying intermediate, transitional forms in the fossil record is the circularity of reasoning involved: Because it assumes (or posits) common descent (or descent with modification), Darwinism must have intermediate, transitional forms;

    Correct, for those organisms whose fossil record is good enough. Hey, just an example off the top of my head, there are no known fossil poison-dart frogs (intermediate or otherwise), because tiny skeletons don’t last long in the acidic soil of a rainforest, if they ever reach the soil in the first place. And here we’re talking about organisms that have a mineralized skeleton. Are there any fossil earthworms? I don’t know, but I bet not.

    Darwinists then identify such forms on the basis of that assumption;

    Wrong.

    Oh, dude, we don’t go around “identifying intermediate forms”. Have you ever read primary paleontological literature? I posted a link to a free pdf of one such paper last night (Central European time).

    There goes the circle.

    ‘The known fossil record fails to document a single example of phyletic (gradual) evolution accomplishing a major morphological transition and hence offers no evidence that the gradualistic model can be valid.’

    Which resolution exactly do you want for “document”, and what if anything is “major”? If you’re content with a gradual speciation in the fossil record, I can give you that. Pacific diatoms of the last few million years have an excellent fossil record — the sea floor consists of them.

    If Spriggina is the evolutionary precursor of trilobites, where in the fossil record is the “unambiguous continuum of transitional species exhibiting a perfect gradation of skeletal form leading unarguably” from Spriggina to trilobites?

    We have already explained that you can’t expect that from the fossil record of organisms without hard parts (and that well over half a billion years ago).

    There is no fourth mode of explanation, David. If an explanation requires the combination of two of the explanatory modes, that combination is not a fourth mode of explanation. ToE appeals to both chance and necessity, but that doesn’t make evolution a fourth explanatory mode.

    Its results differ both from those of random alone and from those of necessity alone, so of course it is a fourth mode of explanation. Don’t come with semantics.

    Judging from his own example, Behe wouldn’t recognize evolution if he saw it. He would automatically confuse it with design. That’s what I’m saying.

    In fact, to say that something evolved is not explanatory at all; it’s merely descriptive.

    Then let me be more precise: to say that something evolved by mutation, selection, and drift is an explanation.

    No, but I am saying that judging that a design is deficient requires us to get into the mind of the designer. Unless we know his objectives, we can’t say that his design failed to meet them.

    Oh, the designer is not stupid — he’s ineffable!

    You have left science, my friend. Claims of ineffability are not testable, so they aren’t science. Are you trying to do science, or are you trying to do theology? I think you should decide between those two.

    “Maybe the designer isn’t all that beneficient or omnipotent,” [Be]he wrote. “Science can’t answer questions like that. But denying design simply because it can cause terrible pain is a failure of nerve, a failure to look the universe fully in the face.”

    I’m not “denying design” because I don’t like the implications. I just wanted to point out that it’s not true that ID makes no claims about the designer. It cannot help making claims about the designer.

    Besides, Anton has explained why it shouldn’t avoid making claims about the designer.

    Unless I misunderstood it, what you wrote can be said in this way: Natural selection means that the fittest organisms will survive to leave the most offspring, the fittest organisms being those that survive to leave the most offspring.

    Yeah, that one again. You forgot to ask why any organisms leave more surviving offspring than others. It’s because of very concrete reasons: they use their food more efficiently, they gather food more efficiently, they are better at escaping predators, whatever. Each of those possible reasons is testable. It won’t surprise you (I hope) to read that lots of literature exist on the question of whether a particular factor is being selected upon in a particular species.

    I remember reading about a bird species where shorter wings make for more efficient flight in reed (lots of twisting & turning in the air required) and are therefore selected for by natural selection, but sexual selection favors longer wings! Result: a compromise. This was shown using lots of measurements of a whole population and lots of math. Hey, multivariate statistics was invented for population genetics, in other words, for evolutionary biology. (Change of allele frequencies in a population = evolution.)

    —————

    Not that Denton’s judgement is necessarily any better now, but why do you only quote his two-decades old statements?

    Hey, why do you quote opinions instead of results, Jim? Have you noticed how papers tend to have a “Results” section and a “Discussion” section?

    I think it comes from the tradition of creationism — a religious tradition where arguments from authority are not considered logical fallacies.

    —————-

    But since all it’s delivered (with respect to its macroevolutionary claims) are wishful speculations devoid of any actual details, I’ve found it quite unpersuasive.

    Then you should, for example, read Jennifer Clack’s book “Gaining Ground” on the origin of limbed (as opposed to finned) vertebrates. Or Carl Zimmer’s “At the Water’s Edge” for a shorter take on that topic and another on the origin of whales. Or preferably both. You will learn a lot.

    The air of certainty presented here by Darwinism’s defenders and their apparent outrage that I dare to question their cherished theory simply demonstrate the sadly dogmatic condition of evolutionary biology.

    It only looks that way because you mistakenly believe you are “widely read” in the topic. Because you aren’t, you don’t understand what we are talking about, but because you believe you already know it all, you don’t get the idea that you still have something to learn.

    This is not something that should be able to happen to someone with an IQ around 150, wherever “north” is.

  17. #17 David Marjanovi?
    September 11, 2007

    This is why I had an allergic reaction to Jim when he showed up on this thread: I remembered the last time he was here. It all played out pretty much the same way.

    Told you he’ll come back. :-)

    He cannot see how or why this approach, which tacitly accuses every defender of Evo of being a mindless adherent to a broken philosophy, will sometimes precipitate hostile responses from those who know significantly more about the subject than he does.

    That’s because he seems not to understand, at least not consciously, that anyone knows significantly more about the subject than he does.

  18. #18 David Marjanovi?
    September 12, 2007

    Thanks, Anton.

    Still laughing about post 300… :-D

  19. #19 Torbjörn Larsson, OM
    September 13, 2007

    Maybe a wrapup, maybe not.

    Jim:

    Dembski (and ID theory) is not concerned with events that have no possible alternatives. But it is concerned with the probability that specified complexity in biological systems could have been randomly generated. Dawkins’s me-thinks-it-is-like-a-weasel algorithm is irrelevant to both ID theory and Darwinism.

    Since you concede that natural selection is an evolutionary mechanism, you should recognize that the weasel algorithm is a relevant evolutionary algorithm. It illustrates how selection speeds up evolution. Note that there are many possible alternatives to the paths taken to fulfilling the fitness constraints.

    It is however not an example of how biological populations and their changing fitness constraints behave. That wasn’t the purpose.

    I’ve found that Darwinian true-believers often take great umbrage when a skeptic refers to natural selection as a tautology, and I didn’t see any point in fanning the flames. But since you’ve brought it up, I’ll simply say that I agree.

    The reason people takes umbrage is that it isn’t quite a tautology. But this argument is besides the point. After you develop a formal theory covering your data, the theory and the data forms a tautology:

    A tautology is a statement which is true by its logical structure. What’s a proof of a statement in logic? It’s a set of basic statements (axioms) which can, by using the inference rules of the logic derive the proven statement. Translate that down a bit and – what’s a proof? It’s a series of statements that demonstrates that a final statement is inevitably true by the logical structure of the proof. So form the proof up into a single statement (by joining steps with appropriate “and” and “or”s), and the proof is a tautology.

    The same holds for scientific theories – except that in general, scientific theories add observations to the set of basic statements.

    His criticisms tend to focus on trivialities

    Demsbki didn’t answer even one of Shalit’s points.

