Home » Complex Specified Information, Design inference, Functionally Specified Complex Information & Organization, ID Foundations, Irreducible Complexity » ID Foundations, 14: “Islands” vs “Continents” of complex, specific function — a pivotal issue and debate

ID Foundations, 14: “Islands” vs “Continents” of complex, specific function — a pivotal issue and debate

In the current discussion on [Mis-]Representing Natural Selection, UD commenter Bruce David has posed a significant challenge:

A junkers Jumo 004 early Turbojet Engine (Courtesy, Wiki)

. . . it is not obvious that even with intelligence in the picture a major modification of a complex system is possible one small step at a time if there is a requirement that the system continue to function after each such step.

For example, consider a WWII fighter, say the P51 Mustang. Can you imagine any series of incremental changes that would transform it into a jet fighter, say the F80 and have the plane continue to function after each change? To transform a piston engine fighter in to a jet fighter requires multiple simultaneous changes for it to work–an entirely new type of engine, different engine placement, different location of the wings, different cockpit controls and dials, changes to the electrical system, different placement of the fuel tanks, new air intake systems, different materials to withstand the intense heat of the jet exhaust, etc., etc., etc. You can’t make these changes in a series of small steps and have a plane that works after each step, no matter how much intelligence is input into the process.

He then concludes:

Now both a P51 and an F80 are complex devices, but any living organism, from the simplest cell on up to a large multicellular plant or animal, is many orders of magnitude more complex than a fighter plane. If you believe that it is possible to transform a reptile with a bellows lung, solid bones and scales, say, into a bird with a circular flow lung, hollow bones, and feathers by a series of small incremental changes each of which not only results in a functioning organism, but a more “fit” one, then the burden of proof is squarely on your shoulders, because the idea is absurd on the face of it.

In responding, UD Contributor gpuccio clarifies:

consider that engineered modifications can be implemented in a complex organism while retaining the old functionality, and then the new plan can be activated when everything is ready. I am not saying that’s the way it was done, but that it is possible.

For instance, and just to stay simple, one or more new proteins could be implemented using duplicated, non translated genes as origin. Or segments of non coding DNA. That’s, indeed, very much part of some darwinian scenarios.

The difference with an ID scenario is that, once a gene is duplicated and inactivated, it becomes non visible to NS. So, intelligent causes can very well act on it without any problem, while pure randomness, mutations and drift, will be free to operate in neutral form, but will still have the whole wall of probabilistic barriers against them.

[U/d, Dec 30] He goes on to later add:

NS acts as negative selection to keep the already existing information. We see the results of that everywhere in the proteome: the same function is maintained in time and in different species, even if the primary sequence can vary in time because of neutral variation. So, negative NS conserves the existing function, and allow only neutral or quasi neutral variation. In that sense it works againstany emergence of completely new information from the existing one, even if it can tolerate some limites “tweaking” of what already exists (microevolution).

I suppose that darwinists, or at least some of them, are aware of that difficulty as soon as one tries to explain completely new information, such as a new basic protein domain. Not only the darwinian theory cannot explain it, it really works against it.

So, the duplicated gene mechanism is invoked.

The problem is that the duplicated gene, to be free to vary and to leave the original functional island, must be no more translated and no more functional. Indeed, that happens very early in the history of a duplicated gene, because many forma of variation will completely inactivate it as a functional ORF, as we can see all the time with pseudogenes.

So, one of the two:

a) either the duplicated gene remains functional and contributes to the reproduction, so that negative NS can preserve it. In that case, it cannot “move” to new unrelated forms of function.

b) or the duplicated gene immediately becomes non functional, and is free to vary.

The important point is that case a) is completely useless to the darwinian explanation.

Case b) allows free transitions, but they are no more visible to NS, at least not until a new functional ORF (with the necessary regulatory sites) is generated. IOWs, all variation from that point on becomes neutral by definition.

But neutral variation, while free of going anywhere, is indeed free of going anywhere. That means: feedom is accompanied by the huge rising of the probability barriers. As we know, finding a new protein domain by chance alone is exactly what ID has shown to be empirically impossible.

In her attempted rebuttal, contributor Dr Elizabeth Liddle remarks:

I don’t find Behe’s argument that each phylum has a radically different “kernel” very convincing. Sure, prokaryotic cells and eukaryotic cells are different, but, as I said, we have at least one theory (symbiosis) that might explain that. And in any case for non-sexually reproducing organisms, “speciation” is a poor term – what we must postulate is cloning populations that clone along with their symbiotic inclusions. Which is perfectly possible (indeed even we “inherit” parental gut flora).

I think you are making the mistake of assuming that because “phyla” is a term that refers not only to the earliest exemplars of each phylum but also to the entire lineage from each, that those earliest exemplars were as different from each other as we, for example, are from trees, or bacteria. It’s really important to be clear when we are talking longitudinally (adaptation over time) and when laterally (subdivisions of populations into separate lineages).

This was largely in response to Dr V J Torley’s listing of evidence:

What evidence [for the distinctness of main body plans and for abrupt origin of same in the fossil record], Elizabeth? Please have a look here:

http://www.darwinsdilemma.org/pdf/faq.pdf
http://www.darwinsdilemma.org/
http://www.nature.com/news/eni…..ria-1.9714
http://www.arn.org/blogs/index.php/literature

In “The Edge of Evolution”, Dr. Michael Behe argues that phyla were probably separately designed because each phylum has it own kernel that requires design. He also suggests that new orders (or families, or genera – he’s not yet sure which) are characterized by unique cell types, which he thinks must have been intelligently designed, because the number of protein factors in their gene regulatory network (about ten) well exceeds the number that might fall into place naturally (three).

This exchange pivots on the central issue: does complex, multi-part functionality come in easily accessible continents that can be spanned by an incrementally growing and branching tree, or does it normally come in isolated islands in beyond astronomical spaces dominated by seas of non-function, that the atomic level resources of our solar system (our effective universe) or of the observed cosmos as a whole cannot take more than a tiny sample of?

Let’s take the matter in steps of thought:

1 –> Complex, multi-part function depends on having several well-matched, correctly aligned and “wired together” parts that work together to carry out an overall task, i.e. we see apparently purposeful matching and organisation of multiple parts into a whole that carries out what seems to be a goal. The Junkers Jumo 004 Jet engine in the above image is a relevant case in point.

2 –> Ever since Wicken posed the following clip in 1979, this issue of wiring-diagram based complex functional organisation has been on the table as a characteristic feature of life forms that must be properly explained by any successful theory of the causal roots of life. Clip:

‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems.  Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

3 –> The question at stake in the thread excerpted from above, is whether there can be an effective, incremental culling-out based on competition for niches and thence reproductive success of sub-populations that will create ever more complex systems that will then appear to have been designed.

4 –> Of course, we must notice that the implication of this claim is that we are dealing with in effect a vast continent of possible functional forms that can be spanned by a gradually branching tree. That’s a big claim, and it needs to be warranted on observational evidence, or it becomes little more than wishful thinking and grand extrapolation in service to an a priori evolutionary materialistic scheme of thought.

5 –> I cases where the function in question has an irreducible core of necessary parts, it is often suggested that something that may have had another purpose may simply find itself duplicated or fall out of use, then fit in with a new use. “Simple.”

6 –> NOT. For, such a proposal faces a cluster of challenges highlighted earlier in this UD series as posed by Angus Menuge [oops!] for the case of the flagellum:

For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

8 –> The number of biologically relevant cases where C1 – 5 has been observed: ZERO.

9 –> What is coming out ever more clearly is this:

when a set of matching components must be arranged so they can work together to carry out a task or function, this strongly constrains both the choice of individual parts and how they must be arranged to fit together

A jigsaw puzzle is a good case in point.

So is a car engine — as anyone who has had to hunt down a specific, hard to find part will know.

So are the statements in a computer program — there was once a NASA rocket that veered off course on launch and had to be destroyed by triggering the self-destruct because of — I think it was — a misplaced comma.

The letters and words in this paragraph are like that too.

That’s why (at first, simple level) we can usually quite easily tell the difference between:

A: An orderly, periodic, meaninglessly repetitive sequence: FFFFFFFFFF . . .

B: Aperiodic, evidently random, equally meaningless text: y8ivgdfdihgdftrs . . .

C: Aperiodic, but recognisably meaningfully organised sequences of characters: such as this sequence of letters . . .

In short, to be meaningful or functional, a correct set of core components have to match and must be properly arranged, and while there may be some room to vary, it is not true that just any part popped in in any number of ways can fit in.

As a direct result, in our general experience, and observation, if the functional result is complex enough, the most likely cause is intelligent choice, or design.  

This has a consequence. For, this need for choosing and correctly arranging then hooking up correct, matching parts in a specific pattern implicitly rules out the vast majority of possibilities and leads to the concept of islands of function in a vast sea of possible but meaningless and/or non-functional configurations.

10 –> Consequently, the normal expectation is that complex, multi-part functionality will come in isolated islands. So also, those who wish to assert an “exception” for biological functions like the avian flow-through lung, will need to  empirically warrant their claims. Show us, in short.

11 –> And, to do so will require addressing the difficulty posed by Gould in his last book, in 2002:

. . . long term stasis following geologically abrupt origin of most fossil morphospecies, has always been recognized by professional paleontologists. [The Structure of Evolutionary Theory (2002), p. 752.]

. . . .  The great majority of species do not show any appreciable evolutionary change at all. These species appear in the section [[first occurrence] without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants.” [p. 753.]

. . . . proclamations for the supposed ‘truth’ of gradualism – asserted against every working paleontologist’s knowledge of its rarity – emerged largely from such a restriction of attention to exceedingly rare cases under the false belief that they alone provided a record of evolution at all! The falsification of most ‘textbook classics’ upon restudy only accentuates the fallacy of the ‘case study’ method and its root in prior expectation rather than objective reading of the fossil record. [[p. 773.]

12 –> In that context, the point raised by GP above, that

. . .  once a gene is duplicated and inactivated, it becomes non visible to NS. So, intelligent causes can very well act on it without any problem, while pure randomness, mutations and drift, will be free to operate in neutral form, but will still have the whole wall of probabilistic barriers against them.

. . . takes on multiplied force.

___________

In short, the islands of function issue — rhetorical brush-asides notwithstanding — is real, and it counts.  Let us see how the evolutionary materialism advocates will answer to it. END

PS: I am facing a security headache, so this post was completed on a Linux partition. Linux is looking better than ever, just now. as a main OS . . .

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412 Responses to ID Foundations, 14: “Islands” vs “Continents” of complex, specific function — a pivotal issue and debate

  1. The problem is analagous to modifying words, sentences, paragraphs by a series of simple “mutations”, to give a significantly different meaning, while maintaining meaning along the way. The task is relatively easy for short words, but as the total number of letters, or words, increases, the fraction of meaningful combinations out of the possible total becomes smaller and smaller, with the result that solution space becomes disconnected. It is not hard to make the step from written human language to DNA sequences.

    I began to make this argument over on Elizabeth Liddle’s blog “The Skeptical Zone” late last summer, and got replies such as the following, which were intended as rebuttal, but actually prove the conjecture — real meaning is lost the longer you make the sentences. Zachriel, for instance has some written some interesting code to mutate phrases, but the best that can be said of them is that they are poetic. I wouldn’t want to build anything based on poetry.

  2. Oops, I made mention of “replies such as the following” in the post above… it’s better to see the original Search Space discussion in the Skeptical Zone blog.

  3. CS:

    Precisely.

    We do not normally write books by mutating “See Spot run,” and if we take it out of the requirement for step by step functionality and use duplication then chance variation then seek to get back to function at a more sophisticated level, we are essentially doing a random walk from an arbitrary initial config in a large space.

    Not a recipe for success.

    To see the point with even greater force, try moving from a hello world program to something a lot more sophisticated, like say a spreadsheet, by this sort of process or the like.

    That dog ain’t gonna bark or bite.

    Happy New Year to all, esp to UD News!

    GEM of TKI

    PS: Deep background scanning but — after some ruthless cleaning and removal of anything that hints of being possibly suspect — the black screen of sudden death seems to be gone for now. Linux is looking better and better, though. I see where Netbooks are going Android. PCs, next?

  4. Poetry presents its own challenge. It’s tough enough to mutate letters to form different words or to mutate sentences to affect subtle changes in meaning. However, to alter poetic verse requires structural changes analogous to replacing the aluminum skin used on a propeller-driven aircraft with the titanium skin needed to survive the high temperatures encountered by a jet fighter. That is, changing a word or two in Hamlet preserves its iambic pentameter. Converting Hamlet to the Iliad or Poe’s Raven requires not only word changes but meter change from iambic pentameter to dactylic hexameter or trochaic octameter, respectively. Coherence must be maintained on multiple levels.

    Another point to make is that while a purpose of life is survival to the next generation, a purpose of natural language is to communicate. So, it is insufficient fitness for a sentence to pass a grammar checker. It needs to merit retransmission.

  5. 5

    To quote from my book :

    An analogy may be useful here. If some future paleontologist were to unearth two species of Volkswagens, he might find it plausible that one evolved gradually from the other. He might find the lack of gradual transitions between automobile families more problematic, for example, in the transition from mechanical to hydraulic brake systems, or from manual to automatic transmissions, or from steam engines to internal combustion engines; though if he thought about what gradual transitions would look like, he would understand why they didn’t exist. He would be even more puzzled by the huge differences between the bicycle and motor vehicle phyla, or between the boat and airplane phyla. But heaven help us if he uncovers motorcycles and Hovercraft, the discovery of these “missing links” would be hailed in all our newspapers as final proof that all forms of transportation arose gradually from a common ancestor, without design.

  6. To take something obvious, an eye and a eye socket. In ‘evolution’ you would expect the eye to move around trying to find the perfect spot, so that it is useful. Should there not be a record of that? Now that also means that the eye socket, has to move around also. At what point to they move to the correct spot together at the same time? These are two different processes. For the eye it also has to have all the muscles, optic nerves, to move with it. If you think of a spine and nerves that travel through that and have to go to certain muscles. If a leg becomes something else and moves to another placement, all of the supporting parts do also. None of this is in the fossil record. The brain also has to know how to use this ‘new’ placement. Or your dinner, and could never past it on.
    To detect ID, there is an easy experiment to do.
    1-Find life just happening on its own.
    2-Or record all the steps necessary, to create life in a lab. Including the knowledge, that goes into it. All of that is ID.
    Compare the two.
    http://patternsofcreation.weebly.com/

  7. You really published that?

  8. Analogies are actually pretty useless, because there is nothing really analogous to chemistry.

    Functional sequence space has simply not been explored sufficiently to draw conclusions about whether it can be navigated by incremental steps.

    In those cases where it has been exhaustively explored, as with Lenski and Thornton, it has been navigable.

    As for words, it is quite easy to navigate to words using a GA. The interesting thing is that the ease differs from one language to another, which demonstrates that you can’t characterize the difficulty of evolution without actually testing sequence space. You can’t decide the spareness using intuition.

  9. Nor, therefore, the brittleness.

  10. To be specific:

    There are three glaring holes in that passage.

    First: if a future paleontologist uncovered the remains of human mechanical artefacts it would be immediately obvious that they were not self-reproducing – there would be no evidence of any reproductive or developmental process.

    Second: if that same paleontologist attempted to map each artefact by character on to a nested tree diagram, she would fail utterly, for exactly the reasons you give – hovercraft and motorcycles would not be assignable to nested hierarchies. The Venn diagrams would overlap. It is the rigorous lack of overlap in biological characteristics that point so strongly at common ancestry for living things.

    Third: there would be copious evidence of human manufacture.

    Even if we ignore for hypothetical reasons the third, you are left with the first two. I’m really surprised you would write such a thing in a published book.

  11. 11

    Good Lord Elizabeth, you always go after the perifery in order to avoid the main point. I’m sure you know I wasn’t claiming my paleontologist would REALLY think that one species of VW evolved from another. The point was that the evolution of human technology is similar to the evolution of species; new technologies are also descended from earlier technologies, but not without the help of design, and the major changes occur in large steps, not entirely gradually, in both cases. But I’m not going to be drawn further into a discussion with someone who is as insulting as you, and isn’t making any effort to see my point.

  12. Good Lord Elizabeth, you always go after the perifery in order to avoid the main point.

    From my point of view it always looks as though IDists only manage to cling to their main point by avoiding the crucial details at the periphery!

    I’m sure you know I wasn’t claiming my paleontologist would REALLY think that one species of VW evolved from another.

    I’m aware of that. But the reasons that the palaeontologist wouldn’t are absolutely pertinent, and subvert what IS your main point AFAICT.

    The point was that the evolution of human technology is similar to the evolution of species; new technologies are also descended from earlier technologies,

    Yes, indeed, but with some absolutely crucial differences. The differences are what completely negate your point.

    but not without the help of design, and the major changes occur in large steps, not entirely gradually, in both cases.

    No, not in both cases. That’s one of the crucial differences.

    But I’m not going to be drawn further into a discussion with someone who is as insulting as you, and isn’t making any effort to see my point.

    I apologise for insulting you. It was not my intention. I was genuinely surprise that someone could publish an analogy so self-defeating. I still am.

    If your “main point” is that both processes occur in leaps, then an analogy doesn’t work to make that point. You’d have to make the point that biological evolution does occur in big leaps, not simply assert that it’s analogous to design lineages which do. It’s precisely because biological lineages do NOT show the features that you even point out in your “analogy” that we can reasonably infer that no very Intelligent Designer was involved.

    And your point about motor cycles and hovercraft remains completely wrong. If you try to make a Venn diagram for bicycles, overcraft, aeroplanes, motorcycles and cars, you will find yourselve with violations of a nested hierarchy, not “missing links” (a silly term anyway). A “missing link” wouldn’t be a link if it spanned two separate lineages.

    A “missing link” (in tabloid parlance) is usually a fossil that has characters from both earlier and later periods, the later ones being more “derived” than the earlier ones. A tetropod with wrists but no ankles might be a missing link between fish and tetrapods with both wrists and ankles. However, a fossil with a mammalian jaw and dynapsid skull would not be a Missing Link – it would be one of your hovercraft and would be a serious problem for nested hierarchies and therefore common descent.

  13. Elizabeth Liddle

    A “missing link” (in tabloid parlance) is usually a fossil that has characters from both earlier and later periods, the later ones being more “derived” than the earlier ones. A tetropod with wrists but no ankles might be a missing link between fish and tetrapods with both wrists and ankles. However, a fossil with a mammalian jaw and dynapsid skull would not be a Missing Link – it would be one of your hovercraft and would be a serious problem for nested hierarchies and therefore common descent
    ———————————————————
    That is of course, if you assume one came from the other naturally. Which there is no evidence for. The evidence we do have is a human comes from humans. There is no monkey business.
    There is no common descent, but there maybe many lines of descent.
    This can be explained by Patterns of Creation*. One life created from existing life. By taking materials from one and making another with slight changes. That also explains why there are no transitional ( mistakes, or trial and error) fossils. Which if ‘evolution’ were true, you would need to see.
    *
    http://patternsofcreation.weebly.com/

  14. Onlookers:

    The above exchange shows why I — with sadness — no longer really believe serious dialogue is sustainable on this topic, given what seems to be typically brought to the table by darwinist advocates. At least, the moderation policy here at UD restrains the sort of abuse, “I can get away with it” rudeness and misbehaviour that so often crop up elsewhere. And, again, typically and mainly from the darwinist side.

    It has now come to a point of letting the sides speak for themselves, and allowing you the onlooker to see where the warrant lies.

    For instance, of course it is easy to go cat –> rat –> ran –> man –> mat, etc. But, once we add significant complexity — say about seven letters for English words, the gaps between words will be all but impossible to consistently bridge (the islands of function issue emerges . . . ).

    And that has been pointed out over and over, just ignored.

    Similarly, it becomes ever harder to vary words incrementally and get a coherent series of sentences that moves from “See Spot run,” to say a report on sustainable energy development.

    As to the abuse of the term “analogy” as a dismissal, that has been pointed out to Petrushka over and over, to no avail.

    I will note, one more time for record:

    1 –> No analogy is a deductive proof, but that is true of all inductive arguments, the only class of arguments that gives us hope of empirical knowledge.

    2 –> In fact, inductive reasoning is closely and inextricably tied to analogous reasoning. The real issue then is the quality — the cogency — of the comparison, not the existence of a comparison and the possibility of making an error.

    3 –> To pretend otherwise is to play at selective hyperskepticism, which reveals its fallacious nature by the double standard of warrant in cases one is inclined to accept vs those one is disinclined to accept.

    4 –> We must also reckon with the power of good analogies, e.g. Power = Torque * Angular velocity, which is so closely analogous to the linear case that some of the names are simply taken over and prefaced.

    5 –> Last time around, P was objecting to how we reckoned that the flagellum incorporates a motor, or how ATP synthetase uses a motor, and indeed how kinesin also uses a linear motor on the cellular “highway” network, as a part of a nanotech “walking truck.” The dismissal was: ANALOGIES — ugh!

    6 –> But a motor is a two-port that converts pressure-volume energy, or fluid flow, or combustion or electrical current — another analogy! — into rotational mechanical energy, power and shaft work.

    7 –> Much like how the old fashioned water wheel and windmill did much the same. (I guess s/he would have objected to how I used to use a rotary water pump, sluice and overshot waterwheel as an analogy for an electric circuit to teach basic electricity, potential difference, work, power etc to students.)

    8 –> Sorry, each and every one of these is a case of INSTANTIATION of what a motor is generically [and of the broader concept of a two-port], as is the Junkers Jumo 004 in the OP above. Genus and difference on distinguishing keys is a legitimate way to analyse and understand phenomena.

    9 –> And in every one of those cases, a very specific pattern of components that have to be present, well-matched and arranged is required, or function cannot begin, or will cease.

    10 –> And, that in some cases we are looking at functional devices that are components of self-replicating automata simply ADDS to the complexity involved. In short — as was discussed here in this series — the presence of a vNSR adds to the case that the system is designed, it does not divert from it.

    11 –> And where there IS an analogy, it is patently an apt one: Kinesin acting as a walking truck and pulling vesicles along the cell’s microtubule highway networks like containerised loads. Indeed, it is typical to describe the stepping action as “zippering” along the microtubule, using up an ATP per step.

    ___________

    In short, we need to pause and look seriously at what is going on in that living cell.

    GEM of TKI

  15. Easy-smeasy:

    Can you imagine any series of incremental changes that would transform it into a jet fighter, say the F80 and have the plane continue to function after each change? To transform a piston engine fighter in to a jet fighter requires multiple simultaneous changes for it to work–an entirely new type of engine,…

    IDiot! First you would duplicate the engine so that you always have one working engine. Then you bang away on the duplicated engine until you have a functioning jet engine. And next you just swap and drop the prop.

    Gall dang creationists can’t think of nuthin’… :)

  16. F/N: Actually, configuration spaces for composite, functional entities are a commonplace, and it is notorious that the right part needs to be in the right place for such to work. Whether, letters and words in a sentence or the engine in your car, or the PC you are reading this on. The claim that biological functional forms are exceptional is what needs to be shown, in the teeth of the known problems that quite simple mutations in genomes often lead to grave defects or even to lethality.

  17. A tetropod with wrists but no ankles might be a missing link between fish and tetrapods with both wrists and ankles. However, a fossil with a mammalian jaw and dynapsid skull would not be a Missing Link – it would be one of your hovercraft and would be a serious problem for nested hierarchies and therefore common descent.

    Actually you would just have to redefine your “nests”. And it is already a given that common descent does not expect a nested hierarchy based on characteristics- OTOH Linnean taxonomy is a nested hierarchy based on characteristics but it has nothing to do with descent with modification.

  18. No.

    And common descent does imply a nested hierarchy.

    A nested hierarchy doesn’t necessarily imply common descent, but it makes common descent more likely than ID. IDs tend to produce artefacts that violate into nested hierarchies.

  19. Of course, the materials — alloys — are very different.

  20. And common descent does imply a nested hierarchy.

    Based on what, exactly? With evolution characteristics can be gained or lost-> it all depends on what works.

    OTOH Linnean taxonomy is based on characteristics, has no regard for descent and was once used by Creationsits as evidence for a common design.

    IDs tend to produce artefacts that violate into nested hierarchies.

    They can but don’t have. but again it all depends on what you are basing your nested hierarchy on.

    The point being is one can construct a nested hierarchy out of just about anything. It all depends on the criteria used.

  21. Through molecular recombination caused by the Illudium Q-36 Explosive Space Modulator, the alloys met the specification qualification described in the documentation making the situation an evolutionary fabrication.

    Any questions?

  22. The point I was trying to make, and which I think often gets lost in these back and forth discussions, is that the state of the evidence as it currently exists puts the burden of proof squarely on the shoulders of anyone who claims that RM/NS is sufficient to explain all of the variety of species we observe in the natural world plus the fossil record. I contend that given my analysis quoted by KS at the beginning of this post, along with the work of Behe, Denton, Dembski, Axe, Sanford, Sewell, Meyer, Wells, and others, coupled with the fact that there is no actual evidence that RM/NS is capable of producing macroevolutionary change (neither observational, experimental, nor in the fossil record), it is incumbent on anyone believes that neo-Darwinism explains the origin of all species to demonstrate that that this is so.

    What I observe about Elizabeth Liddle and others is that she implicitly takes the position that she will continue to believe the neo-Darwinian explanation until ID proponents can prove that it is false. I think that the case has been made many times over that she has placed the burden of proof on the wrong set of shoulders.

    Further, I think that this question of where the burden of proof lies is central to the arguments that each side uses, but is most often implicitly assumed by each to lie with the other, leading to a great deal of talking past one another.

  23. Joe,

    “Then you bang away on the duplicated engine until you have a functioning jet engine”

    Are you being serious?

    You just bang away at a piston engine until it becomes a jet engine?

    Or, do you leave the piston engine alone, as it of new use to a jet, and go off into another shed where with other materials – and a whole new design plan – create a jet engine?

  24. BD:

    You make an excellent point.

    However, as a general point, the burden of warrant issue is not up for debate.

    EVERY scientific theory worth its salt must provide adequate empirical support: a base of solid empirical observations joined to explanations that are as far as possible factually adequate [and all the relevant facts should be on the table], coherent and elegantly simple — neither ad hoc nor simplistic.

    Where, a priori ideological materialism or philosophical impositions that censor out otherwise reasonable explanations, do not constitute such adequate warrant. Where also claiming that science “must” explain naturalistically, is a case in point of ideological impositions.

    And, pretending that such ideological captivity of science is justifiable, even seeking to redefine science under that imposition, is obviously unjustifiable.

    As has been pointed out here at UD over and over and over, and as has been brushed aside, too often with personal attacks added (especially in the penumbra of hate — beyond a certain point, that is the only apt word, as can easily be seen — sites).

    And so we come back to the point raised by Philip Johnson in reply to Lewontin, in 1997:

    For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

    So, now, will we face this issue squarely?

    Is truth-seeking a serious objective of science, and of science education?

    And if so, then how can one justify imposition of ideological a priori materialism and putting it into the definition of science you want to teach, a la NSTA and NAS?

    If not, then will you frankly acknowledge this, and face the fact that science and science education then become simply another ideological turf war?

    One thing is sure, playing ideological games with science, the definition of science, and science education, then pretending to objectivity, is indefensible.

    If you are going to propose a materialistic school of thought, then say so, and move up one level, to comparative difficulties analysis at worldview levels. Then, give a balanced view of the different major views.

    If you fail to do that, you are being at minimum in gross neglect of a major duty of care, and are arguably indulging in false packaging and misleading labelling, of materialist ideology hiding in a box labelled “science.”

    (That was in effect what we used to tell the rabid marxists of my youth, who often thought they were presenting a “scientific” analysis of society, its ills and the logical solution. When you dressed it up with matrix analysis, and did not bring out the issue of the over-determined set of equations, it could look very impressive indeed.)

    I think we need to do some serious reflection on that concern.

    GEM of TKI

  25. PJ: Joe is being sarcastic. He is implying that the proposals of duplicate and then modify then bring back on line are as outlandish as hammering away at random at a Rolls Royce Merlin or Daimler-Benz DB 601 under the impression that by hammering and testing successively, you will get a Junkers Jumo 004 jet as a result, not simply a broken engine. KF

  26. Bruce,

    There are some very good reasons to favor evolutionary theory over intelligent design:

    1. We know that natural selection happens.

    2. We know of no barrier that prevents microevolutionary changes due to NS and drift from accumulating over time, thereby becoming macroevolutionary change. (I’ll address the “islands of function” argument below).

    3. Evolutionary theory predicts that life should form a nested hierarchy. When biologists construct trees based on independent characters, they match to a stunning degree. In fact, the standard tree of life is known to an accuracy of 38 decimal places! See Theobald’s excellent analysis for details.

    4. Intelligent design does not predict a nested hierarchy at all. And contrary to what many ID proponents believe, “common design” does not lead to such a hierarchy. A designer could produce a single nested hierarchy only if he deliberately chose to make evolution appear true, or if he was somehow forced to do so.

    5. The “islands of function” argument against natural selection assumes that there are unbridgeable gaps between most of the “islands”. However, no ID proponent has been able to demonstrate this.

    6. The extraordinary, many-decimal-place congruence between phylogenetic trees is evidence that the gaps aren’t there. If they were actually there, then evolutionary theory’s prediction of a single nested hierarchy wouldn’t have panned out.

    7. The “islands of function” metaphor and the very similar “peaks of a fitness landscape” metaphor are quite misleading. For one thing, they bring to mind a three-dimensional space where the x and y coordinates represent genetic changes and the z coordinate represents fitness. The idea is that evolution can get stuck on a peak, even if there is a higher peak in the vicinity, because incremental movement in the x-direction, or the y-direction, or any combination of the two, will result in a decrease of fitness.

    The reason this is so misleading is that the actual fitness landscape has many, many dimensions. In order for evolution to get stuck on a fitness peak, it would have to be true that incremental movement in every one of those dimensions, and every possible combination of those dimensions. This is much less likely than the simple 3-dimensional visualization would suggest.

    Also, the “fitness peak” metaphor invites us to imagine an unchanging landscape. In reality the landscape will change over time due to changes in the environment, evolutionary changes in other organisms, and even intra-species evolutionary changes. A population that’s stuck on a fitness peak may no longer be stuck in a thousand years as the landscape changes underneath it.

    The take-home message is that evolutionary theory, including the idea that natural selection is responsible for macroevolutionary change, makes a prediction that is confirmed to dozens of decimal digits of accuracy. Intelligent design makes no such prediction. Evolutionary theory is the superior explanation of biological diversity.

  27. In all this it once again is apparent to me its all just lines of reasoning.
    To assert small steps can be seen reasonably to explain macro results in biology and to assert that its unreasonable to see small steps can bring macro results in biology is still a exercise in a line of reasoning.
    There is no actual investigation demonstrating these steps took place.
    Id people by debunking certain plane types evolving innately from other plane types are engaged in the evolutionist reasoning claim as evidence or proof of evolution.

    if evolution is not true then its impossible there was ever good or close to good evidence from scientific investigation.
    therefore it could only be that confidence in evolution as always been from a line of reasoning and other lines of reasoning based on minor data.

    Creationists should aggressively demand if evolution is no further along then a untested hypothesis.

    A clue is this whole, steps can or cannot, lead from a mouse to a moose.
    Whether its reasonable or possible is unrelated to scientific investigation that it did occur.

    Its also not from scientific investigation that steps after steps can lead to macro results.

    Its all just bringing lines of reasoning to great conclusions of rejecting the bible and explaining biology origins.

    A great humbug of human knowledge.

  28. Correction to third-from-last paragraph:

    The reason this is so misleading is that the actual fitness landscape has many, many dimensions. In order for evolution to get stuck on a fitness peak, it would have to be true that incremental movement in every one of those dimensions, and every possible combination of those dimensions, would lead to a decrease in fitness. This is much less likely than the simple 3-dimensional visualization would suggest.

  29. PJ: Joe is being sarcastic. He is implying that the proposals of duplicate and then modify then bring back on line are as outlandish as hammering away at random at a Rolls Royce Merlin or Daimler-Benz DB 601 under the impression that by hammering and testing successively, you will get a Junkers Jumo 004 jet as a result, not simply a broken engine. KF

    That doesn’t really help. It’s still silly.

    Variants of living things aren’t made by damaging them. They are made by changes to the DNA sequence that governs their development.

    There isn’t really a parallel with human manufacturing, unless it’s the sequential tweaking of designs and testing prototypes, and retaining the ones that perform best, then tweaking those. Clearly that process of tweaking is planned though.

    The best analogue of course is a GA, in which the tweaks are random, and the best resulting performers are retained for further random tweaking.

    And of course it works, which is why people use them.

  30. And common descent does imply a nested hierarchy.

    Based on what, exactly?

    Based on inheritance. A family tree is a tree, yes? A nested hierarchy.

    With evolution characteristics can be gained or lost-> it all depends on what works.

    Sure, and “gained” means replicated down the lineage, and “lost” means ceases to be replicated down that lineage. So you get a nested hierarchy.

    OTOH Linnean taxonomy is based on characteristics, has no regard for descent and was once used by Creationsits as evidence for a common design.

    Sure. As I said, the nested hierarchy is an observation, and demands explanation. It’s consistent with common design, but it wouldn’t be evidence for common design, as common design could result in non-nested hierarchies, as human designs do. Common design is consistent with anything. However, common descent requires nested hierarchies.

    IDs tend to produce artefacts that violate into nested hierarchies.

    They can but don’t have. but again it all depends on what you are basing your nested hierarchy on.

    To a limited extent, yes. But what is striking, as Linnaeus discovered, is how readily the characteristics of living things can be used to arrange organisms in a nested hierarchy – much more than would be expected by chance, say, or by human design.

    You get weakly nested hierarchies in human design, but far more violations because human designers are capable of transferring innovations from one design lineage into another. Evolution can’t do that, so we are stuck with inefficient lungs even though far more efficient lungs exist in a parallel lineage. A human designer would be able to install bird lungs into mammals, just as they install car engines into aeroplanes, or lasers into barcode readers.

    The point being is one can construct a nested hierarchy out of just about anything. It all depends on the criteria used.

    Only to a limited extent before you encounter violations overlaps, unless the set of things you are arranging was in fact created by some system that tends to generate deeply nested hierarchies.

    Try constructing a phylogeny of vehicles and compare it with a phylogeny of, say, mammals, and you will see what I mean.

  31. Dr Liddle:

    First, happy new year when it comes.

    On the just above, by overwhelming odds, sufficiently large random [non-purposive] changes to complex digit strings that have been duplicated will . . . damage them, reducing them to gibberish. (And encrypted codes — which only look like nonsense [which is actually part of their FUNCTION!] — require something else somewhere with the decoding algorithm and keys, to work.)

    You have a choice, on the alternatives that have been suggested:

    a: incremental functional changes within an island of function, that can only reasonably explain microevo.

    b: duplication and taking off-line that then can vary but faces the full scope of the relevant config space, which is overwhelmingly non-functional.

    Neither of these seems a credible source for the sort of systematic, organised large scale functionally specific changes required to explain novel body plans.

    Starting of course with the first — the functional organisation of the living self replicating cell needs to be explained on observational evidence.

    But also proceeding tot he range of body plans, which on evidence will require 10 – 100+ mn bits of novel, co-ordinated, functional information.

    Your explanation for such is __________, and your observational cases in support are _______________ .

    All best for the new year

    GEM of TKI

  32. C:

    And your observational — not inferred, and not censored by a priori evolutionary materialism — case that NS can and does account for a novel body plan is ___________ ?

    KF

  33. kairosfocus, even in the light of recent evolutionary literature, champignon’s claims boil down to outdated propaganda found only in low level textbooks.

  34. C:

    The problem with fitness landscape type arguments is that — as the OP highlights — they implicitly imply that we are within an island of function. When we look at he overall configuration space for all the involved components, it is overwhelmingly obvious that the non-functional states absolutely dominate, so the issue is not to move around within an island of function, but to get to the beach of such an island.

    That is what the body plan origin challenge is about.

    When we see a switcheroo that begs the question of getting to the beach first before hill-climbing, that tells us that the real issue is being distracted from.

    Your evidence that chance variation plus natural selection in plausible initial conditions can account for novel body plans is _______________________, and this is backed up by the following observations of the relevant process in action at that level of body plan origination: ____________________ .

    (If you cannot readily and cogently fill in those blanks, you have not got a first level answer. And BTW, computer simulations that work within islands of function are not a good answer.)

    KF

  35. F/N: Please, it is a routine matter in multidimensional situations to use 2 or 3 d toy models for illustration. The real deal requires matrices and vectors of large size, maybe in some cases matrices with Laplace transform elements to get us into operations.

  36. And a happy new year to you, kairosfocus! Good to see you again :)

    On the just above, by overwhelming odds, sufficiently large random [non-purposive] changes to complex digit strings that have been duplicated will . . . damage them, reducing them to gibberish. (And encrypted codes — which only look like nonsense [which is actually part of their FUNCTION!] — require something else somewhere with the decoding algorithm and keys, to work.)

    ONce you have a functional DNA sequence, i.e. a sequence that results in benefit to the organism that bears it, you are correct that most non-purposive changes will tend to damage them. As a result, offspring bearing such damaged sequences will leave few, if any, of their own offspring. Only those bearing undamaged versions will leave offspring. That is the basic principle of Natural Selection. This means that only the very rarer mutations that result in function that is approximately as efficient, or slightly better than the function conferred by the original sequence will be retained in the population. And those that perform the function slightly better will, by definition, become most prevalent.

    However, if we start with a non-functional sequence (“gibberish”) if you like, one that does nothing to effect the organism’s chances of reproduction, then a considerably greater proportion of possible mutations are likely to perform rather better than the original. All others will be retained, unless they actually do damage, in which case they will be lost. So Natural Selection also refers to filtering out of damaging mutations as well as the propagation of more beneficial ones.

    And any that turn out to have even a minor beneficial effect on the organism will tend to be retained in the population and become more prevalent.

    Would you agree that that is the principle of what people here tend to call “neo-Darwinism”?

    You then suggest a choice:

    You have a choice, on the alternatives that have been suggested:

    a: incremental functional changes within an island of function, that can only reasonably explain microevo.

    b: duplication and taking off-line that then can vary but faces the full scope of the relevant config space, which is overwhelmingly non-functional.

    I disagree that this is the “choice”. I don’t even think your choices reflect actuality.

    “Microevolution” is indeed “incremental functional changes” but I see no “islands” of function. I do see constraints, but no islands. And if a gene is duplicated and one of the copies becomes non-functional, it does not “face…the full scope of the relevant config space” if by that you mean every possible sequence. It faces a highly constrained “config space” where it is close (to continue the spatial imagery) to an “archipeligo” if you like of functional sequences. For instance, in a coding gene, many point mutations, which are common, will tend to give rise to a closely related protein, and minor changes to regulatory sequences may simply alter the expression pattern.

    So once you have a functional sequence, there are a great many ways for evolution to go – fine-tuning the sequence, so that a more efficient protein is produced; fine tuning of the regulatory sequences so that it is produced in more optimal contexts; duplication so that a vital function remains able to be performed by one copy, enabling the other to undergo possibly disabling mutations that stand between it and some other useful function.

    As for body plans 9if by that we mean multicellular organisms with cellular differentiation) the key seems to be hox genes. What evidence makes you think that the earliest hox genes would have required “10 – 100+ mn bits of novel, co-ordinated, functional information”?

  37. 37

    The point of my comment was that new human technologies appear suddenly for the same reason major new features appear suddenly in the fossil record: because a gradual transition in most cases would make no sense, involving useless incipient features. You had to know that was my point, since that’s the point of this whole post. The fact that VWs don’t reproduce, or that we don’t find the designer’s tools lying around the fossils IS completely “periferal”.

    And since you seem to be questioning the claim that new features generally do appear suddenly, here’s a quote from George Gaylord Simpson in “The History of Life”: “It is a feature of the known fossil record that most taxa appear abruptly…This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large.”

    Finally, “I’m sorry I said I was amazed you could publish such garbage, but I still am” is not really an apology.

  38. Yes Peter,

    I have a magic hammer and a magic ratchet.

    Ya see Pete mutations are the magic hammer and natural selection is a magic ratchet.

    And no I am not being serious but if I was an evolutionists you gall dang better believe I am serious, seriously.

  39. Elizabeth:

    The best analogue of course is a GA, in which the tweaks are random, and the best resulting performers are retained for further random tweaking.

    In a GA all tweaks are trying to find a solution to a problem.

  40. No, the tweaks are not “trying to find a solution to a problem”. The person who wrote the GA is trying to find a solution to a problem, but instead of making informed intelligent tweaks to a solution, she gets the GA to make uninformed, random (“blind”) tweaks.

    Exactly like mutations in genetics. Which is why they are called Genetic Algorithms.

  41. Elizabeth:

    Based on inheritance. A family tree is a tree, yes? A nested hierarchy.

    Except a family tree is not a nested hierarchy. Any memebr of a family tree can belong to several different family trees. Can’t have that in a nested hierarchy.

    Sure, and “gained” means replicated down the lineage, and “lost” means ceases to be replicated down that lineage. So you get a nested hierarchy.

    Do you even know what a nested hierarchy is?

    Linnean taxonomy is a nested hierarchy as the top set consists of and contains all lower sets.

    If you lose a characteristic then you lose containment.

    Dr Denton goes over all this in “Evolution: A Theory in Crisis”

  42. The whole purpose of a GA is to fing a solution. And the tweaks are defined/ constrained by the resources provided.

    And whoever is calling mutations a genetic algorithm doesn’t know squat about algorithms.

  43. 1. We know that natural selection happens.

    We also know it happens not to do anything.

    2. We know of no barrier that prevents microevolutionary changes due to NS and drift from accumulating over time, thereby becoming macroevolutionary change. (I’ll address the “islands of function” argument below).

    There rare at least two- one is that two new protein-to-protein sites is te limit of stochastic processes and the other is no one knows what makes an organism what it is- and genetics does not say that an organism is the sum of its genome.

    3. Evolutionary theory predicts that life should form a nested hierarchy. When biologists construct trees based on independent characters, they match to a stunning degree. In fact, the standard tree of life is known to an accuracy of 38 decimal places! See Theobald’s excellent analysis for details.

    What is this alleged nested hierarchy based on? If you are using charactrers then it ain’t based on descent, which means evolution wouldn’t predict one.

    Also with evolution we would expect a Venn diagram with overlapping of characteristics during the transition phase.

    IOW you evos are totally clueless.

    As for theobald I can and have taken his “evidence” for common descent and used it to support a common design.

    Just admit it that you do not know what a nested hierachy is nor what it entails.

  44. Why evolution does not expect a nested hierarchy based on characteristics-

    Evolution is said to be a gradual process without any direction except the direction of the surviving reproducers.

    A gradual process would lead to a nice smooth blending of characteristics as would be observed if all the alleged transitional populations were still alive- or with today’s tech we should be able to animate what they should have been-

    The point is that a smooth blending leads to an overlap, which is indicative of a Venn diagram and not allowed by a nested hierarchy.

  45. It seems your post is going to be fairly popular for responses. So it’s probably best if you address a contradiction in your arguments earlier rather than later.

    If we accept your argument #7 then it means that evolution can and will ‘devolve’ to get where ever it needs to be for the purpose of a benefit. But if we accept that then we are required to accept that cytochrome-c and other genetic clocks are entirely unreliable and can tell us nothing. In which case the argument to the strength of the phylogeny matches fails as it is either a mere fluke, or there’s something a bit less than scientific going on.

    If you give up #7 you admit the validity of the “islands of function” argument. If you don’t give up #7 you admit the invalidity of molecular clocks. As you’ve cast your arguments the two cannot stand together and you may want to clear that up before it becomes a thorn for you.

  46. The problem with using jet engines etc, they are designed and built. Which is ID and creation.
    If I thought a Harley would just show up in my driveway, I wouldn’t go out and buy one. After all, its been billions of years.
    The other problem with this is the hypothesis of ‘evolution’ is that it needs life to already be there. Even though many scientists do not how that could happen naturally. So the hypothesis is the evidence. You have a hypothesis ‘evolution’ that needs the start to life be from non creation.That is so , because that is the ‘evolution’some scientists are promoting. No ID involved at all. That really is circular thinking and not scientific.
    The ‘evolutionary’ scientists have designed a method of research that, does not have away of detecting ID. So for even a loaf of bread, they would not be able to say, it was designed. But would try to figure out how it could happen naturally. And of course would end up saying they may never be able to prove it. ( just like they say about the origins of life)
    that is why
    1 life comes from life
    2 a human comes from humans
    3 there is design in life
    Is there any scientific evidence, that does not support these 3 facts? Are there any almost humans, or ex-humans? These are facts just like Gravity is a fact. Even though the scientists do not know everything about it.