  20. #20 David Marjanovi?
    September 13, 2007

    Wow, truth machine… why did you send each of your paragraphs as a separate post? Just to bring the thread back into the “top 5/most active” list?

  21. #21 David Marjanovi?
    September 13, 2007

    :-D

  22. #22 Kseniya
    September 14, 2007

    I’m out of date? Dangit, I knowed I shoulda payed more attenshun in class.

    LMAO @ “soapdishes” !!! :-D

  23. #23 David Marjanovi?
    September 16, 2007

    P.S. A note to David: As you may recall,

    So you have come back, and you have found something of interest to you. I consider two of my predictions confirmed. :-}

    I argued that if species are defined in terms of reproductive isolation, then demonstrating that the primary Darwinian mechanism (i.e., random mutations acted on by natural selection) can cause such speciation doesn’t also demonstrate that the Darwinian mechanism can do all the macroevolutionary work that Darwinists want to attribute to it (such as the generation of new organisms, new organs, new systems, etc.).

    You are fully correct about this. But you overlooked the other half of science: the principle of parsimony. You have not shown that anything other than mutation and selection is necessary for explaining “macroevolution”. As long as you can’t show that, we will continue to hold that nothing else is necessary.

    Probably you have also overlooked how little is ever completely new. What is a lung? An evagination of the esophagus. What is a jaw? A gill arch* with teeth on it. What are the stapes and the hyoid**? The following gill arch. What is an insect wing? The gill part of an arthropod limb.

    And that’s just what we can see with the naked eye! Then there’s developmentary genetics. Behold Sonic hedgehog: this gene is expressed when any outgrowth of the vertebrate body wall begins to form. That includes limbs, teeth, hair, “reptile” scales including feathers, taste buds, everything. Shh has two close relatives (desert hedgehog and another); by “relatives” I mean “strong similarities in sequence, explicable if the three genes result from gene duplication events” — and indeed, Drosophila has a single hedgehog gene. Clearly, the simplest explanation is descent with modification — without a duplication in arthropods, with two duplications in vertebrates. “Evolution is a tinkerer”: it takes what is there and tinkers with it; it does not create ex nihilo. After all, how should it.

    * That’s two rods of cartilage (joined by a joint) between two gill slits that prevent the slits from deforming, one pair per side of the body.
    ** The horseshoe-shaped bone in the throat, above the Adam’s apple.

  24. #24 David Marjanovi?
    September 17, 2007

    I’ll come back later today, probably. Just so much… here is a wonderful cartoon on descending from fish.

  25. #25 David Marjanovi?
    September 17, 2007

    If we demonstrate (as we arguably have) that Darwinian mechanisms can cause minor adaptive changes in the beaks of finches, have we also demonstrated that those mechanisms brought finches into existence in the first place, or that they can cause finches to evolve into something other than finches? Of course not. Such extrapolation is wishful speculation, not rigorous science.

    It seems you keep overlooking the principle of parsimony. No, we haven’t demonstrated that “those mechanisms” did it. We have, however, demonstrated that they are enough to explain all of evolution. If you want to add yet another mechanism, show that it exists; if you can’t, show that it’s necessary (i. e. prove us wrong); if you can’t do that either, give up and realize that you have quit science.

  26. #26 David Marjanovi?
    September 17, 2007

    once he came to his senses – Kseniya

    That’s a she, as you can see simply from her final -a.

    In what sense did Jussieu identify those organisms as “intermediate/transitional” forms? As a matter of logic, it is utterly senseless to describe an organism as intermediate and transitional (in an evolutionary sense) unless evolution is assumed. A platypus exhibits both mammalian and reptilian features, but it can’t be described as intermediate and transitional on that basis.

    You’re still wrong. Something can be intermediate in shape without being intermediate in history.

    Jussieu was, as far as I’m aware (and as one can guess with quite high certainty from the time of his life), a creationist. For him, life was not a tree, it was a tape. Each trait occurred along a certain part of the tape, and all those parts overlapped. (I don’t know if the tape had ends or formed a circle, but in any case it was not branched.)

    For the record, one might well say that, because of its beak, the platypus is intermediate between birds and mammals as well as an intermediate between “reptiles” and mammals. (I don’t know if the platypus was already known to Jussieu, and he was a botanist anyway, so I don’t think he made that argument.)

    Now comes the interesting part. We find only small parts of Jussieu’s tape in nature. However, we find intermediates between those parts — we don’t find a tape, we find a tree. For example, the platypus is not intermediate between the house mouse and the sand lizard; instead, the monotremes as a whole are intermediate between Theria (placentals + marsupials) as a whole and sauropsids (turtles, lizards + snakes, crocodiles, birds) as a whole, and the amphibians as a whole are intermediate between all of the above as a whole and the lungfish as a whole.

    It also turns out that the beaks of the monotremes are actually quite different from bird beaks (and for that matter turtle beaks) in build, and I haven’t mentioned a single fossil yet.

    Given the fact of “microevolution”, it makes sense to interpret this morphological ( = shape) tree as the result of a genealogical tree. But that’s a conclusion; it’s not part of the observation, and it’s not an a priori assumption.

    (You will also have noticed that nobody claims the platypus is our ancestor. Instead, the interpretation goes, Theria and Monotremata share a common ancestor that they do not share with Sauropsida.)

    A platypus may be intermediate between reptiles and mammals on a morphological basis, but we can’t describe it as intermediate AND transitional unless we assume evolution.

    Oh, you only have a different definition of “transitional” than I. OK, I’ll stop using “transitional” when I mean “morphologically intermediate”.

    Perhaps, but if fish evolved into men by way of the gradual accumulation of adaptive variations, where is the unambiguous continuum of transitional species exhibiting a perfect gradation of skeletal form leading unarguably from fish to amphibians to reptiles to mammals to man?

    We have a whole tree full of intermediate species, with ever-increasing resolution. If you aren’t satisfied with that, given the quality of the fossil record (which you seem to consistently overestimate by orders of magnitude), you probably just don’t know what I’m talking about. I’ll go look for some links, and I repeat my recommendation of books like Carl Zimmer’s At the Water’s Edge.

    Why does the fossil record persistently fail to demonstrate incremental Darwinian evolution (as Gould, Eldredge, and others have noted)? Why must we always assume that the problem is with the fossils? Why shouldn’t we entertain the idea that the problem is with the theory?

    Ah, now it gets interesting. Why have neither Gould nor Eldredge ever doubted mutation & selection?

    Because you have misunderstood them. Punctuated equilibrium means that, on timescales of hundreds of thousands of years and less, periods of long periods of stabilizing selection (that is, natural selection working against variation, because the mode of the variation is best adapted to the present environment) are interrupted by short periods of directional selection (that is, natural selection favoring one tail of the Gauss curve, because the mode of the variation is no longer best adapted to the environment, which has recently changed). These short periods they called speciation (which makes sense under some species concepts, and less sense under others).

    Now, tell me if you can read papers on this page. That’s the July 2001 issue of TREE (Trends in Ecology and Evolution), a special issue on speciation. You should, at the very least, read the paper on “Speciation in the fossil record”. If you can’t, tell me your e-mail address, and I’ll send you the pdf.

    Or just read this paper, which is free-access and in HTML, and probably says much the same, including the most important figure, which shows the rarer of the two cases — a gradual speciation, happening among diatoms in the Pacific. Unlike vertebrates, diatoms have an excellent fossil record: much of the ocean-floor mud consists of their skeletons.

    David:”…we don’t go around ‘identifying intermediate forms’.”
    Then why do you insist that such forms have been identified?

    I was trying to say that we don’t go around looking for transitional forms, because we already expect that everything is intermediate. If by “transitional” you only mean “direct ancestors”, then there’s next to no hope of finding any in any group with a fossil record worse than that of diatoms or the like. If you mean “very close to a direct ancestor”, then the collections are full of them.

    Dawkins’s weasel algorithm is irrelevant to Darwinian theory because it has only one possible outcome. The selection function in his algorithm dictates the preservation of randomly generated letters that match the target sequence (“methinks it is like a weasel”). A selection function of that kind is quite un-Darwinian. Rather than mimicking natural selection, it smuggles intelligence into a process that is supposed to operate without any intelligent guidance whatsoever.

    I don’t see where the intelligence is. What the process models is strong and constant natural selection to a very narrowly defined outcome. This is only unrealistic in that the possible outcomes are usually broader — anything that works works. Still, we get the phenomenon of convergence (all over the place — it’s the biggest problem in phylogenetics, and among the most interesting topics in evolutionary biology). The most famous example is that tuna, big sharks, ichthyosaurs, the most strictly marine crocodiles like Metriorhynchus, and dolphins all have the same shape because there aren’t many ways of skinning this particular cat (fast, energy-efficient swimming — as opposed to effective acceleration). I don’t see where Dawkins’ algorithm strongly differs from this case.

    David: “You are fully correct about this. But you overlooked the other half of science: the principle of parsimony. You have not shown that anything other than mutation and selection is necessary for explaining ‘macroevolution’.”
    Perhaps, but since Darwinists have not yet shown that mutation and selection (and associated mechanisms, such as gene flow, genetic drift, etc.) are sufficient to explain macroevolutionary events (such as the origin of organismal forms and biological systems that did not previously exist), the case is not yet closed.

    You still underestimate the principle of parsimony. No case is ever truly closed — but the burden of evidence is on your side. Show me that “microevolution”, accumulated over tens of millions of years, is something other than “macroevolution”.

    exactly what is the evidence showing that Darwinian mechanisms are sufficiently creative to have generated all of life’s diversity and complexity?

    Show me they are not sufficient. I don’t see why they shouldn’t be.

    If we demonstrate (as we arguably have) that Darwinian mechanisms can cause minor adaptive changes in the beaks of finches, have we also demonstrated that those mechanisms brought finches into existence in the first place, or that they can cause finches to evolve into something other than finches?

    What is a finch, other than a titmouse with a thickened beak?

    What am I, other than a short-haired, tall, lanky ape with a babyface?

    What is Tiktaalik, other than Panderichthys without gill lids?

    What is Sapeornis, other than Archaeopteryx with a shrunk tail, lengthened wings, and shrunk 3rd fingers?

    What is Morganucodon, other than a shrunk Chiniquodon with broadened jaw joints and a longer, thinner tail?

    Your use of “bringing into existence” and “something other” is misleading you.

    I almost always sign my reviews if it’s a journal that allows it. If it’s accepted practice to allow reviewers to be identified to the paper’s author(s),

    It is also customary to thank all reviewers in the acknowledgments, whether anonymous or not. Here’s the relevant sentence from the paper I and my thesis supervisor (in this order) published in June:

    The draft was improved by comments from Susan Evans, Norman MacLeod, Roderic Page, Jean-Claude Rage, Armand de Ricqlès, Jorge Cubo, and an anonymous referee.

    R. Page is the editor of the journal, and N. MacLeod is the responsible associate editor. (Both basically did peer-reviews of their own, but had no chance of remaining anonymous.) We gave the draft to A. de Ricqlès and J. Cubo, who are here in the building, to read before we submitted it. The other three are peer-reviewers, two of whom chose to sign their reviews.

  27. #27 David Marjanovi?
    September 17, 2007

    When has it been demonstrated that Darwinian mechanisms are sufficient to have caused all macroevolutionary events, such as the presumed evolution of men from fish (by way of amphibians, reptiles, and some unknown mammal)?

    Why do you believe they are not sufficient? I just don’t get that. That’s something you haven’t even begun to explain, except maybe for implying an argument from personal incredulity.

    What repeatable experiments have been done to demonstrate the ability of Darwinian mechanisms to have produced the extraordinary complexity that characterizes living organisms?

    We can’t run experiments that run for tens of millions of years. We can’t make those observations in the lab, so we have to make them in the field. We can’t make experiments in astrophysics either…

    but when has it been shown that those mechanisms can (or did) generate biological novelty (i.e., new organisms, new organs, new systems, etc.)?

    I said you need to take in mind “how little is ever new” and illustrated it with a few examples. I’m awaiting your reply.

    How would you answer the following, taken from a paper by design theorist Steven C. Meyer?

    He talks about “novelty” — tell me something that really is new.

    (Besides, he misuses the word “epigenetic”.)

    Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest.

    Bullshit.

    “Arrival of the fittest”? Please. Suppose a populations, suppose mutations, and suppose an environment. It follows from that alone that part of the population is fit enough and that the rest isn’t.

    As Goodwin (1995) points out, ‘the origin of species–Darwin’s problem–remains unsolved’”

    Pick any species concept, and this becomes bullshit, too.

    The purpose of intelligent design is to show (with mathematical, logical, and scientific rigor) that Darwinian mechanisms do not suffice to explain all of life’s diversity and complexity

    When has it ever tried to do that?

    Oh, you mean “irreducible complexity”? Arc, meet scaffold. Mouse trap, meet paper clip, cutting board, cheese, and biro spring. Flagellum, meet Type III secretion system. Ad infinitum vel nauseam.

    and that design inferences are often justified by analyses of biological systems.

    That it has tried to do, but only by a priori excluding the fourth possible explanation and then afterwards asserting it can’t have been at work.

    ID does not propose to “add yet another mechanism” because intelligence is creative, not mechanistic.

    Then let’s fiddle with the terminology and say “cause” instead of “mechanism”… you know what I mean.

    How an intelligent agent (or cause, or force) might have actualized design in biological systems is a legitimate line of scientific research

    …as long as Ockham’s Razor doesn’t cut it off. Which it does at present.

    Now, let’s return to Stupid Design. You ended up saying the designer isn’t stupid but ineffable, and I noted that thereby you had left science. Any comments? Or are you happy outside science?

  28. #28 David Marjanovi?
    September 17, 2007

    (former Soviet Premier Nikita Krushchev comes to mind)

    One of the few exceptions, somehow explicable via Greek…

    The tools of intelligent design include: probability theory, recursion theory, the theory of cellular automata, stochastic process theory, information theory, computer science, molecular biology, microbiology, biochemistry, paleontology, genetics, developmental biology, and philosophy of science (to name just those that come readily to mind). You tell me: Which of those tools is religious rather than scientific?

    Assuming an ineffable designer, before even showing (within science theory = philosophy of science) that any designer is needed…

    Whether design theory is, in some ways, superior to Darwinism remains to be seen, but – given the mounting difficulties our increasing knowledge of biological complexity presents to Darwinism – I think the smart money is on design.

    You haven’t mentioned a single difficulty, only alluded to one.

    I’ve already acknowledged that, but if an organism is intermediate in shape (or in morphological structure) between two different organismal forms, it doesn’t follow that it must be an evolutionary transition between those two different forms (which is the only sense of “intermediate, transitional form” that is relevant to ToE).