    So what is the point of debating, jet engines etc.?

    http://patternsofcreation.weebly.com/

  47. Petrushka:

    Analogies are actually pretty useless, because there is nothing really analogous to chemistry.

    Really? What do you call the following terms: genetic code, translation, transcription, messenger, error-correction, stop-frame. “Chemistry” has actually about as much to do with what is stored in DNA as silicon and electrons have to do with computer code. DNA is designed specifically to ensure that chemistry has as little to do with ordering as is physically possible. A crystal is all about chemistry. That’s why there is virtually no information stored there, beyond the unit cell.

    DNA is coded information. It IS a language. It is harder to find attributes which it does NOT share with human languages than it is to find those it does share. Maybe you can come up with some.

    As such, if you now claim that its “search space” is qualitatively and quantitatively different (e.g. extremely sparse yet still connected) than human languages, the onus is on you to show how that is possible. In fact to show it is true of any language encoding lengthy instructions.

  48. The point is that a smooth blending leads to an overlap, which is indicative of a Venn diagram and not allowed by a nested hierarchy.

    “Smooth overlap” down a lineage does indeed lead to blending, but only longitudinally. What you will not see, if common descent is true, is overlap between lineages.

    In other words, you will see: creatures with synapsid skulls; creatures with synasid skulls and mammalian jaws; creatures with synapsid heads, mammalian jaws and mammary glands; creatures with synapsid skulls, mammalian jaws, mammary glands and placentas.

    You will not see:

    Creatures with dynapsid skulls and mammary glands.

    There are no non-nested sets of characteristics.

    On the other hand, among vehicles you will see:

    Vehicles with wheels and no engines.
    Vehicles with engines and skis.
    Vehicles with skis and no engines.
    Vehicles with wings and wheels and engins.
    Vehicles with wings and skis and engines.
    Vehicles with wings and floats and engines
    Vehicles with wings and floats and no engines.
    Vehicles with wings and skis and no engines.
    Vehicles with floats and engines but no wings.

    See? Nothing is nested, everything overlaps.

  49. The analogy fails because you can’t predict the utility of a sequence independently from selection.

    There’s been a whole lot of arguments regarding protein folding, but no one has addressed any of my arguments.

    First, design advocates haven’t demonstrated that there is a better or faster way than chemistry to determine folds. Without that, design is about as practical as putting an airplane on a truck and moving it from one airport to the destination airport. It can be done, but why?

    Second, most of the evolution that Darwin wrote about and that people argue about takes place in regulatory networks, not in inventing new proteins. I haven’t seen anyone even attempt to address the design of regulation any theory that is independent of selection.

  50. As such, if you now claim that its “search space” is qualitatively and quantitatively different (e.g. extremely sparse yet still connected) than human languages, the onus is on you to show how that is possible.

    I think the onus has always been on science to demonstrate that evolution is possible, and I believe that’s what science is doing.

    From the early days the focus was on missing links in the fossil record. There’s a lot of blather about whales and bats and punctuation, but the simple fact is that most lineages have fossil sequences with smaller gaps than between dog breeds.

    We are now int genomics, where there are no fossils, but there is the opportunity to look at the actual carriers of variation, and the opportunity to map out the history of sequences.

    So the onus is accepted. It’s the present and future of evolutionary biology.

  51. “Smooth overlap” down a lineage does indeed lead to blending, but only longitudinally. What you will not see, if common descent is true, is overlap between lineages.

    Yet only Creation predicted reproductive isolation. There isn’t anything in the theory of evolution that prevents once diverged lines from converging.

    As for your list- yes I could make a nested hierarchy out of vehicles- it all depends on what characteristics I choose and how I choose to lay it out.

    For example we would classify it as “Transportation”

    There would be a set for vehicles with no engines. One for vehicles with engines and then ypu just keep adding as you go.

  52. In other words, you will see: creatures with synapsid skulls; creatures with synasid skulls and mammalian jaws; creatures with synapsid heads, mammalian jaws and mammary glands; creatures with synapsid skulls, mammalian jaws, mammary glands and placentas.

    You will not see:

    Creatures with dynapsid skulls and mammary glands.

    Please point to the passage in the theory of evolution that states evolution does not predict a population of organisms with dynapsid skulls and mammary glands.

    What is the genetic basis for such a claim?

  53. Yet only Creation predicted reproductive isolation. There isn’t anything in the theory of evolution that prevents once diverged lines from converging.

    Yes, there is. Speciation actually means diverging lineages that no longer interbreed. And once hybridisation has practically ceased, then those lines can’t converge again. By definition.

    As for your list- yes I could make a nested hierarchy out of vehicles- it all depends on what characteristics I choose and how I choose to lay it out.

    For example we would classify it as “Transportation”

    There would be a set for vehicles with no engines. One for vehicles with engines and then ypu just keep adding as you go.

    Well, do it then. Arrange my list into a nested hierarchy. Go on.

  54. Oh, and you aren’t allowed just to arbitrarily leave characteristics out.

    A violation you don’t mention is still a violation.

  55. Please point to the passage in the theory of evolution

    There is no “passage”, Joe. Evolutionist don’t have a holy book. It’s a theory.

    that states evolution does not predict a population of organisms with dynapsid skulls and mammary glands.

    There is no evolutionary reason why the dynapsid line shouldn’t have taken a turn down the mammary route. But clearly it didn’t, as can be deduced from the fact that we can make a synapsid clade that does not overlap with the dynapsid clade, the former including creatures with uniquely mammalian features that are completely absent from the dynapsid clade.

    In other words, a nested hierarchy. Evolutionary theory predicts nested hierarchies. Obviously it cannot predict, a priori, what those hierarchies will consist of.

    Just as we can predict cold winter weather reliably every year; we cannot predict, until a few days in advance, what the temperature and rainfall and wind speed and direction will be on any given day.

    What is the genetic basis for such a claim?

    It isn’t a claim. But the genetic basis is that genes are, by definition, the units that carry heritable traits.

  56. Petrushka wrote:

    We are now int genomics, where there are no fossils, but there is the opportunity to look at the actual carriers of variation, and the opportunity to map out the history of sequences.

    So the onus is accepted. It’s the present and future of evolutionary biology.
    —————————————————–

    The reason , some scientists have to turn their attention to biology is that the fossil record shows no transitional fossils. Even Darwin knew that would be a problem and hoped that in the future this would be found. But they have not been found.
    You are correct, people have accepted creation for thousands of years, now the scientists come along , and say that is not correct. So it really is upon them to prove it.

    “map out the history of sequences.”
    This is interesting, because, this is what the Patterns of Creation* is about. The creative lines of descent. The idea that from one life, material is taken and used to build another slightly different animal. This would show histories of populations, over time, also the creative breeding of animals for certain traits.
    It may be that these histories that the scientists are looking into, are actually showing what animal was created one from another.
    *
    http://patternsofcreation.weebly.com/

  57. Yup and being human is not a heritable trait- yes being human is heritable but being human is not a trait based on any gene nor genes.

  58. Speciation actually means diverging lineages that no longer interbreed.

    Yet there are many reasons why organisms do not interbreed.

    And once hybridisation has practically ceased, then those lines can’t converge again.

    What is the evolutionary and genetic basis for such a claim?

    Well, do it then. Arrange my list into a nested hierarchy. Go on.

    Denton did it in “Evolution: A Theory in Crisis”.

  59. Elizabeth,

    When are you going to reference some authority as to what is and isn’t a nested hierarchy?

    Above you said a family tree is a nested hierrachy when clearly it isn’t. A hierarchy yes. A nested hierarchy, no.

  60. Evolutionary theory predicts nested hierarchies.

    Yet we do not observe one amongst prokaryotes.

    Does that mean the theory is refuted?

    Or are you just going to flail away?

  61. KF,

    The problem with fitness landscape type arguments is that — as the OP highlights — they implicitly imply that we are within an island of function.

    We are within an area of function, but you are assuming that it is an island.

    Am I merely assuming the opposite? The answer is no, because the evidence supports the idea that functional areas are connected, not isolated. See comment 11 for an explanation.

    When we look at he overall configuration space for all the involved components, it is overwhelmingly obvious that the non-functional states absolutely dominate,

    What matters is not whether non-functional states dominate; rather, the important question is whether the functional states are well-connected.

    …so the issue is not to move around within an island of function, but to get to the beach of such an island.

    Again, you’re assuming that the functional space is dominated by small, isolated islands of function.

    Please, it is a routine matter in multidimensional situations to use 2 or 3 d toy models for illustration.

    Of course, and there’s nothing wrong with that, as long as you remember that the toy model differs from reality in important ways. In this case, a crucial difference is that it’s much harder to get stuck on a fitness peak in the real, many-dimensional case. The toy model fools people (including you, apparently) into thinking that getting stuck on a peak is likely or even inevitable.

  62. I think the onus has always been on science to demonstrate that evolution is possible, and I believe that’s what science is doing.

    Well said, expressing it as a belief and avoiding the past tense.

    So the onus is accepted. It’s the present and future of evolutionary biology.

    Again, well said. It’s in the textbooks now, but the confirmation is always coming soon. Here’s the check, but please don’t cash it until the end of the week.

    Having accepted that onus, you must refer to these ‘possibilities of evolution’ as hypotheses which have not been confirmed.

    How many times must it be said that evolution is a process of selection, and selection cannot be derived from a sequence of fossils? It takes but a moment to reason and realize that neither fossils nor phylogenetic trees demonstrate evolution, ever.

    Do you dispute that? Does anyone? Does anyone wish to disagree and assert that a process of variation and selection can be derived from fossils or genetic trees? Will someone please come out and say it, to offer some justification for the constant, tired mention of them?

  63. In this case, a crucial difference is that it’s much harder to get stuck on a fitness peak in the real, many-dimensional case.

    Exactly. This point can’t be too strongly emphasized. Sometimes oversimplified models can lead to conclusions that are simply wrong.

    Fitness space is extremely high-dimensioned.

  64. C:

    Pardon, but I must correct.

    No, I am not merely “assuming,” as you would have seen if you had done the courtesy of first reading the OP before commenting.

    Functional specificity of multiple, well matched parts sharply constrains the number of possible arrangements that are consistent with that function. Unless one is in a cluster of such workable arrangements — the wiring diagram if you will, the composite entity will not work.

    So, the descriptive image of an island of function in a sea of non-function is not an empty assertion. Let us just start with the number of arrangements consistent with a coherent and contextually responsive message in English in this thread. By far and away most possible arrangements of letters will NOT meet these criteria, as well we all know.

    In fact, it is those who assert that in effect, life forms are different, never mind how we see in them coded digital strings, chained proteins that depend on sequence for their ability to properly fold and work, and organised structures that carry out duties like being motors, or walking trucks, or being a highway network for said trucks etc etc, who need to show such empirically for first life.

    then, when they move up to the dozens of major body plans for life forms, they need to show — per empirical observations — that there is in effect a demonstrated continent of function that leads to an incremental, progressive descent with modification that creates an OBSERVED not inferred branching tree of life.

    In actual fact, the rot of the tree is conspicuously missing, as are the main trunks, and of course the incremental, step by step descent with advantageous modifications — which if the claimed macroevo were so should DOMINATE the fossil record.

    As cited in the OP, Gould is on public record that the actual pattern is that of distinct islands of functional forms, with of course adaptations at that level.

    And no I am not particularly interested in populations at peaks within islands of function. The issue is as I have repeatedly said, getting to the beaches of those islands.

    And, trying to shift the burden of proof to empirically warrant the core macroevolutionary claims, just will not cut it. I am not interested in finch beaks, or circumpolar gulls or in how red deer seem to have a wide variety of populations, or the colour variations and body shapes of cichlids in various places.

    Show us body plan level origin, not adaptations; that is just variation within islands of function. Which BTW, we routinely observe. Or if you want, we see bushes and twigs in a forest of life forms. You need to warrant the claim that these are tips of a wider structure arrived at by chance variation and natural selection incrementally giving rise to the whole. SHOW, with observational warrant.

    And, kindly do the courtesy of reading and responding in light of the OP. Note especially the issue of C1 – 5.

    G’day

    GEM of TKI

  65. Yet we do not observe one amongst prokaryotes.

    Yes we do.

    So no, the theory is not refuted.

  66. Elizabeth Liddle
    Exactly. This point can’t be too strongly emphasized. Sometimes oversimplified models can lead to conclusions that are simply wrong.
    ————————————————-
    Some times , you can’t see the forest for the trees.
    And the obvious answer is correct.
    http://patternsofcreation.weebly.com/

  67. Are you disputing that fitness space is high-dimensioned? Because that was the point I said needed emphasis.

    Your link does not touch that matter.

  68. Red Herring led away to a Strawman, I am afraid. The question is not hill-climbing within islands of function, but arriving at the shores thereof, in a context where most arrangements of parts will be non-functional.

  69. No, it is not a Red Herring, kf, nor yet a Strawman. It’s absolutely crucial. Because fitness space is extremely high-dimensions islands of function will be extremely rare

    So “arriving at the shores thereof” is not a problem because those shores are only shores in a subset of dimensions. Along other dimensions they are not shores but causeways.

    To put it at its simplest. Take a one-dimensional landscape where the only route between A and B is along a line. If that line has a gap in it, you cannot get from A to B.

    Now project that line into a second dimension. Now, while there may be no straight line route between A and B there may will be a curved route, via the second dimension. But let’s say there isn’t – A is a disc that doesn’t overlap with B. Now we are stuck again. Unless we go into a third dimension, whereupon A and B might be connected by a curved cylinder.

    But let’s say it isn’t. A and B are in fact mountains 3D islands, unconnected. But add a fourth dimension, harder to envisage, but we can do with effort.

    And so on. Just because two places are unconnected in low-dimensional space does not mean they are unconnected in high dimensional space. And the higher the dimensional space, the less likely it becomes that there will not be ANY other accessible neighbouring space.

    If you want to use spatial analogies to make a point about “islands of function” it is really important to project that metaphor into high dimensioned space.

    Otherwise, just abandon the metaphor and think just how many ways an organism might be modified in order to take advantage of some environmental resource.


  70. Yet we do not observe one amongst prokaryotes.

    Yes we do.

    No, we don’t

    So if you ignore the evidence and reality than you would be right.

  71. Hey Elizabeth,

    Where would you put ants with wings? How about ants that have wings but then lose them?

    Do you arbitrarily just refuse to acknowledge some ants have wings?

  72. Hello Elizabeth

    I don’t believe there is any disagreement there. Fitness space is highly dimensioned, at multiple levels – from the possibilities of point mutations at any location in a protein to modes of interactions between proteins in a functioning biological machine, to the ordering and quantitities (e.g. regulation) in how that machine is constructed from its components; plus who know how many more once you add gene-transfer, duplication, repetition etc. to the mix.

    Where we disagree, I think it fair to say, is to the degree of “plasticity” in such machines or organisms conferred by the dimensionality of the problem, and whether that dimensionality is sufficient to overcome sparseness of solutions in the overall solution space to deliver “connectedness”, and hence allow real evolution to new forms and functions.

    My reply would be that, despite the high dimensionality, the vast majority of those dimensions provide little or no flexibiliy, and amount to fatal or degradative mutations, while the rest can, at most, allow limited variation in the performance of what is already a highly optimized system, in order to adapt to moderate changes in the environment. It’s difficult to see how what we have observed of living systems today demonstrates more than that.

  73. Hello Elizabeth

    I don’t believe there is any disagreement there. Fitness space is highly dimensioned, at multiple levels – from the possibilities of point mutations at any location in a protein to modes of interactions between proteins in a functioning biological machine, to the ordering and quantitities (e.g. regulation) in how that machine is constructed from its components; plus who know how many more once you add gene-transfer, duplication, repetition etc. to the mix.

    Cool :)

    Where we disagree, I think it fair to say, is to the degree of “plasticity” in such machines or organisms conferred by the dimensionality of the problem, and whether that dimensionality is sufficient to overcome sparseness of solutions in the overall solution space to deliver “connectedness”, and hence allow real evolution to new forms and functions.

    Well, I agree that a “sparse solution space” will result in a “brittle” rather than “plastic” system, but why do you think that the solution space is sparse in the vicinity of any existing solution? Sometimes it is, of course, so you get some highly conserved sequences, although even there, there is variance. But often it isn’t. Many genes have very large numbers of alleles.

    My reply would be that, despite the high dimensionality, the vast majority of those dimensions provide little or no flexibiliy, and amount to fatal or degradative mutations,

    Well, the evidence doesn’t suggest that. Yes, there are mutations that are incompatible with life or at least development, and we see a tail of those, but if they were in the majority, successful pregnancy would be much rarer than it is. Most of us carry hundreds of brand new mutations, and remain perfectly viable, suggesting that most mutations are near-neutral, although, clearly, in a well-adapted population, more will be slightly below than optimal than slightly above average in terms of effect on reproductive success.

    And there are good theoretical reasons, supported by some data, to think that variance-producing mechanisms themselves are subject to natural selection at the population level, including mutation rates. Populations with too-high replication fidelity will tend not to adapt and be more likely to go to extinction if the environment changes too fast, whereas populations with too-low replication fidelity will tend to suffer “mutational meltdown” when populations levels are low. So surviving lineages themselves will have tend to have optimised mutation rates and mutation types. The best example of which, of course is sexual recombination, which shuffles grand-parental genes and part-genes to generate, sometimes, brand new alleles.

    while the rest can, at most, allow limited variation in the performance of what is already a highly optimized system, in order to adapt to moderate changes in the environment. It’s difficult to see how what we have observed of living systems today demonstrates more than that.

    Well, you are absolutely right of course that in an already optimised population (adapted to its environment), natural selection serves to maintain the population at that optimum. However, a constant drip-feed of near-neutral variants means that if there are changes to the environment, allele prevalence can track those changes even generation by generation, as the Grants observed in the Galapagos, and if there is steady, rather than oscillating, environmental change, that too can be tracked, and can be observed doing so (although obviously over human life-times we see very little of that in real time; we can however observe it in the fossil record, and do).

    A happy new year to you!

    Lizzie

  74. Yes we do, if you use phenotypic characters.

    But if you use genotypic characters you may well get bushiness because there are a few ways in which genetic material can transfer “horizontally”, as I’m sure you know. It’s called “horizontal gene transfer”.

    But horizontal gene transfer is very unlikely to result in transfer of a phenotypic character from one lineage to another (although it may do in very simple organisms, I’m not sure, it’s certainly very unlikely to do so in multicellular organisms).

    But even if even if it did, we have a mechanism to explain it.

    However, I will qualify my claim: Evolutionary theory explains nested hierarchies, given that most genetic transfer is longitudinal not horizontal, and predicts nested hierarchies of where that transfer is longitudinal.

    Obviously it doesn’t predict genetic nested hierarchies if there is a horizontal genetic transfer mechanism, and it’s possible that you might occasionally get a horizontal transfer of a genetic material that had the same phenotypic effect in the new host as in the source. I don’t know if this is true.

    Either way, it doesn’t matter, because science is all about finding explanations for phenomena, and horizontal gene transfer is now well-understood.

    It remains the case that phenotypic characters are distributed as a tree – as nested hierarchies – in living things, whereas the characteristics of human artefacts are not.

  75. If you are interested in phylogenetics, why don’t you get a text book on the subject?

    As far as I know, winglessness in ants, like leglessness in snakes appears later in winged lineages.

    In some species of ants, only the queen has wings, so winglessness is probably due to a mutation in a regulatory gene.

    In other words, the genotype must contain wing-making genes that are only expressed in the queen.

  76. What is the use of abstract concepts such as ‘multidimensional fitness space’ when the concrete realities they model are so limited?

    When someone hears such a term, they are likely misled to thinking that it corresponds to such ideas the evolution of the mammalian ear or whales or feathers. Anything modeled using a multidimensional fitness space must be pretty serious. Sometimes I see these terms abbreviated, because if someone talks about a MFS or an GTR than it must be such awfully common knowledge that everyone knows what they mean.

    You can make up a $10 expression but you still have $.50 worth of finch beaks and colored cichlid fish.

    I don’t mean to sound like I’m mocking. But it’s pretty funny when you think about it. I don’t say “LOL” because I’m not, and I suspect that most people who say that are really turning purple and their hands are shaking. But it does make me smile.

  77. >blockquote>But horizontal gene transfer is very unlikely to result in transfer of a phenotypic character from one lineage to another (although it may do in very simple organisms, I’m not sure, it’s certainly very unlikely to do so in multicellular organisms).

    But even if even if it did, we have a mechanism to explain it.

    Once you have mechanisms to explain things that no one thinks ever did or could happen, the sky’s the limit.

  78. What is the use of abstract concepts such as ‘multidimensional fitness space’ when the concrete realities they model are so limited?

    I don’t find them terribly useful myself, but kf likes to use them. So if he talks about “islands in config space” then it needs to be pointed out that “config space” is multidimensional and so islands are rare – most locations will be connected along some dimension.

    But to take your second point: “the concrete realities they model” are very far from “limited”. As I said, just think of the numbers of ways an organism could change to survive better in a new environment. There are hosts of dimensions along which it could change,from size, to patterning, to motility, to sensory sensitivity and resolution, to attack or escape behaviour, to heat insulation, to shock absorption, to predictive accuracy – the list is endless.

    When someone hears such a term, they are likely misled to thinking that it corresponds to such ideas the evolution of the mammalian ear or whales or feathers.

    Yes, it does. That’s exactly the kind of thing it refers to. Any change in any function that tends to promote reproductive success, whether it’s hearing better or being better insulated, or having lower terminal velocity, or being more scary to predators. And then there’s drift as well (changes with no net change in fitness, but which still moves the population through fitness space).

    Anything modeled using a multidimensional fitness space must be pretty serious. Sometimes I see these terms abbreviated, because if someone talks about a MFS or an GTR than it must be such awfully common knowledge that everyone knows what they mean.

    Well, we certainly don’t have to use those terms. But, as I said, kf uses them, and I was responding to him.

    You can make up a $10 expression but you still have $.50 worth of finch beaks and colored cichlid fish.

    I don’t mean to sound like I’m mocking. But it’s pretty funny when you think about it. I don’t say “LOL” because I’m not, and I suspect that most people who say that are really turning purple and their hands are shaking. But it does make me smile.

    Well, I’m all for smiling (as you know :))and I tend to agree that using high-level metaphors and fancy functions can hinder rather than help communication, and even lead to errors. That’s why my point was that if kf is going to talk about “islands of function in config space” he does need to consider the vast numbers of dimensions of config space. If a metaphor is too simple for the job, it can mislead. My position is that kf’s metaphor has misled him into thinking there is a problem where there isn’t one.

  79. Once you have mechanisms to explain things that no one thinks ever did or could happen, the sky’s the limit.

    This is simply wrong. We have explanations for data. That’s what science is about. The sky is not the limit – the data are the limit.

    Data are what constrain science.

    In contrast, if you invoke miracles or Intelligent Designers for which we have no evidence at all to explain our data, the sky, is, literally, the limit. Or the heavens anyway.

    Motes. Beams.

  80. This is simply wrong. We have explanations for data. That’s what science is about.

    Science is not about explaining phenomena that, even according to you, have never been known to occur and most likely never will. What is the data in that scenario?

  81. We have explanations for data.

    BTW, no one has responded to my simple, generous, reasonable challenge to use evolutionary theory to explain something. That amounts to a concession that it explains nothing. All the talk in the world about ‘how science works’ won’t change that.

    (Fine, it’s not a concession from all of mainstream biology – only from those who participate in this discussion.)

  82. Science is not about explaining phenomena that, even according to you, have never been known to occur and most likely never will. What is the data in that scenario?

    The bushy genetic trees of unicellular organisms, and occasionally in multicellular organisms. They demand explanation. One theory is horizontal gene transfer e.g. by viruses. That theory seems to match the data pretty well.

    BTW, no one has responded to my simple, generous, reasonable challenge to use evolutionary theory to explain something. That amounts to a concession that it explains nothing. All the talk in the world about ‘how science works’ won’t change that.

    (Fine, it’s not a concession from all of mainstream biology – only from those who participate in this discussion.)

    What was wrong with the Grants’ finch beaks? There are many others. How about Endler’s guppies? Or many many fruitfly study data? Or adaptive sequences in the fossil record? Or vestigial legs on whales? Or antibiotic resistance? Or ring species? Or island speciation?

    tbh, I can scarcely think of a problem in biology, including my own field, where considering the evolutionary dimension isn’t helpful at least occasionally.

  83. However, I will qualify my claim: Evolutionary theory explains nested hierarchies, given that most genetic transfer is longitudinal not horizontal, and predicts nested hierarchies of where that transfer is longitudinal.

    Umm but the observed nested hierarchies are based on phenotypic traits.

    As you said earlier wrt prokaryotes- which I would still love to see you make the case for a nested hierarchy based on phenotypic traits for prokaryotes.

    And I am still waiting for your reference as to what is a nested hierarchy.

    Is there any reason for the hold-up?

    You seem to be confusing a tree with a nested hierarchy.

    Also you do realize that since the theory of evolution doesn’t say anything about the origins of living organisms it would be perfectly happy with many trees.

  84. Nice non-sequitur.

    My point is seeing that the same species can contain both winged and wingless individuals the wings are arbitrarily thrown out as a defining characteristic.

  85. Elizabeth:

    Vehicles with wheels and no engines.
    Vehicles with engines and skis.
    Vehicles with skis and no engines.
    Vehicles with wings and wheels and engins.
    Vehicles with wings and skis and engines.
    Vehicles with wings and floats and engines
    Vehicles with wings and floats and no engines.
    Vehicles with wings and skis and no engines.
    Vehicles with floats and engines but no wings.

    Can you please define the word “vehicle” and give examples of each.

    Thank you. Then I can get to work on your strawman.

  86. The point of my comment was that new human technologies appear suddenly for the same reason major new features appear suddenly in the fossil record: because a gradual transition in most cases would make no sense, involving useless incipient features. You had to know that was my point, since that’s the point of this whole post. The fact that VWs don’t reproduce, or that we don’t find the designer’s tools lying around the fossils IS completely “periferal”.

    But we DO see gradual transitions and they DO make sense, because “incipient features” aren’t useless. For all you know your nose may be an “incipient” trunk! Contrary to frequent assertion, half an eye is a lot of use. And the fact that VWs don’t reproduce is absolutely key, because clearly a non-reproducing machine can only have been designed. A reproducing machine could have evolved.

    And since you seem to be questioning the claim that new features generally do appear suddenly, here’s a quote from George Gaylord Simpson in “The History of Life”: “It is a feature of the known fossil record that most taxa appear abruptly…This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large.”

    There are many transitional sequences in the fossil records. Of course there are gaps in the record, but that doesn’t mean there were gaps in the reality. Gaylord Simpson himself didn’t think so.

    Finally, “I’m sorry I said I was amazed you could publish such garbage, but I still am” is not really an apology.

    Well, it wouldn’t be, but then it’s not what I wrote. I said what you wrote was “self-defeating”, not that it was “garbage”. If it is an insult to say what I think is wrong with your argument, then there’s no point in having a discussion. And your argument is self-defeating because the very examples you cited as “transitional” are exactly the kind of examples that would violate the predictionsn of evolution, not support it. Chimeras (hovercraft; motorcycles) would be a problem for evolution, not a support of it.

    Hence “self-defeating”. I did not meant to offend you, and I’m sorry if I did. I did mean to tell you what I thought was wrong with what you wrote, which is that it is “self-defeating”. The very property of the collection you cite as something a paleontologist would regard as “transitional” is precisely the property that would make a a palaeontologist think: intelligent design.

  87. KF,

    Your skepticism about the power of natural selection to create macroevolutionary change is unwarranted. One might even call it hyperskepticism in the teeth of the evidence. :-)

    Evolutionary theory predicts that if natural selection and drift are the main drivers of evolutionary change, then life should form a single nested hierarchy. Construct a series of nested hierarchies based on independent characters — morphological, molecular, and genetic — and you should find that they match. They do, and to a high degree of precision — dozens of decimal digits’ worth. This is a stunning confirmation of the idea that microevolutionary changes accumulate to create macroevolutionary change.

    Intelligent design, including the idea of “common design”, makes no such prediction. An intelligent designer has literally trillions of options to choose from, and no particular reason to choose the few that lead to the appearance of a single nested hierarchy. The fact that we do see a single nested hierarchy makes evolutionary theory an overwhelmingly better explanation of the pattern of life’s diversity, compared to intelligent design.

    Life appears exactly as we would expect if microevolutionary changes accumulate to form macroevolutionary change. Life appears nothing like we would expect if intelligent design, including common design, were operative. And the one objection you offer to natural selection’s power — the “islands of function” argument — falls apart for the reasons that Elizabeth and I have been stressing.

    If evolutionary theory is by far the best scientific explanation of the evidence, whence the resistance among ID supporters?

  88. As I commented to Scott Andrews in another thread:

    Scott,

    Your argument brought an analogy to mind. Here’s an imaginary dialogue between you and an astronomer:

    Scott: I agree that the theory of gravity holds within our solar system, but extrapolating it to interstellar and galactic scales is unwarranted.

    Astronomer: What barrier are you aware of that prevents gravity from acting over interstellar distances?

    Scott: Your error is in assuming that it does.

    Astronomer: But we see evidence that it does.

    Scott: Have you ever directly measured the force between two stars?

    Astronomer: We can’t. But stars behave exactly as we would expect if gravity were operating on them. To support your view, we’d have to posit that 1) gravity mysteriously stops working on some scale larger than the solar system, and 2) there is a different, unknown mechanism that makes it appear that gravity is still working on the larger scales! Are you serious?

    Scott: Game over.

  89. champignon: Intelligent design, including the idea of “common design”, makes no such prediction. An intelligent designer has literally trillions of options to choose from, and no particular reason to choose the few that lead to the appearance of a single nested hierarchy.

    On the contrary, a very intelligent designer might want to front load the system to evolve along certain lines. In such a system one might expect to find irreducably complex features within a nested hierarchy. Which is exactly what we find.

  90. OK, so how would you test a front-loading hypothesis? It’s testable, and I would have thought, makes good differential predictions from the predictions of evolutionary theory.

    But “irreducibly complex features wtihin a nested hierarchy” isn’t a testable prediction because there is no test for irreducible complexity. So no, we don’t “find” it :) In a nested hierarchy or anywhere. It’s not findable.

    Can you explain where you think you did?

  91. Anything built by people to transport themselves or goods.

    And, in order:

    Cart
    Skidoo
    Skis
    Aeroplane
    Skiplane
    Floatplane
    Float glider
    Ski glider
    Boat

  92. Eh? What’s that? The sound of someone using the cornerstone of biology to explain something biological? I can’t hear you.

  93. Mike,

    Front-loading, like common design, does not predict a single nested hierarchy.

    For example, a front-loading designer could arrange for an identical feature to appear at the same moment in three widely separated lineages. A nested hierarchy based on that feature would clash with hierarchies based on other features.

  94. Ah, the “I can’t hear you” defense: “La la la I can’t hear the evidence you just gave for a prediction that has been confirmed to 38 decimal places!”

  95. Anything built by people to transport themselves or goods.

    Great, that is so broad as to allow for a nice superset.

    I will get back to you.

  96. Nested hierarchy of vehicles:

    Vehicles without an engine-> land (snow (skis), ice(skates), ground ->wheeled(cart), water(row boat)(sail boat)(kayak)(canoe), air (landing gear – snow(ski glider), ice(ice sailboat), water(float glider), ground( wheels)(glider))

    Vehicles with engines-> land (snow(skidoo), ice, ground (car), water(boat), air-> landing gear- snow (skiplane), water (floatplane), ground ->wheels (aeroplane)

  97. You can make a nested hierarchy out of just about anything.

  98. summary of the principles of hierarchy theory:

    Nested and non-nested hierarchies: nested hierarchies involve levels which consist of, and contain, lower levels. Non-nested hierarchies are more general in that the requirement of containment of lower levels is relaxed. For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army. Pecking orders and a food chains are also non-nested hierarchies.

  99. Michael Flatley couldn’t dance his way out of this. Evolutionary theory explains things. So explain something using evolutionary theory.

    Or, alternately, tell me what is so difficult or unfair about that question that you’ll say anything but not answer it.

    Do you realize how bad it is if you can’t explain the evolution of anything using evolutionary theory? What else can you say that matters?

    I’m bored with everything else. I’m not interesting in anything but how the cornerstone of biology explains something in biology. (I’m so thankful to Dobzhansky for calling it that and everyone since who has quoted it. It makes the irony that much better. But you can backpedal if you want. That’s fun too :))

  100. Possibly if not probably because even if one accepts that it’s the best explanation of *some* evidence it doesn’t explain all or even much of anything else.

  101. Scott,

    I’ve shown you how evolutionary theory predicts a characteristic of the entire tree of life: a single nested hierarchy, confirmed to 38 decimal places.

    To claim that that’s not an example of “how the cornerstone of biology explains something in biology” is ludicrous.

    Also, you must not be very curious if you’ve failed to come across other biological phenomena explained by natural selection, such as the fact that the sex ratio is 1:1 in most sexual species.

  102. Yes, but we’re talking about constructing multiple nested hierarchies based on independent features — morphological, molecular, and genetic — and finding that the hierarchies match to an amazing degree of precision. That’s remarkable, and it cries out for explanation.

    Evolutionary theory explains it. Intelligent design doesn’t.

  103. 103

    I’ve shown you how evolutionary theory predicts a characteristic of the entire tree of life: a single nested hierarchy, confirmed to 38 decimal places.

    Evolutionary theory is genetic variation and natural selection (feel free to throw in whatever else you wish.)

    Please tell me how you get one single variation from a nested hierarchy, or a single selective cause.

    I’m not asking for a skyscraper. I’m asking for a few bricks stacked together. I ask you to explain something using a theory made of variation and selection, and your reply contains not a single variation and not a single instance of one being selected. The only thing missing from your example of the explanatory power of evolution is – you guessed it – the evolution.

    I repeat, please use this cornerstone of biology to explain something biological. I reject as nonsensical your implication that it can explain things without explaining a thing.

  104. Champignon,

    Your compilation of reasons to believe in Darwinism as an explanation for all the variety that is observed in extant and extinct species demonstrates my point: In the entire list, there is no actual evidence that RM/NS has ever produced a single macroevolutionary advance in living organisms. Furthermore, your most compelling points (were they true), numbers 2 and 3, are false.

    Number 2:

    2. We know of no barrier that prevents microevolutionary changes due to NS and drift from accumulating over time, thereby becoming macroevolutionary change.

    I presented a major barrier, quoted at the very beginning of this post by KF. There is also Behe’s idea of irreducible complexity, as well as several authors’ (notably William Dembski) analysis of the amount of new complex specified functional information required and the probabilistic barriers to its arising by chance. All these considerations, coupled with the lack of any evidence that RM/NS has ever produced a single macroevolutionary advance, implies that if you contend that it is possible, you need to supply some evidence. A mere statement that “we know of no barrier” simply doesn’t cut it.

    Number 3.

    3. Evolutionary theory predicts that life should form a nested hierarchy. When biologists construct trees based on independent characters, they match to a stunning degree. In fact, the standard tree of life is known to an accuracy of 38 decimal places! See Theobald’s excellent analysis for details.

    This is also false. See A Primer on the Tree of Life for a detailed refutation.

    The take home is that neo-Darwinism has never been demonstrated to be true. and there is abundant evidence that it is not. The burden of proof is on the supporters of Darwinism, and so far any compelling evidence is conspicuous by its absence.

  105. Champignon, et al:

    I answered your number 11 underneath it (11.4).

  106. Dr. Liddle,
    You wrote: “Contrary to frequent assertion, half an eye is a lot of use.”

    What function is half an eye capable of and how is it of any use?

  107. Participants & Onlookers:

    First and foremost, a happy new year.

    I came back and took a look.

    I particularly notice that the objecting responses conspicuously do not address what is in the OP, much less the onward linked in the series, etc. As for the invitation to actually provide evidence for the assertions and implications of the claimed macroevolutionary origin of major body plans . . .

    For instance, kindly observe from the OP, the way that complex and specific function — which implies a very large number of degrees of freedom thence a large configuration space for components — then normally leads to sharp constraint of the number of possible functional possibilities, and thus to the existence and increasing isolation of islands of function in that space of possible configs. That is particularly so when we deal with coded strings of digital symbols, and when we deal with multiple, matched- part units, i.e machines.

    (In recent days, several such functional units have been put on the table, but in general the context is that we are dealing with organisms that originate from zygotes or the equivalent, and develop complex, functional body plans. In the case of insects etc undergoing complete metamorphosis, we are talking of distinct body plans and a process by which the initial, larval form, is then broken down into a “soup” and re-assembled as a new plan.)

    Instead of addressing such issues squarely on the merits, unfortunately, we keep on seeing the same pattern of distractors via red herrings led out to strawmen, and/or blanket announcements of the wonderful power of chance variation and natural selection to effect macroevolution — with no specific observed cases of body plan evolution with the steps involved provided. Likewise, we see an attempt to turn about the burden of warrant, as though the CV + NS scenario is exempt from the general requirement of scientific theories that they take empirical data seriously, and warrant their claims on such observations.

    We also see blanket declarations that Design Theory does not make predictions etc.

    The fundamental prediction of design theory, of course, is that when we see complex, specified — especially functionally specified — information and associated organisation, and are able to evaluate its causal source by observatio0n or a good stand-in for that, it will turn out to be that the credible cause is dominated by design. There are literally billions of test cases in point, and the prediction is well confirmed and demonstrably empirically reliable.

    Indeed, this and other posts in this very thread provide further confirmatory instances.

    Such is, or should be, well-known, so the attempt to pretend otherwise is a clear case of a red herring — this is an attempt to change the subject — led out to a strawman misrepresentation of design theory and its epistemic status. As just one instance of this problem.

    In addition, we have a longstanding needle in a haystack/infinite monkeys analysis — similar to that used to ground the second law of statistical thermodynamics, and for that matter, similar to the results of sampling theory for relatively small samples of large populations — that explains why. In effect, once we are dealing with a small sample from a very large population, we have no reasonable right to expect that a blind sample will pick up the atypical, by sheer weight of the bulk of the population. In short, some lotteries are unwinnable — and winnable ones are actually designed to be winnable.

    Blend in the further factor that especially complex, specific function based on well matched, multiple parts arranged per a wiring diagram will be strongly constrained relative to the raw number of degrees of freedom for constituent parts, and we see that such FSCO/I (which may often contain an irreducibly complex core of necessary parts) will as a rule be deeply isolated in the space of possibilities.

    Going to the scale of our solar system, just 500 bits worth of yes/no degrees of freedom for constituent parts implies 3.27*10^150 possibilities, where the 10^57 or so atoms of our solar system, since a reasonable date for formation, will have only up to 10^102 Planck time quantum states, or a sample of 1 in 10^48. This is comparable to blindly picking just one straw sized sample from a cubical hay bale 3 1/2 light days across. As has been often directly presented here at UD.

    Even if our whole solar system out to Pluto were lurking within the bale, on sampling theory, we would have only one reasonable expectation of such a sample: straw. (And in fact the fastest chemical reactions take some 10^30 PTQS’s, i.e. we have made a very conservative count here.)

    Expanding to 1,000 bits, we are looking at 1.07*10^301 possibilities for our string of yes/no degrees of freedom. That would so swamp the 10^150 or so possible PTQS’s for the 10^80 atoms of our observed cosmos, that even with millions of universes the size of our observed universe lurking therein, the one-straw sized sample from the hay bale for that one would have the same result.

    And, notice, this is independent of probabilistic calculations and distribution models. We only need to draw on analysis of blind sampling from large populations, and very basic probability, that should be instantly familiar from a first course in inferential statistics that uses the trick of asking whether it is reasonable to expect to see far-tail skirt results on a typical scope of sampling of a population, instead of coming up in the bulk.

    The bottomline is plain:the central issue is to get to islands of function, or else to show on good empirical grounds that we are dealing with continents of function, not islands. Given what is required to knit multiple, well matched components together into a functioning whole on a wiring diagram, the latter is akin to asserting that one has invented a perpetual motion device.

    SHOW us, and show us why and how it works.

    Cases in point of body plan level origin by chance variation and natural selection, or other similar are: _________________________ , and the relevant observed, reported peer reviewed evidence is _______________________ .

    In contrast to this, let us pose how we may test the design inference on a simple expression, on the gamut of our practical universe, the solar system:

    Chi_500 = I*P – 500, functionally specific bits beyond the solar system threshold where blind processes of chance and/or mechanical necessity are plausible explanatory candidates for the origin of such a functional entity

    That is, once we see 500 or more bits worth of degrees of yes/no freedom, the only plausible explanation for the origin of a given object on the gamut of our solar system is design.

    (This has in it room for variations and adaptations within the island of function through incremental variation and hill climbing, etc. In that context, the origin of a self-replication facility additional to the main function in view, is one of the bits of complex, multiple part functionality that needs to be explained. And those who imagine that GA’s do not carry out that sort of exercise in an island of pre-existing function may look at Chaitin’s remark on the subject, here on. GA’s of course have a causal explanation that is well known: design. They are an example in point of the observed origin of FSCO/I. They are programmed to wander about in islands of function, and they are programmed to move “uphill,” generally speaking. As Chaitin points out.)

    To overturn it, just provide a credible observed counter-instance. Let’s just say — as has been reported over and over at UD — that he random text generation exercises to date show that spaces formed to include about 10^50 possibilities are searchable. But we are looking at 10^150 possibilites or more.

    Of course, all of the above has been pointed out on one form or another over and over and over again, just ignored or distracted from, with strawman distortions being all too common. (I think that part of the problem is that those committed to darwinism or its relatives, find great difficulty understanding what design thinkers are saying, as they are filtering through darwinist glasses.)

    Let’s hope that for the new year, we will be able to move on beyond the endless loop as we have again seen above.

    GEM of TKI

  108. Indeed, and kindly provide an observational case.

  109. C:

    And, your observational case in point of body plan origin by incremental macroevolution is?

    KF

    PS: Have you ever done or seen the taxonomy of paper clips or the like, or played animal, vegetable or mineral? The first shows how nested hierarchies can be applied in design cases, and the latter how once we can do a sequence of yes/no keys, we can reduce almost anything to some sort of hierarchy. Besides, actually if we had a gradual incremental branching tree of body plans — as Darwin knew 150 years ago — we would NOT see a nested hierarchy, which is discrete. We would instead see blended populations. Which is precisely what we do not see once we move up to the level of body plans.

  110. In the entire list, there is no actual evidence that RM/NS has ever produced a single macroevolutionary advance in living organisms.

    There is evidence that the mammalian inner ear bones evolved by incremental change. There is evidence that feathers evolved incrementally. There is evidence that the whales spout moved incrementally from the front of the face to the top of the head.

  111. Bruce David said:

    What I observe about Elizabeth Liddle and others is that she implicitly takes the position that she will continue to believe the neo-Darwinian explanation until ID proponents can prove that it is false. I think that the case has been made many times over that she has placed the burden of proof on the wrong set of shoulders.

    Evolutionary theory have at least some thoughts and corroborating evidence about not only when, but also on the how and why of past genetic changes. Actually, not much different from what has been achieved by artificial selection by man for somewhere about ten to twenty thousand years. Maybe beginning as a side effect, then becoming the conscious selection of desirable traits.

    Now please let us see some evidence of ID showing how it really was, to replace the just-so stories of science.

    WRT burden of proof, that may be relevant within the paradigm of ID but AFAIK is a concept not used by scientists.

    IMHO, ID proponents cannot for ever keep insisting that ID explains it all as long as nothing can be said about how when why and where the designers intervened.

    It seems to me that many ID proponents believe it was all done by magic and if that really is the case, we never will know. And if that is the case, how do we know that not everything uder the sun actually is the work of a magician, busy manipulating atoms and molecules?

    Please correct me if I am wrong. Ten years have not taught me anything about ID that makes senese to me. Genetic Entropy, 2nd law of thermodynamics, IC, CSI, FCSI, and all that, how does it all add up, what is the theory of ID on the level above somebody did something somewhere sometime(s)?

  112. Champignon:

    The nested hierarchy argument only supports common descent, not macroevolution as a result of microevolution.

    Human design, especially where reutilization of existing software and object oriented programming is involved, naturally creates netsed hierarchies.

  113. Petrushka:

    Strange that in all the cases you present the molecular basis is not known. How can you talk of microevolution or macroevolution if you don’t know the molecuolar vatiation implied?

  114. Easily. You don’t need to know the genetic basis of a phenotypic feature to observe incremental evolution over time. Nor do you need to know the genetic basis of a feature to infer that it is heritable. The word “gene” was coined long before its molecular basis was discovered.

    And, in fact, we know very little about the genetic basis for any phenotypic feature.