    I agree. And then I went on to explain that the pattern of which intermediates we find and which we don’t find forms a tree. Why of all possible shapes (Jussieu’s tape…) a tree?

    What we find fails to disprove evolution by mutation, selection, and drift.

    I’ve neither claimed nor suggested that they have doubts that mutation and selection (the principal Darwinian mechanism) operates in nature. They do, however, have doubts about the gradualistic model proposed by Darwin and adopted by neo-Darwinists. As you no doubt know, such doubts are what led them to develop punctuated equilibrium,

    And? You seem to agree with me that it was a discussion within the theory of evolution by mutation, selection and drift, not about it.

    which is an ingenious (but unconfirmed) solution to the failure of the fossil record to reflect Darwinian gradualism.

    As you would know if you had read what I suggested you to read, both punc eq and gradualism have been found in the fossil record (the former being more common). When you say they are “unconfirmed”, you are wrong.

    How are those species identified as intermediate and transitional species (in an evolutionary sense) without assuming that evolution occurred?

    I have explained how they (and all others) are identified as intermediate.

    They are not identified as transitional without assuming that evolution occurred. The other way around: evolution is the most parsimonious explanation for the tree-shaped distribution of intermediates.

    Are you saying the designer is trying to fool us, so that the principle of parsimony doesn’t work? That’s fine — if you don’t pretend it’s science. (Keep in mind that “true” and “scientific” are not synonyms.)

    In physics, the theory of relativity has been tested by experiments whose results can be assessed independently of the theory.

    Then let’s talk a bit more about what science is. Because, you see…

    If those independently assessed results match the predictions of the theory of relativity, they serve to confirm the theory (to the extent that the scientific method ever delivers confirmation).

    …this is not strictly true.

    One very important observation that has tested the theory of relativity is not an experiment: gravitational lenses. We observe Einstein arcs, Einstein crosses, and even an Einstein ring out there, and general relativity explains them, but we can’t make them in the lab, simply because no lab can be big enough. There is no proof that there’s no supernatural being out there that bends the light with its bare hands and makes the various Hubble Deep Fields look like what we’d expect from relativity. There’s not even a proof that there’s no unknown force of nature out there that does the bending and produces the same results. There never is proof in science. Thus, we resort to Ockham’s Razor: we have a theory that predicts all those phenomena; we see all these phenomena; therefore we can explain these phenomena without a single additional assumption. Have you seen Conan the Barbarian? Do you remember the ridiculously huge ax Conan wields? That’s Ockham’s Razor.

    Still, the theory of relativity stays science. It are falsifiable. If we hadn’t found what it predicts — if we hadn’t found any such distortions of light –, this would prove that something, however small, is wrong with the theory.

    Likewise, we observe a tree-shaped pattern of morphological intermediates, with good stratigraphic fit. Whenever the quality of the fossil record allows it (and that can be assessed independently), we find the predicted intermediates at the right time on the right continent. This is exactly what we expect from the theory of evolution. It doesn’t prove it, but Ockham’s Razor means that no other explanation is necessary. Still, the theory is science. It remains falsifiable. Find me a Silurian rabbit, just a single little bunny that is 420 million years old, and it will be in big, big trouble. (Er… not the rabbit.)

    Is ID falsifiable?

    David: “What is a finch, other than a titmouse with a thickened beak?”
    Well, it’s certainly not a dinosaur.

    Hah! Just to get started: It has air sacs, like theropods in general. It is bipedal, like apparently dinosauromorphs in general (that’s an even bigger group than dinosaurs alone). It has 3 fingers in its hands, namely numbers 1, 2, and 3, like tetanuran theropods in general. It has 4 toes per foot, numbers 1, 2, 3, and 4, of which numbers 2, 3, and 4 point forward and are used for walking and running. Its ankle joint runs between the astragalus and calcaneum on the lower leg side and the distal tarsals on the other, like in dinosauromorphs generally (in crocodiles, for example, the calcaneum is on the foot side of the joint, and in mammals, both the astragalus and the calcaneum are). It has feathers, like coelurosaurs generally. It has wing and tail feathers, like maniraptorans generally. It has collarbones fused into a wishbone, like in theropods generally. Its collarbones first of all touch in the middle, like in saurischians generally. And that’s just off the top of my head!

    See? Not only is it a dinosaur, we can place it within subgroups of dinosaurs.

    If you can’t see it, just get more intermediates and look at the whole array. I recommend googling for:

    Ichthyornis
    Gansus
    Yixianornis
    Sinornis
    Jibeinia
    Confuciusornis
    Archaeopteryx
    Rahonavis
    Mahakala
    Microraptor
    Jinfengopteryx
    Caudipteryx
    Sinosauropteryx
    Dilong

    (And that’s not the whole array, only the most spectaculary well-preserved fossils.)

    I can also send you papers (as pdf) on those and more. Spend a few hours reading and looking at pictures! You can’t do science as a third job. :-)

    On what grounds can we say that the mechanism that causes minor adaptive changes in the size of finches’ beaks is the same mechanism that caused birds to evolve from dinosaurs?

    On the principle of parsimony.

    Perhaps you’re too professionally invested in ToE

    I’m a PhD student; I don’t work, I mean, for money, and because of bureaucratic reasons, I haven’t even started the thesis yet. If common descent (not just the ToE by mutation, selection, and drift!!!) fell down overnight, half of my PhD topic would evaporate, but the other half would still be enough work, and I could always add some functional morphology or whatever. I don’t see why I should feel threatened.

    to see the evidentiary and theoretical problems with it that are so obvious to me

    You keep saying that. You also keep not mentioning even one of them. All you make is an argument from personal incredulity (a logical fallacy) and ignorance (another logical fallacy): “Waaah, they are all so different, they can’t have evolved by conventional means”. Should such a thing happen to someone with an IQ of 150, let alone more?

    Show me one of the “evidentiary and theoretical problems”, and then we can discuss about it. Put up or shut up.

    (and to many others).

    Argument from majority. The third logical fallacy in this sentence.

    [insert automatic reminder on ineffable designer vs science]

  29. #29 David Marjanovi?
    September 17, 2007

    I forgot Buitreraptor in the list.

    Why do you believe they are sufficient? That’s something you haven’t even begun to explain, except maybe for implying an argument from personal credulity.

    I have explained how little is ever new. I have tried to give you an idea of how closely we can today trace the origin of limbed vertebrates, mammals, birds, and even arthropods.

    Whatever that first life form was, it certainly didn’t possess a heart, or lungs, or a nervous system, or legs, or feet, or wings, or teeth, or eyes, or skin (and so on and so on). When such biological features made their first appearance in life’s history, they were novel biological features.

    That’s what I wanted to read, thank you!

    Now, let’s see… Heart? Highschool biology: earthworms don’t have a heart, but several of their segmental blood vessels contract like a heart. Now let the guesswork begin. Localize the contraction, enlarge the vessel, and you get a heart. To get the contraction, express gut peristalsis in the wrong place. To get gut peristalsis, get a few muscle cells, a few nerve cells, and natural selection… I’m guessing because this is far from my specialty.