    What we do know now is a fair bit about which genes, and alleles of which genes, are implicated in the development of phenotypic features – it’s what evo-devo is all about, but it’s still very much in its infancy. Phenotypic features are the result of highly complex interactions between many genes and the expressed products of many others.

  115. Elizabeth:

    That’s exactly my point. If you don’t know the molecular basis, you don’t know the informational content of the variation. It can be incremental, it can be heritable, but we cannot classify it as microevolution or macroevolution. You will probably remember that I have given an operational distinction based on dFSCI.

  116. That’s exactly my point. If you don’t know the molecular basis, you don’t know the informational content of the variation. It can be incremental, it can be heritable, but we cannot classify it as microevolution or macroevolution. You will probably remember that I have given an operational distinction based on dFSCI.

    But it’s your side, not ours, that is attempting to so classify!

    As far as evolutionary theory goes, adaptation over short term and long term are essentially the same, except that over the long term, population-level selection starts to play a role, and speciation – the subdivision of populations into two non-interbreeding and thus independently adapting populations – also becomes apparent. It’s just different scale views of the same phenomena.

    If you want to claim that microevolution and macroevolution are two different things based on some measure of informational content of – the step size? I’m not sure – then yes, of course, you will have to measure that.

    But that’s your claim, not ours.

    All we are doing is showing that phenotypic features, such as the mammalian ear, evolved incrementally over many generations, just as finch beaks evolve incrementally to cope with new seed sizes, from generation to generation.

  117. A light sensitive spot on the skin surface is capable of telling its owner when a shadow passes over – potential warning of a predator, or, conversely, information that the owner has reached shelter.

    A light sensitive spot in a slight depression is capable of relaying directional information about the source of the shadow (and may be the reason our brains are wired so strangely, with the left hemispher controlling the right side of our bodies and vice versa).

    A light sensitive spot in a deeper depression is eve nmore capable of relaying directional information.

    A light sensitive spot in a depression with only a pinhole is capable of resolving an actual image.

    A light sensitive spot covered with translucent tissue is better protected than one without.

    A light sensitive spot in which the translucent tissue is concave will focus the light more sharply, improving resolution.

    A light sensitive spot on a body part that can be angled independently is capable of being focusssed on a particular region of space, enabling the creature to maintain “fixation” while it moves towards the fixated point e.g. prey.

    Will that do for starters? There are extant animals with eyes like each of these.

  118. Elizabeth:

    That’s only because your side is not really interested in explaining what is observed (functional information in biology at he molecular level), and is content with a non explanation. Your choice, but we beg to differ.

  119. 119

    A light sensitive spot on the skin surface is capable of telling its owner when a shadow passes over – potential warning of a predator, or, conversely, information that the owner has reached shelter.

    Actually what you’re describing is a light-sensitive spot plus the nerves to transmit the message plus the behavior to respond. In how many iterations did the organism ignore the shadow or perhaps move toward it? In how many iterations did it do something totally unpredictable like flip on its back or spin in circles when it sensed a shadow? It sounds silly, but so many complex behaviors, in order to have evolved, must have begun with seemingly odd responses to stimuli. Take the bird that feigns injury to lure away predators. That must have begun with a behavior that would be far less beneficial, like simply fleeing, or feigning injury right on top of the nest.

    Anything can be simple if you oversimplify it. It’s when we apply the scrutiny of critical thought which is so sorely lacking from this field and actually attempt to apply the theory that we see how far short it falls.

  120. That’s only because your side is not really interested in explaining what is observed (functional information in biology at he molecular level), and is content with a non explanation. Your choice, but we beg to differ.

    Not in the least, gpuccio! That is completely untrue. Evolutionary genetics is a huge field, as is evo devo!

    Let’s recap:

    Bruce David: In the entire list, there is no actual evidence that RM/NS has ever produced a single macroevolutionary advance in living organisms.

    Petrushka: There is evidence that the mammalian inner ear bones evolved by incremental change. There is evidence that feathers evolved incrementally. There is evidence that the whales spout moved incrementally from the front of the face to the top of the head.

    gpuccio: Strange that in all the cases you present the molecular basis is not known. How can you talk of microevolution or macroevolution if you don’t know the molecuolar vatiation implied?

    Me: Easily. You don’t need to know the genetic basis of a phenotypic feature to observe incremental evolution over time. Nor do you need to know the genetic basis of a feature to infer that it is heritable. The word “gene” was coined long before its molecular basis was discovered.

    gpuccio: That’s exactly my point. If you don’t know the molecular basis, you don’t know the informational content of the variation. It can be incremental, it can be heritable, but we cannot classify it as microevolution or macroevolution. You will probably remember that I have given an operational distinction based on dFSCI.

    Me: But it’s your side, not ours, that is attempting to so classify!

    gpuccio: That’s only because your side is not really interested in explaining what is observed (functional information in biology at he molecular level), and is content with a non explanation. Your choice, but we beg to differ.

    In other words, as I read it, Bruce challenged evolutionists to come up with a “macroevolutionary advance” (not a term that evolutionists generally use). Petrushka cited evidence that “advances” generally regarded as “macroevolutionary” by IDists (feathers; the mammalian ear) emerged incrementally i.e. by micro-evolutionary steps. In other words, that microevolution, which your side generally regard as accountable by “RM+NS” is also responsible for macroevolutionary change.

    Then you object that we don’t know the molecular basis for these changes. I agree, but say that that doesn’t stop us observing incremental, i.e. microevolutionary steps.

    You then say that you can’t tell the difference between macro and micro unless you know the genetics because genetics is how you define macro and micro evolution!

    See those goal posts move!

    So I say: but that’s your definition. If you want to claim that some changes demand big step changes in dFCSI, feel free, but that’s your case, not ours. Our case is simply that macroevolutionary change occurs in microevolutionary steps, which are perfectly explicable, as we all agree, by “RM+NS”.

    Or, as I would much prefer to describe it (because much more direct): heritable variance in reproductive success within the current environment.

    You guys agree that happens on an observable micro scale. All we are doing is showing that if you extend that micro scale longitudinally, you end up with “macro” evolution – as long as you don’t move those goal posts!

    Obviously WE can’t demonstrate that evolutionary processes are capable of step changes of 150 bits because we don’t think it is!

    So the whole thing amounts to:

    You guys: show how evolution can produce macroevolution.
    Us: look at incremental evolution of feathers.
    You guys: no, that’s not macro evolution, macro evolution is when you get a step increas of 150 bits.
    Us: but our whole point is that there aren’t big step changes! Look at these incremental changes that amount to big changes in the long term!
    You guys: you aren’t interested in genetics.
    Us: ???????????!!!!!!!!!

  121. 121

    Easily. You don’t need to know the genetic basis of a phenotypic feature to observe incremental evolution over time.

    This is true. But you must know the genetic basis, or at least have a few solid examples, to attribute that evolution to a process of genetic variations and selection. You know neither, and yet attribute the changes to both. How? Why?

    How can you in one sentence state that you can observe incremental evolution while conceding that you cannot observe the increments or even know that they are? That is contradictory and makes absolutely no sense.

  122. Elizabeth:

    No. You are wrong.

    Petrushka cited evidence that “advances” generally regarded as “macroevolutionary” by IDists (feathers; the mammalian ear) emerged incrementally i.e. by micro-evolutionary steps.

    As an IDist, I have never regarded a phenotypic “advance” whose molecular basis is not known as “macroevolutionary”. I don’t know if othyers have done that, but I can respond for myself.

    The macroevolutionary events I usually debate (as you should know) are the emergence of new basci protein domains.

    Speciation is usually considered a macroevolutionary event, and I would agree, but that’s exactly because there are clear, observable and quantifiable genomic differences between species.

    The relation between genomic information and some morphologic aspects of phenotype is sittl not understood, so I maintain that we cannot use those examples to debate our causl explanatory models. I have always stated that, and I will go on stating that.

    Us: but our whole point is that there aren’t big step changes! Look at these incremental changes that amount to big changes in the long term!

    You don’t know the cause of the incremental change. You don’t know the cause of the big change. You cannot know, therefore, how incremental, or how big, those changes are at genomic level.

    Is that clear?

  123. OK, well, it is difficult to keep track of these multi-person discussions!

    But Petrushka’s response seemed to me an appropriate one to Bruce’s – your objection to his response brought up a quite different issue.

    But there are a couple of things that need clearing up anyway. If “speciation” is a “macroevolutionary event” that is a very different definition from an event requiring a > 150 bit step change in dFCSI (however you ascertain that).

    Speciation events often result in populations that are far more similar, at least at first, than, for example a descendent population and its ancestral population, and does not require any “step changes”.

    Nor, IMO, does adaptation, but that is what is under dispute!

    So I’m still finding your argument circular: you are first of all saying: macroevolution is evolution that requires a step change, then challenging us to account for it, without first demonstrating that such step changes ever actually occurred!

    You certainly can’t assume that speciation events require such step changes, and, as Petrushka points out, new features such as feathers also show incremental evolution, not step changes.

    If you want us to explain step changes, please present evidence show that they actually occurred!

  124. This is true. But you must know the genetic basis, or at least have a few solid examples, to attribute that evolution to a process of genetic variations and selection. You know neither, and yet attribute the changes to both. How? Why?

    We have overwhelming evidence that “genes” – the units responsible for inheritance – are molecular. Are you disputing that heritable phenotypic features are genetic as we now understand the word (i.e. carried by DNA sequences)?

    Why should we doubt that incremental morphological changes observed in the fossil records are genetic? Do you, in fact, doubt it?

    Now, we have discovered a lot, recently, about just how genes combine to produce developmental processes, and also about epigenetic effects, which is fascinating, and complicates the picture somewhat, but that has only enhanced our understanding of the kinds of genetic variation, particularly to regulatory genes, that give rises to morphological variance. And we can also make genetic phylogenies that can tell us a lot about what genes are responsible for what features in extant animals, and when they must have appeared, doing what, in their forebears. But clearly we can’t actually do genetics on fossils because there is no genetic material.

    How can you in one sentence state that you can observe incremental evolution while conceding that you cannot observe the increments or even know that they are? That is contradictory and makes absolutely no sense.

    Yes, you can observe incremental evolution – look at the Grants’ work in on the Galapagos finch beaks, and how mean size tracked mean seed size in every generation. And you can then investigate the alleles responsible for those morphological changes, as has been done.

    What on earth is contradictory about it?

  125. Dr. Liddle,

    The spot on the skin surface is not capable of telling its owner anything unless, as Scott Andrew pointed out, there’s a system in place by which it A) can convey its message and B) there’s reason enough for the owner to respond to it and does so properly.

    What was the purpose of that spot-message-conveying-system before the spot came along?

    And if the system wasn’t in place what was the purpose of the spot before the message system was in place?

    Or if they developed simultaneously, how?

    Finally, what are those extant animals you mentioned?

  126. Right, but you asked what use half an eye was. I have told you that :)

    But you are absolutely right that any eye, even a fractional eye, is no use unless it is connected to the rest of the system. But that is a different question – you askes what use half an eye was. I hope that is now clear.

    Right, so let’s look not at “half an eye” but a rudimentary visual system, which makes a lot more sense.

    The most elementary visual system is probably one in which a light sensitive spot reacts to light in such a way that a muscular movement is triggered in the organism. In other words the light-sensitive cells would need to have some way of signalling to muscle cells. Could be chemical, could be ionic. Both kinds of signalling systems were probably already in place before eyes first appeared, certainly chemical signalling systems, as they are essential for multi-cellular life.

    For any prey creature for whom a passing shadow tended to be caused by a predator, a creature who reflexively moved when a shadow fell might pass on more offspring. That’s just a hypothetical. But it is fairly easy to set up simulations in which such visual-systems evolve. And once you have a functional connection between a light (or sound, or chemical) detector and the motor system you have the beginnings of a functional sensory system. And once you have a beneficial sensory system, it can evolve.

    I’ll have to check the extant animals. I’m not a zoologist, so I can’t remember them offhand. Jellyfish are one – I think they just have a light sensitive pigment in a depression.

    And I think a nautilus has a pinhole eye. There’s a book, I think, called “Animal Eyes”. Can’t remember the author. I got it from the library a while back.

    Ah, here it is:

    http://ukcatalogue.oup.com/pro.....8575641.do

  127. Actually what you’re describing is a light-sensitive spot plus the nerves to transmit the message plus the behavior to respond. In how many iterations did the organism ignore the shadow or perhaps move toward it? In how many iterations did it do something totally unpredictable like flip on its back or spin in circles when it sensed a shadow? It sounds silly,

    It’s not silly at all. Just look at the way moths fly into candleflames. They haven’t yet evolved to respond appropriately. They may. The selective pressure is there.

    But recall that sight must have been preceded by other sensory systems and cell-signalling systems.

    but so many complex behaviors, in order to have evolved, must have begun with seemingly odd responses to stimuli. Take the bird that feigns injury to lure away predators. That must have begun with a behavior that would be far less beneficial, like simply fleeing, or feigning injury right on top of the nest.

    Yes indeed.

    Anything can be simple if you oversimplify it. It’s when we apply the scrutiny of critical thought which is so sorely lacking from this field and actually attempt to apply the theory that we see how far short it falls.

    Yes, anything can be simple if you oversimplify it.

    But that doesn’t mean that simple systems can’t be precursors to complex systems, or that coevolution can’t happen. The palaeontological record suggests exactly that.

  128. You are mistaken as the theory of evolution only expects a nested hierarchy based on the vague notion of “all life”.

    Based on characteristics we would expect a Venn diagram.

  129. There still isn’t any genetic data that demonstrates one type of vision system can evolve into another type.

    That should be a big problem for your theory.

  130. OK Elizabeth I will take your silence as an admission that one can construct a nested hierarchy out of vehicles.

    Anything else I can help you with?

  131. Finches “evolving” into finches, guppies “evolving” into guppies and fruit flies “evolving” into fruit flies all support baraminology, not universal common descent.

    Also there aren’t any vestigal legs on whales, anti-biotic resistance doesn’t help you and the fossil record requires genetic confirmation which it currently lacks.

    But the real problem is that you do not understand ID nor Creation- neither reject evolution outright.

  132. Elizabeth:

    But there are a couple of things that need clearing up anyway. If “speciation” is a “macroevolutionary event” that is a very different definition from an event requiring a > 150 bit step change in dFCSI (however you ascertain that).

    Please, read again what I wrote:

    “Speciation is usually considered a macroevolutionary event, and I would agree, but that’s exactly because there are clear, observable and quantifiable genomic differences between species.”

    As you can see, I consider speciation a macroevolutionary event because, in general, it offers evidence of “observable and quantifiable genomic differences” that are in themselves macroevolutionary.

    For instance, the occurrence of even one new de novo protein in a species would most probably be a macroevolutionary event, if we can confirm that the protein has at leal 150 bits of dFSCI.

    We have at least 1000 macroevolutionary events observed after OOL (the emergence of each of the about 1000 new protein domains during natural history). Isn’t that enough to begin?

  133. Whaa….???!!!!

    Sheesh, Joe. Gimme a chance.

    No, you have not constructed a “nested hierarchy”. Look at all the overlaps.

    Try again. Use an actual Venn diagram. Then draw a circle round vehicles with skis. That circle does not nest. Do the same for wheels. That circle does not nest.

    It seems that you don’t understand the principle of nested hierarchies.

    I’ll try to explain, but it’ll have to wait.

  134. You seem to be using a non-standard definition of “speciation”.

    Could you give it?

  135. What overlaps? Everyting is in its own set.

    You are clueless, thanks.

  136. Elizabeth:

    Yes, you can observe incremental evolution – look at the Grants’ work in on the Galapagos finch beaks, and how mean size tracked mean seed size in every generation. And you can then investigate the alleles responsible for those morphological changes, as has been done.

    The problem is that you don’t know what molecular changes are responsible for the size of the finch beaks, or what is the molecular difference between alleles.

    On aminoacid can make a big phenotypic difference, for instance by inactivationg a fundamental protein, and yet the change is very simple at molecular level. On the contrary, the emergence of a completely new protein is a very complex event, but the phenotipic effects need not be huge.

    That’s why discussions about the phenotype are pointless, if we don’t know the moleculare cause. It’s about causes that we are discussing. (By the way, have you answered my epistemologic comments?)

  137. Nested hierarchy of vehicles:

    Vehicles without an engine-> land (snow (skis), ice(skates), ground ->wheeled(cart), water(row boat)(sail boat)(kayak)(canoe), air (landing gear – snow(ski glider), ice(ice sailboat), water(float glider), ground( wheels)(glider))

    Vehicles with engines-> land (snow(skidoo), ice, ground (car), water(boat), air-> landing gear- snow (skiplane), water (floatplane), ground ->wheels (aeroplane)

    Superset = Vehicles (as defined by Elizabeth)

    next level has two sets- one for powered vehicles (engines) and one for no engines- (human powered).

    Under the engine set we have three sets for land vehicles, air vehicles and water vehicles.

    Under the no-engine set we have the same three sets.

    From there each vehicle sits nicely in its own set.

  138. I think the truth is that you do not understand evolution, Joe.

    Do you think that mammals evolve into non-mammals?

    Or dogs into non-dogs? They don’t. No-one claims they do.

    As for vestigial legs on whales, yes there are.

    Saying there aren’t doesn’t make it so. I’ve seen vestigial leg bones on a whale skeleton with my own eyes.

    And yes, I know that antibiotic resistance doesn’t help me. It’s a great problem, but luckily evolutionists understand it, and so help combat it. If it was left to authors like the one in your link, we’d be in much greater trouble. Pseudo-scientists who are prepared to sign a declaration that they will only support conclusions that conform to a priori assumptions.

    And the fossil record does have genetic confirmation – remarkably so. Genetic phylogenies have remarkable congruence with phenotypic phylogenies except in certain very well-accounted for instances.

    I’ll take a break from responding to you, I think. It seems to be a waste of both my time and yours.

    Have a very happy new year.

    Cheers

    Lizzie

  139. Elizabeth,

    “Speciation” is ambiguous at best. Ya see we do have so-called seoarate species that can interbreed.

    And if speciation = macroevolution then YECs accept macroevolution because they accept speciation. However with speciation there has never been any observed new body plans with new body parts.

  140. I think the truth is that you do not understand evolution, Joe.

    Great another false accusation.

    Do you think that mammals evolve into non-mammals?

    No. But if the ToE is true they may.

    As for vestigial legs on whales, yes there are.

    Wrong again. Evos only think they are legs because they think whales evolved from some land mammal that had legs. The structures could very well be from FLIPPERS that are no longer developing.

    And yes, I know that antibiotic resistance doesn’t help me. It’s a great problem, but luckily evolutionists understand it, and so help combat it.

    You are clueless. Using baraminology we can fight bacteria and anti-biotic resistance.

    The fossil record can’t have genetic confirmation as no DNA is recovered with the fossils and no geneticist even knows if teh changes required are even possible.

    Yes take a beak and go out and gather some evidence to support your nonsensical claims.

  141. Actually just about anything can be put into a nested hierarchy. It all depends on your defining criteria.

    That said common descent does not predict a nested hierarchy based on traits for the simple reason that a nested hierarchy based on traits requires the traits be immutable and additive and evolution is not like that.

  142. kairosfocus wrote:
    (I think that part of the problem is that those committed to darwinism or its relatives, find great difficulty understanding what design thinkers are saying, as they are filtering through darwinist glasses.)
    ——————————————————-

    One of the mind blowing comments made to me by a well known scientists,lecturer, on ‘evolution’ and the state of science today. Said to me, “we are not set up to detect ID, we don’t need to to.”
    That statement, set me back a bit, it is not about evidence, or what the science says, its about attitude, or should I say altitude.
    So discussing the science (evidence)will not get you anywhere.
    Its better to deal with the attitude. That they are the ones to tells us all the answers.And because they have done and learned a lot, they feel justified, that in time they will know it all. They have faith.
    Why else would some say ‘evolution’ is a fact. It is attitude.

    http://patternsofcreation.weebly.com/

  143. 143

    But that doesn’t mean that simple systems can’t be precursors to complex systems, or that coevolution can’t happen. The palaeontological record suggests exactly that.

    Of course simple systems can be precursors to complex systems. I’ve designed a number of each. What does that have to do with what we’re discussing, the origin of simple and complex systems?

    Your reason is circular, as the existence of both simple and complex systems is explained by evolution, and then you use them as evidence confirming that explanation.

    Let no one be mistaken that the existence of simple and complex systems are evidence confirming any theory of their origins. They are what must be explained. They are not the evidence.

    Further, the palaeontological record is not evidence of evolution as evolution consists of variations and selections which cannot be inferred or otherwise determined from it. That point can’t be made enough, and certainly not while anyone presents fossils as evidence of darwinian evolution. People have heard that so many times that it starts to sound like it makes sense. It doesn’t.

  144. 144

    I’m not sure whether you are begging the question or conceding that this is evidence of nothing. You seem to be straddling the fence.

    What we do know now is a fair bit about which genes, and alleles of which genes, are implicated in the development of phenotypic features – it’s what evo-devo is all about, but it’s still very much in its infancy. Phenotypic features are the result of highly complex interactions between many genes and the expressed products of many others.

    Of course genetic differences correspond to phenotypic features. That’s common knowledge. The genes and alleles and their phenotypic expressions are exactly what require explanation. It’s the question, not the answer.

    It’s a no-brainer that two fossils with different forms came from two organisms with varying genes.

    But you have absolutely know way of knowing, given any two or two thousand fossils which genes or how many vary between them, which ones vary, which genetic variations form the pathway between two variations, and how, why, or whether they were selected.

    That’s what evolution is supposedly made of. And that is why the ‘mountains’ of fossil evidence and phylogenetic trees contain no evidence of evolution.

    That leaves you with finch beaks and the fantastic, wishful notion that the variations between them can be extrapolated to the explain the differences between lizards and finches.

    I think the point has been made repeatedly that this assertion requires some sort of confirming evidence. That evidence would consist of explaining something, anything, using evolutionary theory.

    Frankly I don’t expect anyone to produce anything. No one has yet. All the talk of fitting models to data is irrelevant, abstract fluff without it.

    I can respect even abstract fluff, but not when it’s called the ‘cornerstone of biology,’ taught as fact, and supported by evidence that obviously isn’t evidence.

  145. What “reason is circular”?

    I’m simply saying that simple systems work (as we can see) and can therefore be the precursors to complex systems, thus disposing of the “what use is half an eye?” canard. We see creatures with half eyes and they find them useful.

    Job done.

    Or is your question now: if simple eyes are the precursors to complex eyes, why are there still simple eyes?

    That’s awfully like the proverbial “why are there still monkeys?” :)

    Simple answer: because not all lineages undergo the same adaptations, but some still thrive.

    Remember: it is not evolutionists who proposed the “ladder of being”. We do not see evolution as progress towards complexity, but as increase in diversity.

  146. Recall that there is no lineage that connects lizards with finches.

    Scott, I’ve tried honestly to explain. I don’t think there is any evidence or example you would accept because your thinking is so far from the way evolutionists think. This you may regard as a virtue, of course! But from where I’m standing, you have a monumental straw man, based, I think, on a lack of understanding of how evolutionary investigations are conducted and why.

    It seems back to front to me. Darwin knew nothing about genetics; genetics gives us the mechanism for heritability. So now we can infer that inherited change is transferred genetically, even though we can’t, obviously, trace the exact genetic change for every morphological change – though we can date the evolution of relevant genes, and map those on to morphological changes in the fossil record. So we are gradually building up a good picture of just how those adapted changes happened, and what genes were involved.

    But you seem to think that until we know everything we can draw no conclusions.

    I’m not sure why. There is far more that we don’t know than we know, and the fossil record can only be a smattering of the total number of populations that have ever lived, and we don’t have tissues from fossils.

    We do, however, have genetics from extant organisms, and increasingly, especially with evo-devo, we start to undertand the role that genes (especially regulatory genes) play in the evolution of morphological features that we see in the fossil record.

    Sure, we don’t know, and never will know, for sure, just what genetic changes resulted in what selected features, so if that’s what you are waiting for, you will wait a long time! But in the mean time, science will go on, and we will keep uncovering this wonderful picture of how life came to be.

  147. 147

    I’m simply saying that simple systems work (as we can see) and can therefore be the precursors to complex systems

    Of course they can. As I said, I’ve designed both. But if you’re using that to support an explanation of the origin of those systems then it is circular.

    If you’re just pointing out the consistency between evolutionary theory and the existence of simple and complex systems in that chronological order, so be it. It’s a weak correlation, and as I’ve said no fewer than a dozen times, there is no application of evolutionary theory to account for it. I could respond that a designer might start simple and build complex, or that it makes more sense to build an ecology from the ground up. You wouldn’t start with elephants and then add grass a million years later, followed a million years later by bacteria to consume the remains of the elephants that starved and the grass they weren’t around to eat.

    There could be half eyes or no half eyes, monkeys or no monkeys. There is absolutely no evolutionary explanation for any of it, no exceptions, period. For the theory to allow them is meaningless. The flying spaghetti monster permits half eyes and monkeys.

    Despite the majority opinion, evolutionary theory is playing defense. I’ve asked repeatedly for the simplest, most reasonable substantiation. Use evolutionary theory to explain something. Every single reply that does not do so is tap dancing. If no one has a direct answer then the best move would be pretending to be too busy to reply.

  148. You have been given many examples of evolutionary theory explaining something.

    But you reject them. I can only conclude that you do not understand what evolutionary theory claims to explain.

    Could you perhaps give an example of a phenomenon that you think should be able to be explained by evolutionary theory but hasn’t been?

  149. 149

    You have been given many examples of evolutionary theory explaining something.

    You have been given many examples of evolutionary theory explaining something.

    Explain gecko feet. Why does my cat have retractable claws? Why do I have toenails? (Odd – I did’t mean to focus on feet.)
    Why do I have earlobes? Why do clovers usually have three leaves? Why do trees have bark? Why do dogs have tails?

    Am I being unreasonable? I’m not asking anything hard, like orbital spiderwebs or what have you. I’m setting the bar as low as I can. That’s a good ballpark.

    What, at this level, can you explain using evolutionary theory? Don’t use one of my examples if it’s going to make you guess.

  150. 150

    Actually, let me clarify even further. I’m trying to set a ballpark, but I would really rather not have you respond to one of my examples. Again, because I’m so reasonable. Even if it could eventually explain everything, it’s not reasonable to expect that all or even any of the examples I had provided had been fully researched. I don’t want an ad-hoc explanation. I want whatever it is that has been carefully researched and documented, providing basis for using evolution as an explanation for biological phenomena in general.

    As far as I can tell it’s kept in an underground vault guarded by a secret society and a two-headed devil dog. But maybe you know somebody.

  151. No, I don’t think any one of those things has been fully researched.

    But I’m still not at all sure why you are rejecting the Galapagos finch beaks, which were actually observed evolving.

    And then there is then there is the broader level at which evolutionary theory explains adaptation. I’m not sure why you think it doesn’t.

  152. Elizabeth, to Scott:

    But I’m still not at all sure why you are rejecting the Galapagos finch beaks, which were actually observed evolving.

    Or the 1:1 sex ratios I mentioned in comment 25.

    Or the congruence of the nested hierarchy to 1 part in 100 trillion trillion trillion trillion.

    Or the gradual transformation of reptilian jaw bones into mammalian inner ear bones through a series of functional intermediates, as mentioned by Petrushka.

    Or the bizarre hormonal warfare between mother and fetus in gestational diabetes.

    Scott, you asked for examples of “how the cornerstone of biology explains something in biology”. Evolutionary theory explains all of these. Intelligent design explains none of them.

  153. 153

    What do we make of stuff like this? It’s clearly a combination of highly derived traits from one part of the hierarchy or tree (bicycles) with highly derived traits from a completely different part of the tree (motorized vehicles). Such a thing would be the equivalent of finding feathered monkeys in the animal kingdom.

    Or better yet, someone who takes a car, puts floatation devices on the sides, and paddles their way up and down a river on it (something I’ve seen people do). Let’s say someone does this with a Nissan Sentra SE-R. You have then what is clearly a barely modified Nissan Sentra SE-R that is not only not classified with other Nissan Sentra SE-Rs, but not even with other Nissan Sentras, nor even with other compact cars, nor even with other cars, nor even as a motorized vehicle. This “Nissan Sentra SE-R” would be classified with vehicles that are about as far as possible from Nissan Sentra SE-Rs on the tree (as a row boat or something I guess).

    Of course, that we’d encounter such problems is easily anticipated – after, all, we’re clearly dealing with “intelligent design” here, and so there’s no reason that a piece of technology in one area wouldn’t be borrowed in very different areas, and breakthroughs in one area are going to be quickly applied to other unrelated areas. And this is why no one (or hardly anyone) would bother trying to put vehicles into a nested hierarchy or taxonomic tree; it’s going to be completely arbitrary and useless.

  154. 154

    But I’m still not at all sure why you are rejecting the Galapagos finch beaks, which were actually observed evolving.

    Now you see why even mainstream biologists use terms such as micro and macro-evolution. Because we’re using the same word to describe the origin of finches and the variations of their beaks.

    Even the most casual reader can tell that we’re talking about – what did Darwin call it – the origin of species.

    You’ve made it quite clear that you think the two are the same. Your opinion is noted. Now will you attempt to make a case for it or not so that those of us who value empirical evidence can have a reason to share your opinion? If so, please do. Or don’t. But that’s where the eyes are.

    And then there is then there is the broader level at which evolutionary theory explains adaptation. I’m not sure why you think it doesn’t.

    Why don’t you explain why it does? As you’re fond of pointing out, that’s how science works.

    Use the ‘broader level of evolutionary theory’ to ‘explain an adaptation (Now you’re making me double up on tags.)

    If I have pennies, I have a penny. If I do not have a penny, it follows that I do not have pennies. Am I inaccurate? I think it’s beyond question.

    Therefore, explain an adaptation. If it can explain adaptations then it follows that it must explain an adaptation, and the converse is true.

    And if the answer is finch beaks or colored cichlid fishes, then congratulations, you get the ribbon for explaining variation within species, and will have conceded that evolution does not explain the origin of species.

    How many times can I repeat such a simple question and receive so many non-answers? I’ve conceded that even if its explanatory power is what you think, the origin of a species is too much to ask. But if you can’t explain the origin of something, only its variations, then it’s dead in the water. Game over. Give the cornerstone a headstone.

    I’ve asked enough times, and what should be off-the-shelf information either does not exist or is a well-guarded secret. Whether or not the discussion continues, it is conceded, past tense, pending new input, that evolutionary theory does not explain the origin of species. We have the evidence we have, not what we hope for or are confident we will have.

  155. 155

    Champignon,

    You’ve recited the same tired list. As much as it annoys me, I’ll point out again that the hierarchies and fossils provide not a single instance of a genetic variation or the selection of a genetic variation. Have I been saying this to myself?

    These are what evolution is made of! And they are entirely missing from your evidence of evolution. They are not sparse. They are missing! How can evidence of change through genetic variation and selection specify no, none, zero genetic variations or selections of them?

    I sure hope whoever taught you that fossils and hierarchies constitute evidence of the mechanisms of evolution at work didn’t get any of your money. And if they did, I hope you kept your receipt. You’ve been boondoggled. There’s nothing under any of the shells.

  156. Tell me what part of genetics forbids a feathered monkey. Tell me what part of genetics forbids any of the alleged hybrids that would allegedly foil the theory of evolution.

    Geez Louise if we saw a bunch of jumbled-up organisms we would think that is the norm

  157. Scott,

    Even the saintly Elizabeth Liddle must be getting exasperated with you. You asked us to explain “something, anything, using evolutionary theory.”

    We did.

    You asked us to use “the cornerstone of biology to explain something biological.”

    We did, as anyone reading the thread can see.

    Yet you pretend we didn’t. You’re not fooling anyone, except perhaps for yourself.

    Here are some questions for you:

    1. How does ID “theory” explain the fact that there is a single nested hierarchy, to a precision of 38 decimal places?

    2. How does ID explain the 1:1 sex ratios of so many sexual species?

    3. How does ID explain gestational diabetes, which pits mother against fetus in a hormonal battle?

    4. Which is scientifically preferable: a theory that makes predictions that are confirmed to an amazing degree of precision, or one that does not?

    5. Which is preferable: a theory that provides explanations for otherwise mysterious phenomena, or one that does not?

  158. Joe,

    Are you arguing against goodusername or for him?

    Think about what you just wrote.

  159. champignon,

    I am saying that there isn’t anything in either the theory of evolution nor genetics that prevents the mixture of characteristics that would alledgedly refute the theory.

  160. 160

    Champignon,

    Neither of you provided either. Elizabeth mentioned the finches, although she declined to explain them using evolutionary theory. That’s fine. If you wish to scale back the grandiose claims of TOE and call it an explanation of how finch beaks and lizard heads vary slightly and fish change color, I will find less to object to.

    You also provided your checklist of items that contain no specific content regarding the operation of darwinian mechanisms. There’s no points for that.

    I’m not speaking as an ID advocate right now. I’m just having fun repeatedly pointing out that no one is able to use this awesome explanatory power to explain anything.

    I don’t split hairs over the little stuff like the finches or the lizard heads. Living things change. They get smaller, bigger, smaller again, the beaks get longer, shorter, and longer again. If you want to amass evidence that evolution produces such minor variations, go for it.

    I’ve been quite reasonable with regard to the scope of change I’ve asked you to explain. Rather than picking really tough cases, I’ve asked you to chuck a few stones off the ol’ mountain of evidence my way.

    I’m not asking you to explain the giraffe’s neck. I’m asking you for any example you can provide as a basis for thinking that TOE can explain the giraffe’s neck. (You’re still saying that evolved, right?)

    Please don’t pretend that you’ve answered. An explanation using genetic variation and selection must involve genetic variations and selections. It’s almost surreal that I must even point this out more than once.

    I know you’re in a big hurry to change subjects and talk about ID. But TOE is taught in public schools, and its proponents are fond of pointing out that it’s been explaining biology for 150 years. Please either back it up or concede before moving on. Or don’t. Failure to explain any evolutionary transitions in terms of genetic variation and selection is concession. The request is far too reasonable to be objectionable. If you can explain A-Z, demonstrate it by picking one and explaining it.

    If you don’t have a response that involves genetic variations and selections, my advice is pretending to be too busy to answer. That’s always fair. We all have other things to do. But every non-answering post reinforces your implicit concession that you cannot reply.

  161. 161

    I am saying that there isn’t anything in either the theory of evolution nor genetics that prevents the mixture of characteristics that would alledgedly refute the theory.

    If we discovered a species of monkey with feathers, I would believe that it originated via intelligent design.

    To say that the odds of two independent lineages coming up with such a specific trait is astronomical, would be an understatement. I would say, given our current knowledge of genetics, that such a thing is statistically impossible. And so I would believe that someone (God, aliens, a human super-genius) fiddled with the genetics to create such a creature.

  162. Scott,

    I’ve answered your questions. Now it’s your turn to answer mine. I’ve reproduced them here for your convenience, so that you don’t have to page back to find them.

    If you’re unable to answer them, that’s understandable. After all, it’s the predictive and explanatory power of the theory of evolution vis-a-vis its rivals that makes it such a successful theory, accepted by more than 99% of biologists. ID simply can’t compete.

    The questions:

    1. How does ID “theory” explain the fact that there is a single nested hierarchy, to a precision of 38 decimal places?

    2. How does ID explain the 1:1 sex ratios of so many sexual species?

    3. How does ID explain gestational diabetes, which pits mother against fetus in a hormonal battle?

    4. Which is scientifically preferable: a theory that makes predictions that are confirmed to an amazing degree of precision, or one that does not?

    5. Which is preferable: a theory that provides explanations for otherwise mysterious phenomena, or one that does not?

  163. C:

    Pardon, but you are changing the subject again.

    The issue is not about nested hierarchies or the causes of diabetes, but about the empirically warranted source of functionally specific, complex organisation and associated information, and the linked point that such FSCO/I strongly points to isolated islands of function in configuration spaces.

    In short, there is a pivotal phenomenon on the table, and a reasonable, empirically warranted account of it needs to be had.

    Assertions as to how much darwinian evolution “explains” are useless if it cannot account for how we get to islands of function. Or, failing that, if it cannot show that on observed cases in point, body plan origin is explicable on incremental changes to a few initial single celled forms. Or, even, that we have good observations that show how by such mechanisms, we have specifically got to significant organ systems.

    Just so stories with a few highlights with some hand waving driven by a priori evolutionary materialism will not do.

    As a case in point, how — on actual observed evidence, step by step — did birds get their specialised lungs and wings?

    Or, the like.

    Perhaps, the definition of ID at NWE in its ID article will help clarify the proper focus:

    Intelligent design (ID) is the view that it is possible to infer from empirical evidence that “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection” [1] Intelligent design cannot be inferred from complexity alone, since complex patterns often happen by chance. ID focuses on just those sorts of complex patterns [ --> specific, info rich ones, especially functionally specific ones, or irreducibly complex ones, with fine tuning of the cosmos we observe being also on the table] that in human experience are produced by a mind that conceives and executes a plan. According to adherents, intelligent design can be detected in the natural laws and structure of the cosmos; it also can be detected in at least some features of living things.

    Greater clarity on the topic may be gained from a discussion of what ID is not considered to be by its leading theorists. Intelligent design generally is not defined the same as creationism, with proponents maintaining that ID relies on scientific evidence rather than on Scripture or religious doctrines. ID makes no claims about biblical chronology, and technically a person does not have to believe in God to infer intelligent design in nature. As a theory, ID also does not specify the identity or nature of the designer, so it is not the same as natural theology, which reasons from nature to the existence and attributes of God. ID does not claim that all species of living things were created in their present forms, and it does not claim to provide a complete account of the history of the universe or of living things.

    If indeed the inference is cogent, theories that purport to explain say life forms on blind chance and/or mechanical processes will run short of specific, step by step observational evidence.

    Which seems to be the precise problem behind how much of this discussion has been so repeatedly on side tracks.

    So, let us refocus.

    The expression, below — and as discussed here — may help us:

    Chi_500 = I*P – 500, functionally specific bits beyond the solar system threshold.

    GEM of TKI

    PS: Marxists were fond, too, of how much their theory seemed to explain. But in fact, that was symptomatic of its flaws. It was so broad that it could explain just about anything and its opposite.

  164. OK,you ask me to explain the origin of a species by means of evolutionary theory.

    Sure.

    Here goes: Evolutionary theory explains the origin of species as follows:

    A single interbreeding population subdivides into two sub-populations which decreasingly interbreed. This may be because they become geographically separated, by a mountain range, or by a stretch of water, or it may that the population simply spreads over a wide area, even though each member’s territorial range remains small, resulting in clustering.

    Thereupon each interbreeding group starts to adapt to its own local conditions, independently of the rest of the population. For example, finches on a particular island might evolve larger beaks because of some locally available large seed, while finches on a neighbouring island evolve smaller beaks because of a locally available small seed.

    Over time, because the species rarely hybridise, the populations grow increasingly dissimilar, both because of genetic drift (which doesn’t travel beyond each population) and because of adaptation to local conditions. Eventually, they become so dissimilar that interbreeding cannot occur successfully, even if the species come to inhabit the same territory.

    At that point we say we have two species of finch instead of the original one.

    One of those species may closely resemble the ancestral population, and may be given the same name, while the other is given a new name. But that’s just a question of nomenclature. Sometimes two new names are given.

    Either way, there are two species where before there was only one.

    This has been observed in real time, and is also indicated by ring species, in which populations at the extreme ends of a territorial range do not interbreed (even if they have the opportunity to do so) but each population hybridises with the neighbouring population along the range.

    Northern herring gulls are such an example.

    But clearly it is a slow process, and we do not see dramatic divergence on the timescale of human eyewitnesses.

    We do, however, see those divergences in the fossil record, and also in the genetic record, which is why we can construct branching phylogenies aka nested hierarchies. The more remote from present day the bifurcation point, or node, the more dissimilar the descendents of the common ancestral population will be.

    And are.

  165. Dr Liddle:

    The problem is not generic origin of a “species” — a particularly vague target — but the origin of functionally specific body plans or significant organ systems or structures that exhibit FSCO/I and perhaps IC.

    That is what needs to be documented on empirical observation, not something like how populations of gulls in the North grade from one species to another by the time we get back around the circle. That sort of variation is within islands of function and is not even a serious issue.

    GEM of TKI

  166. 166

    Elizabeth,

    I’m afraid you’ve misunderstood the question. You’ve attempted to explain the origin of species in general.

    If you can explain the origin of species, why not demonstrate it by explaining the origin of a species using genetic variation and natural selection (and whatever else you wish to throw in?)

    Naming a species is not an explanation. I can open a book and read the names of many species.

    I looked up the northern herring gull. Frankly I’m disappointed that you would retreat to an example of simple variation that starts with a gull and ends with a gull that only a birdwatcher could distinguish from the first.

    Is this what Darwin had in mind when he used the term “origin of species?” Did he revolutionize biology by proposing how gulls come from gulls?

    I feel trifled with. If I tell you specifically what to explain, even I see why that might be unreasonable. But if I don’t, you and others retreat to these meaningless examples that tell us nothing about the origin of anything at all.

    Anyway, I looked it up. As is typical, the research focused on taking samples from various birds and comparing their DNA, and then looking for identifiers that would separate them in a manner corresponding to their taxonomy.

    The specific variations are uncertain. Natural selection is not even mentioned in the paper. Now you’ll mention that not all speciation is caused by natural selection. Some is caused because a population spreads out and is geographically prevented from interbreeding.

    That’s very interesting. But it tells us nothing of the evolution of anything about a herring gull, only the way that separated populations have different colors. (Wow, cichlid fish again!) And it tells us nothing of the mechanics of natural selection.

    If these are your examples of what evolution explains, and they don’t even mention natural selection, what am I to understand? That you had a better example but preferred to make your point with northern herring gulls?

    You’re making my point for me. My point is that you cannot explain anything in biology beyond trivial variations within species using the mechanics of evolutionary theory, namely genetic variation and natural selection.

  167. Cabal:

    I suggest you take some time out to read say the NWE survey on ID, the FAQ’s at UD at top under the resources tab and perhaps the summary article here. [Take time to view the two introductory videos.] Then, kindly be specific rather than blanket dismissive.

    I particularly note that many objections to the design inference on empirical signs, and the warrant for that, pivot on talking point distortions such as are addressed in the FAQ above.

    In the meanwhile, this thread is about something specific, which should not be distracted from.

    I note to you — IIRC, yet again — that the inference that design is the best explanation for an object, on well tested signs, is prior to evaluating who or what may be a good candidate. And, the answer that design is on evidence the best explanation of a given object is of the order of the conclusion that arson is the best explanation for a given fire. It is specific in itself and foundational to further investigations.

    GEM of TKI

  168. GUN: How many times did vision and flight allegedly evolve convergently again? The echolocation systems of bats and cetaceans? Marsupial and placental analogues? What about mosaic organisms like the platypus? [Cf discussions here on in context.] KF

  169. Hi goodusername,

    Tell me what part of genetics forbids a feathered monkey. Tell me what part of genetics forbids any of the alleged hybrids that would allegedly foil the theory of evolution.

    Geez Louise if we saw a bunch of jumbled-up organisms we would think that is the norm

  170. Elizabeth,

    I’m afraid you’ve misunderstood the question. You’ve attempted to explain the origin of species in general.

    I think the problem lies in the question, then, Scott :) I think you think that evoltution claims to answer a question that it does not attempt to answer – that the theory, in fact, says is not the right question.

    The theory of evolution is the theory that all modern variety came about by two means: adaptation down lineages, and speciation across lineages.

    It disputes the notion that there are large longitudinal leaps between the characteristics of populations and claims instead that all change is incremental. And not only is it incremental, that each bifurcation (speciation point), at the time it happens, results in species that are, as you say, as similar as two non-interbreeding populations of herring gull at the extreme ends of a range, or two species of finch. However, and this is important, once interbreeding between those two populations has ceased, adaptation within each of the two lineages will proceed independently, resulting not only in descendents that may differ profoundly from their ancestors, but also in descendents, down different lineages, that differ profoundly from each other.

    So when what we now call phyla first diverged, they were a similar as closely related species are today; ditto with what we now call kingdoms, classes, genuses, etc. The reason we have different words for them is that since kingdoms etc speciated, there have been large numbers of subsequent subdivisions. But at the time it happens, all subdivisions are simply speciation events, resulting, at first, in two extremely similar populations.

    I’m not trying to persuade you what did happen; I’m trying to explain what evolutionist claim happened, because it seems to me that you are challenging evolutions to explain something that the actually claim did not happen – which obviously we can’t do!

    I’ll respond in more detail below:

    If you can explain the origin of species, why not demonstrate it by explaining the origin of a species using genetic variation and natural selection (and whatever else you wish to throw in?)