    Lungs? That’s closer to my specialty. Breathing air with the gut is easy. If you get air in your gut, you can’t help extracting the oxygen at least (the concentration difference alone does that). If you do that, and be it by accidentally swallowing air, you aren’t dependent on the oxygen content of the water. There are plenty of fish species today that do just that when the oxygen in the water becomes too little. But there is another advantage: Behold the blood circulation of any “fish”. The blood gets from the heart to the gills, then to the whole body, and then back to the heart. At that point, little oxygen is left. You can chase a salmon to death because of this stupid design. (Explained at more length in Carl Zimmer’s At the Water’s Edge.) In the same circulation, much blood goes to the gut shortly before reaching the heart. Get it? Now imagine a mutation that produces an evagination of the intestinal tract (it happened to be the esophagus), such as a crop for example. That is a lung (e.g. of a lungfish or amphibian), and has the massive advantage of speeding air-breathing up, because used air can easily be vomited instead of having to pass the entire gut and coming out at the other end. The trachea comes later (as mentioned, even today’s amphibians lack it, apart from a short stalk between lung and esophagus).

    Nervous system? Sponges have cells that are muscles, nerves, and connective tissue at once. A few gene duplications, and you’re all set.

    Legs and feet? Of vertebrates? Take Tiktaalik, switch off the production of fin rays (that can be done by a single mutation in a single gene), and make the bones near the end grow for a little longer than usual (that can be done by overexpressing another gene, which in turn might require a single mutation in a regulatory gene). Of arthropods? That’s harder (for my ignorance at least), but I already mentioned the hedgehog genes. How did these get their function? I suppose they started their career as growth factors.

    Wings? Of birds? Just arms with wing feathers and enlarged musculature. Of bats? Just arms with extra-long fingers (which is done by overexpression of a single gene — this research has been done) and that webbing (I don’t know where that comes from, but I suspect a bit of fibroblast growth factor overexpression in the right place should do it). Of pterosaurs? Ditto, except a single finger is lengthened. Of insects? Read PZ’s post “Flap those gills and fly!”. (Pharyngula has a working search function.)

    Teeth? Very similar to general vertebrate scales. Much has been written on that topic. Scales in general? Outgrowths of the body wall (see hedgehog), plus mineralization (calcium and phosphate are present, so wait for osteocalcin or amelogenin or whatever protein to appear by mutation and apply selection.

    Eyes? Read more. That has been explained hundreds of times all over teh intarwebz. I really don’t need to repeat that one.

    Skin? What do you mean? Epithelia in general? Cell-adhesion proteins happen — mutation & selection. The dead outer layer? Overexpress epidermal growth factor, and overexpress keratin — two mutations, plus selection against desiccation.

    Did you know that one of the proteins in the eye lenses of chickens is a dysfunctional enzyme that just happens to make transparent crystals?

    I submit (again) that you are only arguing from ignorance which has led to personal incredulity.

    I’ve always found “bullshit” to be a quite compelling argument. Well done.

    Thank you very much. Let me elaborate.

    Biological Species Concept? Wait for a mutation to appear that prevents fertile offspring with organisms that lack that mutation. For example, that can be a chromosome fusion — donkeys and horses have different chromosome numbers, so that mules have an odd number of chromosomes, which means meiosis doesn’t work properly. I really don’t understand where the mystery is supposed to be. Just wait for a mutation, and it will happen — sooner or later. There are cases where it is “later”; google “intergeneric hybrids”.

    Ecological Species Concept? Wait for a mutation that allows exploitation of another niche. Select for individuals that fit into a niche, and against individuals that fit in between ( = fit badly into any niche).

    Morphological Species Concept? Wait for the phenotype to change by mutation (selection of course helps, but is not even necessary, drift will do). Sooner or later it will happen.

    If you want me to go on, I will.

    I’m not the one who keeps bringing up the designer. Neither are design theorists. Indeed, so far as they’re concerned, questions about the identity, nature, and purposes of the designer don’t belong to science, they belong to philosophy and theology.

    A few posts above truth machine’s rant it was explained why you can’t infer a designer and then just stop asking questions without stopping doing science.

    I must say that I’m quite impressed by the open-mindedness of Darwinism’s defenders. They are all so open to the possibility that there are some rather serious problems with ToE.

    We are. That’s why we keep discussing instead of running away screaming. We are waiting for you to mention one such problem. So far (see above), you haven’t — the only problem you have shown is your own lack of knowledge, your own belief to be “widely read” even though you aren’t.

    I’ll try to find Kevin Padian’s Dover testimony for you. It will teach you a lot about the origin of limbed vertebrates.

  30. #30 David Marjanovi?
    September 17, 2007

    Good grief. There is no extrapolation involved in saying that the same force that causes toast to fall to the floor will also cause toast to fall to the floor of the Grand Canyon. The law of gravity applies to toast regardless of where the toast falls (or how far it falls).

    That is quite an extrapolation. Newton is famous for extrapolating from the force that made the mythical apple fall on his head to the force that keeps the moon on its orbit (doesn’t even make it fall down).

    Now, this extrapolation is a testable hypothesis. It has been tested again and again, and never disproven, so it continues to be accepted.

    You mentioned relativity. It got started by Einstein equating, just for the sake of esthetic simplicity, mass-as-relevant-to-gravity with mass-as-relevant-to-inertia. There’s nothing bad about extrapolations, as long as they result in testable hypotheses. To the contrary: they are always more parsimonious than postulating an extra explanation for what is outside the known range.

    When have we ever observed the Darwinian mechanism causing a macroevolutionary event – or even inducing a directional change in an organism that might lead to its evolving into a different kind of organism?

    Give me a grant that runs ten million years…

    It instead focuses on detecting design in biological systems. If it succeeds in that regard (meaning that it becomes widely accepted),

    The argument from majority again. No, if it succeeds, that will mean it will have found instances where the theory of evolution fails to explains a shape, no matter how many people know about that.

    A theory wholly committed to material causes cannot explain, even in principle, the origin of information (which is immaterial).

    Every time we get you into a corner, you pull out decades-old creationist nonsense…

    For it is nonsense, and you know that full well, you’re just desperate. Matter + laws of nature => shape. If you really believe methodological naturalism doesn’t include laws…

    Where does the shape of a crystal come from? From electrostatics. Period. Where does the shape of a water molecule come from? From electrostatics. Period. Where does the shape of DNA come from? From electrostatics. Period. Where does the shape of a protein come from? From electrostatics and thermodynamics. Period.

    Where does the shape of a leg come from? Read a textbook on developmentary genetics… Where does the gene sequence come from? From mutation, selection, and electrostatics.

    Actually, I should replace “electrostatics” by “quantum electrodynamics” throughout the above. Or just by “QED”.

  31. #31 ?????? ?????????? ?????????, ??, ???
    September 17, 2007

    Why is it all right to infer that trilobites had a designer (and legs), but not all right to infer that they had an ancestor?

    Great question. Answer? Because random chance could not have produced a human being!

    ?-?

  32. #32 David Marjanovi?
    September 17, 2007

    Dude, you just totally called Shiva a girl.

    Only works in languages that have borrowed words with “ks” but not the letter for it. Not in languages that lost the manly life-giving final -s at least 4000 years ago. And even in those it works for long -a (which Shiva doesn’t have).

    —————–

    Rather, we’re ordered to prove a perfect sequence of ‘transitional’ forms showing tiny little steps in between one species and another

    And if I’ve correctly understood Jim, he doesn’t just want that “in between one species and another”, because that would be microevolution — he wants it between one “kind” and another, in spite of never having defined “kind”, ideally all the way between “fish” and man.

    David: “Show me one of the ‘evidentiary and theoretical problems’, and then we can discuss about it.”