    Sure. How about the apple maggot fly? Obviously within living observation, there will be few unambiguous speciation events outside the lab (i.e. naturally occurring – there are plenty with lab fruitflies). Here is Talk Origins:

    5.5.1 Apple Maggot Fly (Rhagoletis pomonella)

    Rhagoletis pomonella is a fly that is native to North America. Its normal host is the hawthorn tree. Sometime during the nineteenth century it began to infest apple trees. Since then it has begun to infest cherries, roses, pears and possibly other members of the rosaceae. Quite a bit of work has been done on the differences between flies infesting hawthorn and flies infesting apple. There appear to be differences in host preferences among populations. Offspring of females collected from on of these two hosts are more likely to select that host for oviposition (Prokopy et al. 1988). Genetic differences between flies on these two hosts have been found at 6 out of 13 allozyme loci (Feder et al. 1988, see also McPheron et al. 1988). Laboratory studies have shown an asynchrony in emergence time of adults between these two host races (Smith 1988). Flies from apple trees take about 40 days to mature, whereas flies from hawthorn trees take 54-60 days to mature. This makes sense when we consider that hawthorn fruit tends to mature later in the season that apples. Hybridization studies show that host preferences are inherited, but give no evidence of barriers to mating. This is a very exciting case. It may represent the early stages of a sympatric speciation event (considering the dispersal of R. pomonella to other plants it may even represent the beginning of an adaptive radiation). It is important to note that some of the leading researchers on this question are urging caution in interpreting it. Feder and Bush (1989) stated:

    “Hawthorn and apple “host races” of R. pomonella may therefore represent incipient species. However, it remains to be seen whether host-associated traits can evolve into effective enough barriers to gene flow to result eventually in the complete reproductive isolation of R. pomonella populations.”

    Naming a species is not an explanation. I can open a book and read the names of many species.

    No indeed, but it’s important not to be mislead by nomenclature. Complaining that finches that speciate “are still finches” is merely arguing from nomenclature. Moreover, from nomenclature designed to deal with categories rather than continua, and the whole thesis of evolutionary theory is that populations are continually evolving, and periodically speciating. We will probably always call the descendents of dogs “dogs” even if they turn out to look more like marine mammals, just as we still call snakes “tetrapods” even though they have no legs.

    I looked up the northern herring gull. Frankly I’m disappointed that you would retreat to an example of simple variation that starts with a gull and ends with a gull that only a birdwatcher could distinguish from the first.

    Is this what Darwin had in mind when he used the term “origin of species?” Did he revolutionize biology by proposing how gulls come from gulls?

    Yes, actually :) See above. Living things come from living things. Mammals always have mammalian descendents. Synapsids always have synapsid descendents. Tetrapods always have tetrapod descendents. Vertebrates always have vertebrate descendents. Chordata always have chordata descendents. Bilateria always have bilaterian descendents.

    We don’t yet have separate names for the layers below species (well, subspecies) and will always be somewhat defeated because nature isn’t that orderly. There is no absolute difference between a twig and a branch, a branch and a bough, a bough and a limb. And you can trace all twigs back to the trunk, incrementally, even though you pass bifurcations on the way.

    I feel trifled with. If I tell you specifically what to explain, even I see why that might be unreasonable. But if I don’t, you and others retreat to these meaningless examples that tell us nothing about the origin of anything at all.

    No, you aren’t being trifled with, but the fact that you think so is a clue to what is going wrong here I think. As I tried to explain above

    Anyway, I looked it up. As is typical, the research focused on taking samples from various birds and comparing their DNA, and then looking for identifiers that would separate them in a manner corresponding to their taxonomy.

    The specific variations are uncertain. Natural selection is not even mentioned in the paper. Now you’ll mention that not all speciation is caused by natural selection. Some is caused because a population spreads out and is geographically prevented from interbreeding.

    Yes, and speciation isn’t caused by natural selection. It’s caused by two populations spreading out and evolving independently. Some of that evolution will involve natural selection and some will simply be drift. If you separated one populations into two and placed each in identical, but separate, environments, you’d end up with two species, i.e. species that would or could no longer interbreed, even if no adaptation at all had occurred in either population (i.e. no natural selection). However, adaptation pretty well always does occur, so that would probably happen to. But the point is that speciation is a horizontal event, natural selection is a longitudinal event.

    That’s very interesting. But it tells us nothing of the evolution of anything about a herring gull, only the way that separated populations have different colors. (Wow, cichlid fish again!)

    Exactly. It tells you about speciation. It does not tell you about adaptation (which is where natural selection comes in).

    And it tells us nothing of the mechanics of natural selection.

    No, because you asked about speciation. Both happen together of course, but they are different processes. Speciation can happen in the absence of natural selection. But adaptation results from natural selection.

    If these are your examples of what evolution explains, and they don’t even mention natural selection, what am I to understand? That you had a better example but preferred to make your point with northern herring gulls?

    That you are a little confused about the difference between speciation and adaptation :)

    You’re making my point for me. My point is that you cannot explain anything in biology beyond trivial variations within species using the mechanics of evolutionary theory, namely genetic variation and natural selection.

    But “trivial variations” are exactly the “incremental variations” that evolutionary theory posits are responsible for adaptation. Every single adaption is trivial. Just as every millimetre on a journey is trivial. Stack them up, though, and you’ll get from New York to Los Angeles. Travel in convey, then one car takes a different turning at Denver and they end up in Portland.

    The adding up is adaptation (natural selection) + drift. The different turning is speciation. For a while after Denver, the convoys will be a trivial difference apart. But the time you both reach the Pacific, you won’t need a birdwatcher to tell you that you are in very different locations!

  171. Dr. Liddle,

    Clearly, we meant different things by “half an eye” which may further evidence of my having only half a brain. I apologize for the misunderstanding.

    I wonder, though, if you see the difficulty some have in making the leaps made by those on your side of this discussion?
    For example, the rudimentary light sensitive system you described still sounds extremely complex so that the problem seems to not have been resolved at all. It only leads to more questions and what appear to be further leaping for answers. A light sensitive spot that reacts in a way that triggers muscular movement? From my experience light sensitive spots tend to result in itchy rashes and visits to the pharmacy not muscular movements. How do we know that such a spot, in its initial formation before it could signal anything, wasn’t detrimental to the creature it resided on? Such a spot on our little friend’s skin could just have easily allowed for infections that would lead to its demise.

    And a prey creature who reflexively moves when a shadow passes is likely to live in the kind of environment where sitting still may be be the best thing to do when a predator nears. Movement may be the very thing that alerts a predator to prey since no one, as yet, has a functional vision system. If so, our spotted friend is doomed.
    And how is any of this demonstrable?

  172. And if it were linked in such a way that it led to the creatures demise, then it wouldn’t leave offspring. Only those creatures in which the link led to safety would leave offspring.

    Hence the evolution of a beneficial link.

    But recall, that visual systems would have evolved much later than other sensory systems. As far as we know,the earliest sensory system was smell, i.e. chemical.

    And no need to apologize :)

    Cheers

    Lizzie

  173. 1. How does ID “theory” explain the fact that there is a single nested hierarchy, to a precision of 38 decimal places?

    A common design based on common standards. That and the fact the we humans are good at clasifying things.

    Accumulations of random mutations does not predict a nested hierarchy based on characteristics.

    2. How does ID explain the 1:1 sex ratios of so many sexual species?

    How does your position even explain sexual reproduction? How many failed experiments were there before the current system was found?

    3. How does ID explain gestational diabetes, which pits mother against fetus in a hormonal battle?

    Random effects introduced to the design.

    4. Which is scientifically preferable: a theory that makes predictions that are confirmed to an amazing degree of precision, or one that does not?

    Your position doesn’t make any predictions based on the proposed mechanisms.

    5. Which is preferable: a theory that provides explanations for otherwise mysterious phenomena, or one that does not?

    Your position’s “explanations” are as good as my explanations to my teachers as to why my homework was not completed on time.

  174. Hi Cabal,

    What is the theory of evolution on the level above something happened at some point in time and other things just kept happening and here we are?

    What is the theory of evolution on the level above mother nature + father time + some still unknown process(es) = the diversity of life on earth?

  175. ScottAndrews2

    As an aside, the difference between a lesser black blacked gulland a herring gull is pretty significant. You would have to be pretty obtuse not to notice when confronted with the two of them. One has light grey wings and other black wings among other things.

  176. Allow me to expand a little regarding Champignon’s point #1:

    The notion that there is a single tree of life, ie, that trees derived from chemistry agree with each other and with that derived from the morphology of fossils and extant species, has been shown to be false. This is a prediction of Darwinism, like many others, that has turned out to be wrong. However, failed predictions don’t seem to make much difference to Darwinist proponents.

    From an article by Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009):

    “For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

    Further in the article:

    Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts—also known as tunicates—are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren’t chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says.

    Other scientists agree. The conclusion of Antonis Rokas, Dirk Krueger, and Sean B. Carroll in “Animal Evolution and the Molecular Signature of Radiations Compressed in Time,” Science, Vol. 310:1933-1938 (Dec. 23, 2005) is,

    Despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.

    Likewise, Carl Woese, a pioneer of evolutionary molecular systematics, observed in “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998) that these problems extend well beyond the base of the tree of life:

    Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.

    Or again, from Patterson et al., “Congruence between Molecular and Morphological Phylogenies,” Annual Review of Ecology and Systematics, Vol 24, pg. 179 (1993):

    As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.

    Or, from Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” Journal of Molecular Evolution, Vol. 44, pgs. S117-S120 (Supplement 1, 1997):

    That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.

    Darwinists often cite the Cytochrome C phylogenetic tree as matching and confirming the phylogeny of many animal groups derived from morphology. However, they rarely talk about the Cytochrome B tree, which is quite different from the classical animal phylogeny. As Michael S. Y. Lee states in “Molecular phylogenies become functional,” Trends in Ecology and Evolution, Vol. 14:177-178 (1999),

    [T]he mitochondrial cytochrome b gene implied…an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.

    Note that these quotes are all from authors who are Darwinists. My source for them is A Primer on the Tree of Life which contains more examples. In other words, there is no “single nested hierarchy”.

  177. Bruce,

    The funnoest part of a single tree of life is that the theory of evolution is silent on the origins issue which means it is perfectly OK with multiple trees seeing that the number of trees is an origins issue.

  178. Since the topic of ring species has come up, let’s add that to the list of phenomena that are explained by evolutionary theory but not by intelligent design.

  179. Hi Bruce,

    Your post reflects some common misunderstandings about phylogenies and congruence. I highly recommend reading Theobald’s treatment of the issue.

    Here are some key quotes:

    In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are “When comparing two measurements, how much of a discrepancy does it take to be a problem?” and “How close must the measurements be in order to give a strong confirmation?” Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).

    When two independently determined trees mismatch by some branches, they are called “incongruent”. In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al. 1984; Penny et al. 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al. 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see “Statistics of Incongruent Phylogenetic Trees”.

    The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

    “Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106.” (Penny and Hendy 1986, p. 414)

    For a more realistic universal phylogenetic tree with dozens of taxa including all known phyla, the accuracy is better by many orders of magnitude. To put the significance of this incredible confirmation in perspective, consider the modern theory of gravity. Both Newton’s Theory of Universal Gravitation and Einstein’s General Theory of Relativity rely upon a fundamental physical constant, G, the gravitational constant. If these theories of gravity are correct, independent methods should determine similar values for G. However, to date, very precise independent measurements of the gravitational constant G disagree by nearly 1% (Kestenbaum 1998; Quinn 2000).

    Nevertheless, a precision of just under 1% is still pretty good; it is not enough, at this point, to cause us to cast much doubt upon the validity and usefulness of modern theories of gravity. However, if tests of the theory of common descent performed that poorly, different phylogenetic trees, as shown in Figure 1, would have to differ by 18 of the 30 branches! In their quest for scientific perfection, some biologists are rightly rankled at the obvious discrepancies between some phylogenetic trees (Gura 2000; Patterson et al. 1993; Maley and Marshall 1998). However, as illustrated in Figure 1, the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants. For comparison, the charge of the electron is known to only seven decimal places, the Planck constant is known to only eight decimal places, the mass of the neutron, proton, and electron are all known to only nine decimal places, and the universal gravitational constant has been determined to only three decimal places.

  180. goodusername,

    For clarification- are you trying to imply that our definition of what is (and isn’t) a mammal (monkey) somehow a barrier to evolution?

  181. Check this out- I fixed it:

    According to the theory of common design, modern living organisms, with all their incredible differences, are the progeny of one single design standard in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1) replication, (2) heritability (characteristics of descendents are correlated with those of ancestors), (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a design standard tree.

    If every living species is designed from an original design standard that had these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus, a basic prediction of the design relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes.

    (the above was taken and fixed from champignon’s link to Theobald on talk origins)

  182. Joe,

    Here’s the part of Theobald’s discussion that you need to focus on. It explains why evolutionary theory predicts a unique nested hierarchy while design does not:

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

    The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

    Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

    Interestingly, Linnaeus, who originally discovered the objective hierarchical classification of living organisms, also tried to classify rocks and minerals hierarchically. However, his classification for non-living objects eventually failed, as it was found to be very subjective. Hierarchical classifications for inanimate objects don’t work for the very reason that unlike organisms, rocks and minerals do not evolve by descent with modification from common ancestors.

  183. 183

    the difference between a lesser black blacked gulland a herring gull is pretty significant. You would have to be pretty obtuse not to notice when confronted with the two of them. One has light grey wings and other black wings among other things.

    Are you playing a trick on me? Have you switched sides?

  184. champignon,

    I do not hold Theobald as any type of authority on anything, let alone nested hierarchies. He seems to think a family tree produces a nested hierarchy. He also doesn’t seem to understand anything about design standards.

    And guess what Linnaeus saw his nested hierarchy as evidence for a common design

  185. 185

    Since the topic of ring species has come up, let’s add that to the list of phenomena that are explained by evolutionary theory

    You’re getting way ahead of yourself. In any of your nested hierarchies, evolutionary theory does not explain the difference between any species and any other species. (The exception is if you place gull A and gull B that looks almost like gull A and lives 100 miles away next to each other. But then you’re using geographical isolation rather than natural selection, so it has nothing to do with the actual case you’re trying to make.)

    If evolutionary theory, genetic variations and natural selection (plus HGT, drift, and the kitchen sink) cannot explain the difference between any two organisms in the hierarchy, how can it explain the hierarchy?

    You’re right back to the same challenged I’ve issued and you’ve ducked. You say that evolutionary theory explains nested hierarchies. Is it somehow unfair of me to turn around and say, okay, then use evolutionary theory to explain the hierarchy?

    Saying that a theory explains something is easy. You said it explains it, so explain it.

    This is where the tap dancing begins. There won’t be a retraction of the claim that evolutionary theory explains it, but justification for why you can’t produce the explanation you plainly said exists. Or why you shouldn’t. Or questioning the extremely simple question. Or changing the subject.

    I’m repeating for emphasis. If evolutionary theory explains a hierarchy then use it to explain a hierarchy. Or use it to explain the relationship between two items in the hierarchy. I think you made that statement without expecting you’d be called on it, or without even thinking through what it means. Prove me wrong if you can.

  186. KF,

    You wrote:

    The issue is not about nested hierarchies or the causes of diabetes, but about the empirically warranted source of functionally specific, complex organisation and associated information, and the linked point that such FSCO/I strongly points to isolated islands of function in configuration spaces.

    The issue, as it always does in science, centers on the evidence: What theory does the best job of explaining the evidence? What theory does the best job of making distinct predictions that are confirmed by the evidence?

    When evaluated according to these criteria, intelligent design does poorly and evolutionary theory does extremely well, as demonstrated by the evidence laid out elsewhere in this thread. It’s understandable that you would prefer to deflect attention away from this embarrassing fact.

    Assertions as to how much darwinian evolution “explains” are useless if it cannot account for how we get to islands of function.

    Arguments based on “islands of function” are useless if you cannot demonstrate that such islands do in fact predominate. You haven’t done so.

    In fact, the evidence of the nested hierarchy is exactly what we expect to see if 1) natural selection is operating, 2) variation is gradual, and 3) “islands of function” are not a significant barrier to evolution.

    On the other hand, if intelligent design were true, we would not expect to see a nested hierarchy at all — that is, unless you add the totally superfluous assumption that the designer fastidiously mimics unguided evolution for some mysterious reason.

    As a case in point, how — on actual observed evidence, step by step — did birds get their specialised lungs and wings?

    How, on actual observed evidence, step by step, did birds get their specialized lungs and wings — according to ID ‘theory’?

    PS: Marxists were fond, too, of how much their theory seemed to explain. But in fact, that was symptomatic of its flaws. It was so broad that it could explain just about anything and its opposite.

    Except that evolutionary theory doesn’t explain everything and it’s opposite. For example, evolutionary theory explains the 1:1 sex ratio of most sexual species. If evolutionary theory is as flexible as you claim, you should be able to come up with a convincing evolutionary explanation of why the sex ratio should actually be 5:2. Good luck.

    The irony is palpable: an ID proponent charges evolutionary theory with explaining everything and its opposite, not realizing that that is exactly the problem with ID.

    How does ID explain the nested hierarchy? “That’s just the way the designer did it.” What if there were no nested hierarchy? “Of course — that’s the way the designer did it.”

    What about the 1:1 sex ratio? “That’s the ratio the designer chose.” What if it were 5:2? “That’s the ratio the designer chose.”

    And so on. ID is the ultimate just-so story. That accusation boomerangs on you.

  187. 187

    Joe,

    What I’m saying is that if Linnaeus found a species of feathered monkey, I’m pretty sure he would have thrown up his hands and given up his endeavor, as it would be obvious that animals in fact don’t fit such the topology that he was attempting. Monkeys and feathered creatures are no where near each other on the taxonomic tree, and for good reason. And any attempts to modify the tree so that monkeys and such creatures are linked would result in a tree that looks absolutely ludicrous. It’s precisely because things like feathered monkeys aren’t found that a taxonomic tree exists.

    The reason for organizing a group of objects into a nested hierarchy/taxonomic tree is because the various characteristics of the individual objects fit a pattern. The only thing I know of that can create that pattern is when there is a descent from a common ancestor, and changes are passed from parent-to-child, and the changes aren’t very large. Other than living things, the only other example of things that I can think of, off the top of my head, that fit this pattern are groups of languages.
    http://andromeda.rutgers.edu/~jlynch/language.html

    Organizing languages into a nested hierarchy or tree is often problematic though. The reason is that the changes are not passed exclusively from parent to child. Languages, even distantly related languages, often borrow words from each other (shortly after “ok” appeared in English it had spread to Asian languages). In other words, the bifurcations are often not complete, and a kind of “horizontal gene transfer” is very common. Languages can even converge in a sense; a good example is English. IIRC, old English came from German, but today English is more similar to French than to German.

    And so while languages can be organized into tree-like topologies, on close inspection, the trees will often look kinda funny, with little twigs connecting the branches, and sometimes even branches converging. This is similar to what we see among prokaryotes, and for the same reasons. (I wonder if taxonomic work on prokaryotes is more similar to linguistics than to zoology).

  188. Languages have horizontal gene transfer, but it is still possible to trace their evolution, at least since the invention of writing.

    Except for Basque. I’m not sure what the status is for Basque. It sticks out like one of gpuccio’s isolated protein domains. Maybe it was specially created.

  189. champignon,

    The problems I alluded to in 34.1, eg the fact that 50% of the sea squirt genome places it in one location in the tree and 50% places it in another, or that cytochrome B gives a completely different phylogeny than morphology or cytochrome C does, are not simply problems of measurement, like the limitations to physicists’ ability to measure the charge of the electron. In other words, you can’t just chalk them off to experimental error. They are falsifications of common descent. Statistical correlation of the different trees compared to the number of possible trees is completely irrelevant here.

    Furthermore, the tree of life is a prediction of common descent, not RM plus NS. The two are separate issues. Even if common descent were true, which it apparently is not, that would not imply that the mechanism by which variation in biological organisms is produced is RM/NS.

    To repeat, what is missing from the neo-Darwinian synthesis is any actual evidence, either from observation of extant species, from experimental evidence, or from the fossil record, that RM plus NS has ever produced a single maocroevolutionary advance. It is a theory entirely unsupported by evidence.

  190. The problems I alluded to in 34.1, eg the fact that 50% of the sea squirt genome places it in one location in the tree and 50% places it in another…

    You have a reference for that?

  191. Bruce,

    Statistical correlation of the different trees compared to the number of possible trees is completely irrelevant here.

    This couldn’t be further from the truth. To falsify common descent, you have to show that the evidence we have for the nested hierarchy is either 1) purely due to chance, and not indicative of an underlying mechanism, or 2) due to some other mechanism. The statistical analysis is crucial, because it answers the first question.

    The answer, as I explained earlier, is one trillion trillion trillion trillionth of a percent. The fact that cytochrome b (or any other gene) yields an incongruent hierarchy is not an issue as long as the totality of the evidence yields a strong signal that is clearly not due to chance. As Theobald explains,

    Genetics and heredity are stochastic (i.e. probabilistic) processes, and consequently we expect that phylogenies constructed with single genes will be partially incongruent. However, including multiple independent genes in a phylogenetic analysis should circumvent this difficulty; in general more than five independent genes are needed to accurately reconstruct a species phylogeny (Wu 1991). Phylogenetic trees constructed with multiple genes should thus be more accurate than those constructed with single genes, and indeed combined gene trees are more congruent (Baldauf et al. 2000; Hedges 1994; Hedges and Poling 1999; Penny et al. 1982).

    As for the other possibility — a mechanism other than undirected evolution that explains the nested hierarchy — I am unaware of any. ID does not qualify, since it does not predict the nested hierarchy.

  192. goodusername,

    goodusername,

    Tell me what part of genetics forbids a feathered monkey. Tell me what part of genetics forbids any of the alleged hybrids that would allegedly foil the theory of evolution.

    Geez Louise if we saw a bunch of jumbled-up organisms we would think that is the norm

    I am still waiting and your avoidance tells me that you have nothing, as I thought. Thanks for your time.

  193. champignon,

    Common descent does not predict a nested hierarchy based on characteristics. Common descent via some gradual mechanism would produce a blend of characteristics indicative of a Venn diagram which allows overlapping- nested hierarchies do not allow overlapping.

    The point is that you don’t know what you are talking about. But that is typical of evos…

  194. C:

    Let me be relatively brief and selective, as I have several other things that require focus today, first working day of the new year here.