    I’ve already done that. Among the evidentiary problems I’ve mentioned are:

    We’ve already shot all of them down several times, just scroll up… but I can always do it once more for you…

    1) the Cambrian explosion of life, which is at odds with the Darwinian notion that life evolved by way of the gradual, step-by-step accumulation of minor adaptive changes;

    This is simply wrong. You act as if the Cambrian Explosion took a few thousand years (or for that matter 6 literal days). It didn’t. Firstly, we are talking about up to forty million years, depending on the definition of the explosion (some “explosion” when you can quibble about when it began and when it was over!). Secondly, we are talking (among other things) about the evolution of hard parts. Most fossiliferous Cambrian rocks contain only or almost only trilobites, not just because trilobites were common, but because almost only the trilobites were capable of being fossilized. Even then, the legs are missing, as are the other parts that are not calcified. Trilobite legs, and animals without hard parts, are only preserved under exceptional circumstances, and that’s from where all the arthropodian and near-arthropodian wonders have flooded us over the last few decades: one place in Canada, one place in China, one in Australia, one in Sweden, and one on the north coast of Greenland, and all that spread across forty million years. Makes one such site every eight million years. That means we have on average nothing except trilobite armor for 8 million years.

    2) the persistent failure of the fossil record to reflect the continuum of life posited by Darwinism;

    Your persistent failure to grasp the fact that dead things rot.

    Fossilization is the absolute exception. It requires special and rare circumstances.

    Where are the fossil arrow worms? Where are the fossil nematodes?

    Once we take that into account, however, what we see is amazingly close to what we expect. For example, in this paper, I and my thesis supervisor calculated the quality of the fossil record of amphibians in the strict sense. The probability that the congruence between the shape of the tree and the order of stratigraphic appearance of the salamanders, frogs, caecilians, and albanerpetontids in question is due to random is less than 0.0001. Drop me an e-mail address, and I’ll send you the pdf. You can download the appropriate appendix yourself. I think the program we used is available for free somewhere online, too.

    3) the absence of any evidence showing that random mutations can induce the kind of directional changes needed to cause one kind (say, fish) to evolve into a different kind (say, amphibians);

    I’ve already told you that there’s no difference in kind between Tiktaalik and Acanthostega. Into how much anatomical detail do you want me to go? (Preferably next week, though, when I’ll have all the relevant papers at my disposal.)

    In the absence of evidence for the idea that macroevolution is anything else than microevolution over serious time spans, all we need is Ockham’s Razor.

    and
    4) the failure of the fossil record to reflect the Darwinian tree of life, which predicts that the number of phyla should be more numerous in the branches of the tree than they are at its base (the reality being very nearly the opposite).

    Wow. You have repeated the dumbest mistake of Gould’s whole life. And even then, Gould didn’t use it to argue against mutation & selection, but needlessly fabulated about possible and impossible body plans.

    I’ll give you Dawkins’ reply: Have you ever noticed that, on an old tree, all the thick branches are near the bottom? Isn’t it strange that no thick branches have grown in the last 100 years? Surely this requires an explanation! Surely this means that something fundamental about the growth of the tree has changed!!!1!

    “Phylum” is what the more traditionally inclined among us call a group when it has reached a certain “size” in number of species or diversity of shape or whatever (these criteria are never made explicit and never quantified). “Phylum” is also what they call anything that doesn’t fit into an already acknowledged phylum, even if it’s a single species: if they don’t want to make paraphyletic groups ( = consisting of an ancestor and some but not all of its descendants), and want to follow the International Code of Zoological Nomenclature, that’s what they are forced to do.

    Absolutely nothing in that code, however, can stop me from publishing a classification where each phylum is hacked into 10 new phyla, or 100, or 1000 (except for those phyla that already contain fewer species than that, assuming I can’t manage to subdivide the species). Likewise, nothing can stop me from publishing a classification where 5 or 10 or 20 closely related phyla are merged into a single one. Though not to this extent, this kind of thing happens all the time. Like all ranks, the rank of phylum is entirely subjective. Phyla are not countable. It is meaningless to say “in the Cambrian there were more phyla than today”.

    The main theoretical problem with Darwinism is that its total reliance on material explanations makes it incapable, even in principle, of accounting for the biological information that shapes matter into complex organisms.

    Read my previous post.

    “Waaah, they are all so different, they can’t have evolved by conventional means!”

    I think the argument that the differences between organisms entails that Darwinian evolution fails to account for any evolutionary changes is stupid, which is why I’ve not made that argument.

    Sorry for not being precise enough, then. By “all” I meant the “kinds”, not the “species”. I know you acknowledge “microevolution”. So I didn’t mean “any evolutionary changes”.

    1) It is not mere personal incredulity to have doubts about the sufficiency of unguided mechanisms to produce specified outcomes when probability militates against the ability of those mechanisms to produce the outcomes. Doubts in the face of high improbability are rational, not personal.

    You seem not to have taken selection into account in your calculations. Obviously, I agree that “probability militates against” a tornado sweeping through a junkyard and building a 747.

    Also, as you have noted yourself in connection to the “weasel” algorithm, the outcomes are usually not very narrowly specified.

    2) I’ve never argued that Darwinism must be rejected on the basis of inadequate evidence for its macroevolutionary claims (as I would have to do to commit the fallacy of argumentum ad ignorantium, or argument from ignorance). I’ve instead argued that the evidence lends little support to the macroevolutionary claims of Darwinism. Surely you can see the difference between saying that a proposition must be rejected due to a lack of evidence (which I’ve not said) and saying that a proposition lacks evidentiary confirmation (which I have said).

    Yes, and that’s not what I was talking about. I was talking about your insistence that there are differences between “kinds” that evolution by mutation, selection & drift would have great trouble bridging. I maintain that such a claim can only derive from ignorance.

    Thanks, Anton, for catching the two words “macroevolutionary event”. That alone is evidence for ignorance on Jim’s part.

    Also, one thing about SETI. Radio waves do not reproduce. Therefore they cannot evolve, and therefore it is a good idea to a priori exclude evolution in the “necessity, random, design, or evolution” question.

    Organisms do reproduce, and inherit. If left on their own, they are expected to evolve even in a completely stable environment, because nothing stops mutation and drift.

    ——————-

    Jim, here is Padian’s testimony I promised, complete with very nice slides. Warning: huge page, takes a long time to load, and several hours to read. I would like to ask you to read the whole page and look closely at every single picture. (Open the pics in new windows or tabs to avoid having to load the whole page again.) Then please come back and discuss with us.

  33. #33 David Marjanovi?
    September 17, 2007

    (Previous comment pending for approval, probably because of its links.)

    ?-?

    ?-??

  34. #34 David Marjanovi?
    September 18, 2007

    Kseniya has blown her cool. And damn right she is about that.

    Jim, I get the impression that you simply don’t read some of my posts. Yesterday I spent a lot of time hunting through teh intertoobz to find you the TREE paper on speciation in the fossil record, and what do you do? Nothing. You don’t tell me if you have access, you don’t tell me if you want the pdf, nothing. You don’t even mention the paper.

    And yet you repeat the falsehood that no lineages have been found in the fossil record! Both in that paper and in the HTML article which I mentioned in the same post you will find a description and an illustration of a branching lineage in the fossil record. There it is, right in front of your nose, and you ignore it.

    I suggest you google about the most famous intermediates between Tyrannosaurus and the Darwin finches, kindly glossing over the fact that transitional forms wouldn’t disprove ID (so I don’t understand why you ask us for transitional forms anyway), and likewise, you don’t even mention the issue afterwards.

    I try to explain the nature of the fossil record (like the universe, it consists mostly of vacuum, and cannot help doing so), and you never even try to argue with me — you just keep on pretending that we can expect to find the skeletons of every generation!

    What’s up with you?

    Remember: You have not fallen among the rhetoricians here. You have fallen among the scientists. You cannot shame us into retracting any of our questions to you. You cannot make arguments from ignorance. It’s just not possible.

    As I wrote last night: go read, and then come back to discuss. If you don’t know anything, you can’t discuss about anything. Everyone smarter than Captain Unelected understands that.

  35. #35 David Marjanovi?
    September 18, 2007

    Obviously, I haven’t fallen among the rhetoricians either. I, too, must answer every single argument. Here goes:

    Jim: “A theory wholly committed to material causes cannot explain, even in principle, the origin of information (which is immaterial).”

    Josh: “That statement seems to me to contradict what you said to me in #129, namely that ‘ID theory makes no claims about the designer.’ The statement above definitely seem to imply some claims about the designer. What am I missing?”

    That implications aren’t claims.

    You don’t believe that yourself.

    You know full well that in science there’s no difference between an implication and a claim. It doesn’t matter for an implication whether anyone actually holds it or not; the implication is part of the hypothesis, not part of the people who work on it.

    As a scientist, you must search for and face every single implication that ID makes, because each of them might be testable, therefore making ID testable. That’s how science works, in case you really don’t know that: we look for ever more tests for each speculation, hypothesis, and theory.

    Such handwaving just-so stories, which are bereft of actual details, don’t amount to rigorous explanations.

    Hm… wait a little.

    Least importantly, I made some of these up because the animals in question simply aren’t my field. I did take care to keep them feasible and falsifiable, however. Others I didn’t make up. For example, as I mentioned and you elided, perhaps in an attempt to deceive yourself, the developmentary genetics of bat wings has been researched. It was all over the Internet a few months ago. Just google for it — do your homework. The stuff on lungs is directly from (my memory of) At the Water’s Edge. What are you waiting for? Go to a library, get that book, and read!

    More importantly, I don’t need to show that this is how it actually happened. I don’t need to prove — I can’t do that anyway, it’s science, not math. All I need to make are falsifiable predictions (i.e. I must keep asking myself the question “if I were wrong, how would I know, even if it takes decades till the relevant fossils are discovered/the relevant developmentary genetics experiments are done?”), and I must check whether they are more parsimonious than all others.

    Now, finally, let’s get some perspective.

    Does ID do anything but hand-waving? “The designer wanted it that way” is a just-so story, too — and worse, it is not falsifiable: as you explained, the designer is ineffable, so we don’t know his mind or anything else about him, so we can never know if anything was done by the designer or not. Actually we don’t even know that if it looks precisely like the result of pure random or the result of pure necessity.

    If the ToE makes falsifiable just-so stories, and ID makes unfalsifiable just-so stories, ID loses.

    Let me also note that you haven’t even tried to disprove a single of my just-so stories. Why don’t you? Surely you don’t think science is an exercise in rhetorics?

    Newton’s law of gravitation demonstrably affects objects large and small.

    Ah, “demonstrably” you say.

    Go ahead, disprove the theory of Intelligent Falling (there is no gravity, there is an intelligence that pushes things down). No, the fact that it was published in The Onion does not count as an argument. Even if nobody accepts it, it can still be real.

    You can’t disprove the “theory” of Intelligent Falling, just like I can’t disprove the “theory” of Intelligent Design. We are forced to resort to the Principle of Parsimony in both cases.

    Why do you apply it in physics but not in biology?

    Does electrostatics explain the highly aperiodic sequencing of nucleotides in DNA molecules that allows those molecules to be the bearers of vast amounts of complex biological information? Nope.

    Indeed not. For that, you need mutation and selection. BTW, I have a pdf of a paper that proposes an explanation of how the genetic code evolved. Do you want it?

    ID theorists don’t insist that Darwinists must “prove” their claims; they instead contend that Darwinists need to show that the inferences they draw are justified by the evidence.

    See above. The ToE makes falsifiable inferences which are more parsimonious than all others that have so far been proposed, including ID. The ToE wins.

    Gould called the lack of transitional forms among the fossils “the trade secret of paleontology”

    And you have never wondered why he didn’t become an ID adherent?

    I can tell you why: because the gaps are in the very places where we expect gaps based on the nature of fossilization, and because they are small enough to leave us a great deal of data anyway. Do you want the paper by me and my thesis supervisor, yes or no?

    If we “confirm” evolution (understood as descent with modification), we’ve delivered a description of life’s history, not an explanation of it.

    Then we have shown that no further explanation is necessary. Mutations happen, selection happens, and together they can produce an eye or a wing or whatever — so we have no reason to assume that they didn’t.

    The validity of that description is, however, much more important to Darwinism than it is to ID theory.

    That’s true, and that’s bad for ID. This is because ID is compatible with everything and its opposite. It can “explain everything”. It can, therefore, not explain anything.

    Why don’t we find rabbits in Silurian rocks? The ineffable designer must have wanted it that way. Why don’t give dogs birth to cats? The ineffable designer must have wanted it that way.

    Suppose we find a complete rabbit skeleton in Silurian rocks. The skeleton is identical to that of a modern rabbit, the dating is beyond all reasonable doubt, and so on.
    Me: Hm. Something we thought we understood about the history of life is very, very wrong.
    YEC: Told you so.
    Jim: Whatever. Mysterious are the ways of the Designer.

    Suppose a YEC gives a lecture on YEC. For illustration purposes, he has put a bitch on the table. Right when he gets to the part where he says dogs don’t give birth to cats, exactly that happens, in front of a packed audience, cameras, and so on. Meow!
    Me: Uh… wow. Either the bitch is a surrogate mother, or we’re dealing with a miracle.
    YEC, ignorantly believing I must be happy: RRRRAAARGH! VADE RETRO SATANA! (starts praying that Jesus take the demon Darwin away)
    Jim: Whatever. Mysterious are the ways of the designer.

    Why do I need to spend kilobyte after kilobyte trying to explain to you how science works, again and again and again? What’s so difficult to understand about it?

  36. #36 David Marjanovi?
    September 18, 2007

    Apologies to Dembski for the harsh wording.

    Why do you apologize for an accurate description? He doesn’t publish anything, not even math in math journals.

  37. #37 David Marjanovi?
    September 19, 2007

    I’d be a little more precise. Electrostatics certainly does explain why DNA nucleotide sequences are “highly aperiodic”–there’s no physical constraint forcing them to be periodic, as there is in many other crystals, so statistically we’d expect any randomly-assembled sequence to be highly aperiodic. No mystery there.

    Thanks for bringing this up. I disagree only in that electrostatics doesn’t explain why DNA is highly aperiodic — because there’s no necessity for it to be periodic, the fact that it is aperiodic simply doesn’t need an explanation. Jim got carried away by his talking-points in the heat of the argument, methinks.

    (The fact that large stretches of our genome are periodic [and therefore junk] does require an explanation: copying mistakes that make subsequent copying mistakes easier.)

    Also thanks to Ichthyic for repeating what I said in different words. That often makes it clearer. :-)

  38. #38 David Marjanovi?
    September 22, 2007

    Copied from this thread:

    How many ID proponents does it take to screw in a lightbulb?

    Undefined. One to claim the creator of the bulb is the only one who can change it, one to quote-mine Bulbwin’s Theory of Illumination, and the rest of the sheep to argue with the Bulbwi[ni]sts’ argument that ALL THEY NEED TO DO IS UNSCREW IT AND PUT A NEW ONE IN.

    – Caucasian Jesus

    If ID were arithmetic, everyone would accept that small numbers can be built by “micro-addition”, but no amount of micro-addition could provide the macro-arithmetic necessary to build numbers larger than 6,000.

    – Blake Stacey

    If ID was a computer manual

    There would be one page that says “This page intentionally left blank.”

    – Tracy P. Hamilton

    If ID was… SPACE EXPLORATION

    Behe would write a book about the moon landing hoax called “Apollo’s Black Box”. In it, he’d claim that the moon landing was impossible because Zeno’s paradox shows that there are an infinite number of “one small steps” between here and the moon.

    During the Dover trial, Behe would complain that if he wasn’t shown every single “small step” betwen here and the moon, all the proof that there was “wasn’t good enough”.

    Meanwhile, instead of testifying, Dembski would voice a Jib-Jab style Flash animation where a big-headed Neil Armstrong farts his way to Mars.

    – Siamang

    I don’t understand your analogy PZ. You must be God.

    – Allen

    If ID were a legitimate theory… nah, that’s just stretching the imagination too far.

    – Fnord Prefect

    If ID was a supermarket

    It would be a store full of empty shelves. There would be desks up front where clerks would tell you how terrible it is to buy and consume food from other supermarkets.

    They would give you pamphlets with stories of the devastating effect of consuming supermarket food. These pamphlets will also contain quotes from supermarket managers and food buyers saying that they don’t believe in their own business.

    When customers ask if they can get something to eat they will be repeatedly told, “Yes, but don’t get it from a supermarket.”

    Eventually, they will sue other supermarkets demanding that they be allowed to put ID empty shelves into their stores.

    – eewolf

    If ID was…

    Noah Webster, the dictionary would only contain exhortations against Samuel Johnson.

    – Flex

    If ID were Criminal Law

    - there wouldn’t need to be a body, blood or other physical evidence to establish that a crime had occurred. If a “victim” disappeared under circumstances that were analogous to cases we know involved a homicide, we can conclude that a murder occurred.

    Unfortunately, since we cannot say anything about the motive, means or identity of the perpetrator, nobody can ever get convicted for the crime.

    – John Pieret

    IF ID WAS MY LAWYER…

    …it would successfully argue at said trial that, even though i appear on security camera to have shot the victim, i did not actually do so, and the bullet that miraculously killed the victim simply poofed into existance in his chest. the fact that it is strongly homologous to the one that left my gun would be insignificant. and since the video only captures 30 frames a second, the bullet only APPEARS to be moving across the frame. in reality, you can’t prove that it’s the same bullet from one frame to the next, or that it’s actually moving. it might be 5 or 6 different stationary bullets, individually created and subsequently destroyed by an invisible intelligent entity. he would also argue that there is no scientific consensus about the chemical reactions needed to produce such extreme motion, demonstrating that fire simply does not create projectiles.

    – arachnophilia

    If ID was geology…

    Channels must have been dug by a landscape designer to make sure that water reached the sea, as water isn’t clever enough to work out which direction to flow.

    Strata are irreducibly complex because if your removed just one layer, it would all collapse.

    The possibility of coal deposits forming from dead vegetation are so improbable that it couldn’t have happened by chance, therefore The Landscape Designer a landscape designer did it.

    Miners and farmers are so wedded to the theory of natural geology that honest debate about the designed landscape is stifled.

    The Brochure document explains how landscaping will be insinuated into geology lessons, as the begining of the replacement of natural surface philosophy.

    The lanscaping may have started 6,000 years ago or it may have been much longer, but we will worry about the details once the past activities of a lanscape designer have been accepted.

    – Bunjo

    If ID were an auto mechanic

    He’d tell you that at some time (can’t know when), for some reason (can’t know why), by some means (can’t know what) your car was busted by an (unidentifiable) intelligent being, whose work happens to look suspiciously like it occurred as the result of normal wear and tear from operating a car. But since he can’t understand how wear and tear can do that, it must be the work of some kind of (unidentifiable) intelligent being. He hasn’t ruled out gremlins. That’s because he’s open minded about these things, unlike all the other auto mechanics who are so dogmatic they actually went so far as to open the hood and take a look at the engine.

    – Wes

    The music theory one reminds me of an ID talk I attended in high school with a friend. At one point the speaker commented that no one would find a Beethoven symphony on the ground and conclude that symphonies must create themselves. I leaned over to my friend and said, “You show me two symphonies that can reproduce and I WILL show you symphonies that create themselves!”

    – Susan B.

    If ID was post-modern literature analysis then if one examines the darwinist paradigm of evolutionary narrative, one is faced with a choice: either reject subsemiotic dialectic theory or conclude that theoretical identity, ironically, has significance, given that explication of randomosity is interchangeable with truth. The subject is contextualised into a Batailleist `powerful communication’ that includes probability as a whole, whilst choosing between neo-darwinist ‘realism’ and subconstructive mathematical possibility.

    Thus, any number of theories or hypothesi [sic] concerning not darwinism, but neo-darwinism exist. The subject is contextualised into a socialist realism that accidentally and incidentally includes foreign evolution as a totality.

    Thus, the premise of darwinistic natural realism suggests that eventual identity has intrinsic meaning, but only if Darwin’s critique of the evolutionary paradigm of cohesive contiguousness is invalid. Dembski suggests the use of Behe’s `explanatory filter’ to read and modify “fact”.

    If one examines postdarwinian cultural theory, one is faced with a choice: either accept National Socialist realism or conclude that truth is capable of significance and difference, given that evolution is distinct from Meinongian Junglarity. Thus, the primary theme of the works of Dembski is the difference between society and ‘society’. Predarwinian narrative holds that society, somewhat surprisingly, has objective value.

    In a sense, an abundance of theories concerning subdialectic darwinianism may be revealed. The premise of the atheistic paradigm of derivitive pre-consciousness suggests that narrative comes from the collective morality.

    QED

    – Sam (with help from the pomo generator)

    If ID where [sic] my credit card

    I could charge $10 every minute for a week, and yet the bill could never add up to more than about $200.

    The only place I could use it would be Steve’s bait and gun emporium, but the card would claim thousands of locations nationwide where it was accepted (it just wouldn’t name any of them.) It would furthermore claim that thousands of people who don’t own a business would accept them if they did own a business.

    Despite claiming all these locations, it would claim that it wasn’t able to be accepted at more locations because of unfair competition from the other credit companies.

    They would give out credit cards to anyone they possibly could, including high school students, the unemployed, and the mentally handicapped. This is an effort to “teach the controversy” that credit cards work just like cash. They’d try to pass laws making themselves immune from the usual lending scrutiny and bankruptcy laws.(Hey, wait a minute now…)

    Disputing a bill would be impossible. No matter how ridiculous the charge was, it happened in the past and therefore can’t ever be proven. (“But, how could I possibly have bought a gumby doll on Io? It’s a freaking volcanic moon!”)

    The dates of purchases on the monthly statement would be all out of order. When questioned, they will reply that this is consistent with all the charges coming in in a “flood” of data.

    – TheFeshy

  39. #39 David Marjanovi?
    September 22, 2007

    Ironically, I should have inserted an empty line between “/blockquote” and the author attributions, to prevent two empty lines from appearing and the one between the author attribution and the next quote from disappearing. Scienceblogs is ineffable, too.

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