    So I clip and comment on points on an exchange just above:

    KF: The issue is not about nested hierarchies or the causes of diabetes, but about the empirically warranted source of functionally specific, complex organisation and associated information, and the linked point that such FSCO/I strongly points to isolated islands of function in configuration spaces.

    C: The issue, as it always does in science, centers on the evidence: What theory does the best job of explaining the evidence? What theory does the best job of making distinct predictions that are confirmed by the evidence?

    When evaluated according to these criteria, intelligent design does poorly and evolutionary theory does extremely well, as demonstrated by the evidence laid out elsewhere in this thread . . .

    1 –> And, what is the best, empirically warranted explanation for FSCO/I? ANS: design, and also the following talking point tactic of trying to turn about the utter want of empirical evidence that blind chance and necessity can account for FSCO/I whilst we see design accounting for FSCO/I all around us, into empty claims about “evolution” vs design, is telling.

    2 –> In short, the evidence has spoken, and what it says is that via whatever mechanisms used — INCLUDING evolutionary ones — design is the best explanation for FSCO/I

    3 –> In addition, for the evidence on the table, FSCO/I, there is but one empirically warranted causal factor known to be adequate to account for it. So, to try to divert form the key point to vague claims about “evolution” is a red herring led away to a strawman.

    4 –> There is also a slippery slope fallacy of ambiguity, on the terms “evolution” and “evidence.”

    5 –> For, evolution covers a very wide range of claims where the one by no means implies the other, and evidence for the one does not entail it being evidence for the other, save to those who have swallowed the evolutionary materialistic a priori error of Lewontin et al. Which is a patent case of worldview level question begging and ideological imposition.

    6 –> For instance, adaptation of body plans within families of animals or the like, is well accepted and empirically warranted, e.g. circumpolar gulls or the red deer or the like. But this is plainly within an island of function. (And BTW, you are out of order to try to pretend that the reason why such islands are reasonable has not been explained or e4gvidenced, starting with the original post that you have yet to respond to cogently.)

    7 –> Indeed, such is not disputed by even the young earth creationists. Though, there may be reason to suggest that particular cases are disputable on at least some aspects; e.g. the pepper moths or the Darwin’s Finches as distinct species claim — given the famous case of the very fertile pair of birds of different “species” observed in the 1980′s, etc.

    8 –> As was highlighted in the OP, once we get beyond that sort of level, we run into a very different problem, as Gould testifies. The predominant pattern of the fossil record and the observed modern world of life, is abrupt appearance, stasis, and disappearance or continuity. At all levels of the tree of life patterns. (Speaking of which, there is no one molecular level tree, so the differing trees stand in mutual conflict. Hence the plural.)

    10 –> In addition, ever since Wallace, the co-founder of modern evolutionary theory, there have been believers in common descent (i.e., evolution) who are design thinkers, and in some cases also Biblical Creationists.

    11 –> Indeed, leading design thinkers such as Behe and I believe Dembski, accept common descent; as do most leading design advocates here, a leading ID blog. So, there can be no proper argument that runs design VS evolution.

    12 –> No, the proper contrast is design thought vs evolutionary materialist naturalism. Where evolutionary materialism is a philosophy and ideology that is as old as the days of Plato [who identified and exposed it in The Laws, Bk X], and which has always been self refuting (and prone to moral hazards linked to its inescapable amorality and radical relativism), never mind its intellectual and scientific pretensions.

    ________

    So, pardon, but your bluff is not particularly impressive.

    GEM of TKI

  195. F/N: A nice summary, by Abel, of some of that evidence that C cannot find, again in the peer reviewed literature.

    Abstract:

    Abstract: Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity—heat agitation and the cause-and-effect determinism of nature’s orderliness—cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.

  196. goodusernam wrote

    he reason for organizing a group of objects into a nested hierarchy/taxonomic tree is because the various characteristics of the individual objects fit a pattern. The only thing I know of that can create that pattern is when there is a descent from a common ancestor, and changes are passed from parent-to-child, and the changes aren’t very large. Other than living things, the only other example of things that I can think of, off the top of my head, that fit this pattern are groups of languages.
    ——————————————————
    Well, wouldn’t the Patterns of Creation fit that also?
    The idea that from one member of a population, materials were taken and used to build another animal but slightly different, or even quite a bit different. As long as the efficiency is worth doing that. The evidence says there is no common descent, but many lines of descent.
    After all, the creator said he did that. Not just DNA but also body materials, that would carry histories of past populations. If this also, was done many times, would there not be a record of at least some lines of descent?. The Patterns of Creation is an answer to that.

    http://patternsofcreation.weebly.com/

  197. 197

    Champignon,

    I’ve answered your questions.

    You have not. If you’ve explained some aspect of a nested hierarchy or the relationship between two or more of its elements using evolutionary theory – genetic variations and natural selection – then please direct me to the post.

    I predicted that you would attempt to change the subject rather than answer my simple, reasonable question.

    That amounts to a concession that you cannot. No one else seems interested in trying, either.

    How many times have I asked this question? Onlookers should question the basis for calling evolution the cornerstone of biology, as well as every single sentence containing the words “evolutionary theory explains.” Apparently it isn’t, and it doesn’t.

  198. Champignon:

    To falsify common descent, you have to show that the evidence we have for the nested hierarchy is either 1) purely due to chance, and not indicative of an underlying mechanism, or 2) due to some other mechanism. The statistical analysis is crucial, because it answers the first question.

    This is incorrect. To falsify a theory, it is sufficient to show that a prediction of the theory is false. The examples I gave do this. This is simple logic, by the way: If A implies B and B is false, then A is false.

    It is a common misperception among many people that you haven’t falsified a theory unless you can give a viable alternative explanation. Scientist often work this way, as Thomas Kuhn pointed out in The Structure of Scientific Revolutions, but nonetheless, an alternative theory is not required for falsification of an existing one.

    I am also aware that the common response in science to a false prediction of a theory is to modify the theory to include the results that contradicted the prediction. However, the very act of modification is an acknowledgment that the theory as originally formulated was false.

    Petrushka: “You have a reference for that?”

    See my post 34.1

  199. Champignon,

    Oh, and by the way, while it is true that ID does not predict a nested hierarchy of species, a nested hierarchy does not contradict it, either.

  200. To falsify a theory, it is sufficient to show that a prediction of the theory is false. The examples I gave do this.

    No, because evolutionary theory does not predict that every gene will produce a perfectly congruent tree. Did you miss that part of the Theobald quote?

    Genetics and heredity are stochastic (i.e. probabilistic) processes, and consequently we expect that phylogenies constructed with single genes will be partially incongruent.

  201. Thanks for the reference. An interesting hybrid.

  202. 202

    Champignon,

    While I’m waiting for an explanation of anything in biology using evolutionary theory, I’ll answer your questions at 33.

    I’m neither defending nor championing ID in this discussion. I’m far more interested in observing the cornerstone of biology playing defense. And make no mistake, it appears in need of some serious defense.

    In how many other hundreds of posts and articles have you seen nested hierarchies proposed as empirical evidence of ID? Why, then, should ID depend on a correlation between them? You are correct in saying that it is compatible with them or with the absence of them. It is not a proposal to explain either. If you think otherwise then you not even begin to understand it. I think that you do understand, but this mischaracterization is the best you can muster.

    Evolution claims to be an explanation of precisely such things. And yet despite repeated inquiries and searches I find that the explanation is not incorrect, but missing altogether. How can the hypothesis that one species descends from another via genetic variations and selections be confirmed or refuted if no one will propose what any of those genetic variations or selections might be?

    Everyone is quick to point out how difficult it is to refute. But this leads us back to where I entered the discussion. It is not a strength, but a weakness. Evolutionary theory is beyond the reach of the scientific method. It proposes mechanisms but offers no specific application of them which can be tested, confirmed, or falsified. If there is a specific application, neither you nor anyone else seems to know what it is. Perhaps it’s in a box in a giant warehouse next to the ark of the covenant.

  203. 203

    From the “Holy crap, I can’t believe they’re actually saying this” category.

    So far, the only specific example of evolution anyone has proposed is speciation by geographical separation, which involves no natural selection, and explains nothing of how the species originate. It tells us that gulls come from gulls which happen to come from gulls.

    This story, involving sharks, tells us what happens next. These species turn around and reproduce together. Who would have imagined it? And as they prove that the previous instance of evolution which separated them is absolutely meaningless, what is it called? To quote, “Evolution in action.”

    Wow. Do you folks want to add that to your list, or shall I add it to mine? It’s tentatively called “Applications of evolutionary theory you find when looking for any containing actual examples of genetic variation and selection, but which omit any mention of natural selection or specific genetic variations, and in some cases explicitly exclude one or the other.” I’ll have to work on the name. (I hate it when people say LOL, but I’m cackling like Dr. Evil.)

  204. champignon,

    Re. 34.1.2.2.5: I would say that an organism (the sea squirt) half of whose genome puts it in one phylum and half in another, falls way outside the bounds of “stochastic variation”.

    But in any case, the tree of life, if valid, is evidence for common descent, not the assertion that random mutation plus natural selection can and did produce the immense variety, complexity, and functional sophistication of all extant and extinct species. That is what my comments, beginning with the quote by KF at the top of the OP, have been addressing, and it is that for which you have not supplied any evidence to counter the large body of evidence (to which I referred in #s 10 & 11.4) that it is totally inadequate for that task.

  205. 205

    Joe,

    Tell me what part of genetics forbids a feathered monkey.

    Nothing, that’s kind of the point.  So why don’t we ever see such animal hybrids?

    The only reason I can think of, is that mutations are random, and speciation occurs via bifurcation producing a tree-like topology to the patterns of characteristics we see.

    In other words, the reason for not expecting to find any feathered-monkeys is the statistical unlikelihood of two unrelated organisms having a huge chunk of dna match, by chance. It’s the same reason for not expecting the same lottery number to come up a hundred times in a row. There’s nothing to prevent it, other than that it’s so statistically unlikely.

    If hybrids like feathered-monkeys occurred, I’d take that to mean that mutations are very non-random (to say the least) and/or there was a lot of “intelligent design” going on.

    Geez Louise if we saw a bunch of jumbled-up organisms we would think that is the norm

    Yes, we would think it the norm. And in that case there would be no taxonomic tree, and any theories of evolution would be nothing like what we currently have.

  206. Bruce,

    Imagine you were reading a book which was perfectly intelligible except for one paragraph that was out of order on each of pages 73 and 129. Would you throw up your hands and say “There’s no book here! It’s just a random jumble of letters?” Of course not. Why? Because, as ID proponents are fond of pointing out, letters don’t randomly form themselves into words that randomly form themselves into sentences and books. A couple of misplaced paragraphs does not change the fact that you’re clearly looking at a book. Calling it a random jumble of letters would be absurd. An actual jumble of letters would look completely different.

    In case it’s not obvious, book = nested hierarchy and misplaced paragraphs = sea squirt data.

  207. 207

    Champignon,

    I don’t believe Bruce is saying that hierarchies fail to demonstrate darwinian evolution because of their anomalies. They fail to demonstrate it even without the anomalies. At best they show common descent, but not the mechanism by which one species descended from another.

    But your example of the book falls short anyway. The examples Bruce cited are not analogous to a book with a garbled paragraph. They are analogous to a book with a paragraph that is somehow garbled and forms a coherent paragraph on a different subject.

    How’s it coming with finding an example that uses evolutionary theory – genetic variation and natural selection (plus whatever, whatever) to explain an instance of evolution? I would stop beating the horse, but you keep trying to ride it.

    Honestly, while that goes unanswered there’s nothing on that front to even talk about. It’s dead. It’s not an untested hypothesis. It’s an unformulated hypothesis. It’s a thought, an idea.

  208. SA: if you got a hammer and a cat’s paw extractor, everything is going to look like a nail . . . KF

  209. Scott,

    I don’t believe Bruce is saying that hierarchies fail to demonstrate darwinian evolution because of their anomalies. They fail to demonstrate it even without the anomalies. At best they show common descent, but not the mechanism by which one species descended from another.

    Darwinian evolution is the only mechanism I know of that actually predicts the nested hierarchy. ID certainly doesn’t, unless you assume that the designer perversely chooses to mimic evolution over and over again.

    But your example of the book falls short anyway. The examples Bruce cited are not analogous to a book with a garbled paragraph.

    I wrote ‘misplaced’, not ‘garbled’.

    They are analogous to a book with a paragraph that is somehow garbled and forms a coherent paragraph on a different subject.

    The book is analogous to the totality of genomic information. The section on sea squirts contains paragraphs that seem to fit better in another part of the book.

    How’s it coming with finding an example that uses evolutionary theory – genetic variation and natural selection (plus whatever, whatever) to explain an instance of evolution?

    Already done, earlier in the thread. How’s it coming with finding ID-based explanations for the phenomena I cited, such as sex ratios and gestational diabetes?

    Oh, wait. That’s right, you’re “neither defending nor championing ID in this discussion.” We wouldn’t want to actually compare ID to evolutionary theory to see how it holds up, would we?

  210. Scott,

    Who would have imagined it? And as they prove that the previous instance of evolution which separated them is absolutely meaningless, what is it called? To quote, “Evolution in action.”

    You may well find this hilarious, but your imagining of ‘an instance of evolution’ is pretty cacklesome too. As speciation is not an instant process, and evolution is simply genetic change, in whatever set of organisms can currently access each other for mating, there is no contradiction whatsoever in calling both the divergence that led to the separate shark lineages, and the apparent re-merging of some of their descendants, ‘evolution’ – that thing we are constantly told, in the face of much contradictory evidence, that “ID is not anti”, at this low level at least.

    Genes flow down the generations and spread around the population, but if a barrier to transverse flow is created, different mutations and stochastic processes on either side will inevitably lead to different genetic changes – evolution – on either side. If this proceeds for long enough – and there is no rule as to how long is ‘long enough’ – then the physical barrier may become redundant, due to an emerging biological barrier. NS has little if anything to do with it.

    ‘True’ speciation can only really occur when two subpopulations have stopped producing compatible gametes, or have developed physical barriers to successful mating. The principal driver of this divergence is differential mutation-fixation processes across the barrier. But apparent species – groups distinguished both by us and by their members as forming separate types – can potentially hybridise – up until the point at which they can’t.

  211. 211

    Chas,

    My point isn’t that some immediate instantaneous speciation is expected. My point is that for all the bluster, these are the examples of evolution that are provided. When members of one species separate geographically and one turns a different color, that’s evolution. When they come back together and breed, that’s evolution – (putting on my David Caruso sunglasses) – in action. Someone interested in why sharks have fins or cartilage or lateral nerves will just have to keep looking.

    I’ve issued this challenge a dozen times, and after a few questions about the question the discussion has fizzled or the subject has changed.

    Evolution is genetic variation (in all of its varied forms) and natural selection. I’m not trying to oversimplify. It also includes whatever else you say it does. HGT, drift, have at it.

    Evolution explains diversity in biology, right? So use evolutionary theory to explain something in biology. In the interest of being reasonable, you pick. But if it’s finch beaks that change and then change back or cichlid fishes in different colors then you’re just trifling. We will then have agreed on evolution as the theory that explains such things, and you may join the growing number of those who have implicitly conceded that it explains nothing more.

    Please do not beg the question. It’s not my place to determine why or whether such variation has limits. This is the cornerstone of biology. It cannot boil down to “why not?”

    Save fossils and nested hierarchies. Evolution is individual genetic variations, however they may accumulate, and selection. These cannot be determined from fossils or hierarchies.

    So, please use evolutionary theory to explain something. As I’ve said every time, there is no reason why this should not be at your fingertips. If you even have to think about it then the alarm should be ringing.

  212. Your question needs clarification.

    Astrophysics and orbital mechanics “explains” how solar systems form, but does not explain why ours is the way it is.

  213. Champignon:

    Darwinian evolution is the only mechanism I know of that actually predicts the nested hierarchy. ID certainly doesn’t, unless you assume that the designer perversely chooses to mimic evolution over and over again.

    Darwinian evolution predicts that the chemically derived trees should match the morphologically derived trees. They don’t. I have supplied abundant evidence of this. The fact that the various trees you get are close to each other compared to a totally random tree is no evidence at all.
    Furthermore, systems that are known to be designed (human technology) do tend to be arranged in trees, if you look at their development over time. Take aircraft, for example. The root of the tree is the Wright Brothers’ flyer, which branched into the early variations on that body plan, which branched into the different types of military aircraft during WWI, which branched into the various types of military and civilian aircraft between the wars, including the introduction of metal skin. Then during WWII there was even more branching including the introduction of jet powered aircraft, and so on. So if ID is true you would expect a hierarchy of development, or at least it would be no surprise. Therefore, the existence of a hierarchy does not support Darwinism over ID or vice versa. However, the fact that chemically derived trees differ from each other and from morphologically derived trees is strong evidence against Darwinism.

    Finally, as ScottAndrews and I keep pointing out, you continue to ignore my point that 1) there is abundant evidence that RM plus NS is incapable of producing macroevolutionary change, which I have cited already, and 2) there is no evidence that RM/NS has ever produced a single macroevlutionary advance.

    The book is analogous to the totality of genomic information. The section on sea squirts contains paragraphs that seem to fit better in another part of the book.

    I beg to differ. The sea squirt is like a book composed of two other books of roughly equal length but of entirely different subject matter interleaved with each other—a paragraph from Principia followed by three paragraphs from Wuthering Heights followed by two from Principia, etc. You are trying to claim that stochastic variation can account for this. I find that ridiculous.

  214. Please do not beg the question. It’s not my place to determine why or whether such variation has limits. This is the cornerstone of biology. It cannot boil down to “why not?”

    Why not?

    The existence/non-existence of barriers is the central point. If I decided that there was an undetectable barrier between here and Mars that humans could not cross, I suspect the onus would be on me to demonstrate it. But no, apparently you have decided that evolution is permitted to diverge one Galapagos finch from another, say, but the same process cannot explain how finches diverged from sparrows. Or maybe it can, but not finches and ostriches. By what heuristic do you draw your sets of explicable and non-explicable sister groups – the beaches of these ‘islands’?

    We are in agreement about the evolutionary process in operation at a branching point – speciation, mediated by reproductive isolation and stochastic processes on either side of the barrier. That same process mediates change within a single lineage – anagenesis. Following branching, two lineages are free to diverge – as far as anyone has been able to determine, without buzzing against the glass of your inferred container. Thus, evolutionary theory explains diversity in biology. It does not explain how lineages transcend imaginary barriers.

    So, please use evolutionary theory to explain something.

    You want something specific?

    To satisfy you, I must give you the series – the genetic series, no less – including the selective advantage of each fixed allele against the rivals that have been irretrievably lost by the very process. I can’t use fossils and I can’t use the signals of common ancestry in the organisms – sequential, protein-structural, karyotypic or morphological – as they are not demonstrative of mechanism (though I’d be interested to know if you agree that they are demonstrative of ancestry).

    I can use evolutionary theory to demonstrate that your demand is not answerable even in principle. The fundamental process of evolution is iterative population sampling. Sampling, as is readily demonstrated mathematically, distorts distributions in the original population. If you no longer have the original population, you have no way of knowing its composition. Those genes are gone.

    If a sample for a clinical trial consisted solely of Chinese women, and someone demanded to know what biases of the selection process led to this, we would need to know what the original population contained. If it was all Chinese women, there was no systematic bias. If it contained a mix of Chinese women and Norwegians of both sexes, the causal factor may actually have been hair colour.
    So your demand (couched in such open-handed “look how reasonable I’m being” terms) is akin to repeatedly determining, for many hundreds of alleles, what the lost populations contained, and what biases, systematic and nonsystematic, were in effect, taking into account lost developmental, environmental and ecological constraints … yes, I’m sure you will self-declare victory on this one and do the Rumpelstiltskin dance. But I do not concede that it explains nothing more than minor change. From iterative minor, we get major – unless a barrier intercedes.

  215. … yes, I’m sure you will self-declare victory on this one and do the Rumpelstiltskin dance.

    Heh. You know Scott very well.

  216. Kindly stick to substance, I will not tolerate veering off into personal abuse. KF

  217. Chas:

    Pardon, but I believe there is something crucial that is being overlooked in your rush to extrapolate from finch beaks to say origin of birds, and beyond.

    Kindly review the statistical basis for the second law of thermodynamics. There is no hard barrier to a macroscopic fluctuation, but the balance of statistical weights of clusters of accessible microstates is such that by overwhelming likelihood, we will never observe a SPONTANEOUS fluctuation on that scale.

    As a second toy example, a needle in the proverbial haystack is quite hard to find on a sampling based search, due to the similar problem of overwhelming statistical weight. Likewise, a million monkeys at keyboards typing at random will be utterly unlikely to produce say a paragraph of coherent text in English. On the scope of atomic resources of the solar system or even the observed cosmos.

    There is not a hard barrier, but simply the balance of overwhelming statistical weight being towards gibberish possibilities.

    The basic problem is then, that once we look at the functional specificity and complexity of the organisation of life systems like the avian lung, or the avian wing and flight mechanisms, etc, as the OP highlights, that very specificity points away from: “any old config” will get us started up the smooth back-slope of Mt Improbable. (That is, GAs and the like START within islands of function, and do not address the material question.)

    This has been pointed out over and over again, with examples from many domains, including life, but the implication, that only fairly restricted and relatively rare zones of possible configs will function in such a system exhibiting FSCO/I, is resisted.

    Not, because it has actually been shown that such FSCO/I has been observed to originate by blind chance and necessity, but that there is an imposed ideological a priori that insists that something like this MUST be so, for it censors “science” to exclude the possibility of intelligent intervention where that is inconvenient for the philosophy of evolutionary materialism.

    That is why, to those who have been primed to think that things MUST have happened that way, any instances of minor variability and diversity in function will seem to justify making grand extrapolations from micro evolution to macro evolution.

    But, absent actual empirical support for FSCO/I arising by blind chance and necessity, the only empirically known source for FSCO/I — with billions of cases in point all around us — is intelligence. The random walk across config space to hit on islands of function analysis is a reason why this makes sense, but it stands apart from the actual fact of observation. Just as, the stat mech analysis as to why macro fluctuations will be unobservable stands apart from the fact of observation summed up in the 2nd Law and related classical conclusions and analyses.

    In short, if you want to assert that macroevolution is a “fact,” that needs to be warranted on observations adequate to the claim. If you want to then conclude — a further step — that [Neo-] Darwinian ans similar mechanisms account for it, that too needs to be separately observationally warranted, and not on extrapolations from micro-evo.

    Or else — hard as it may be for you to accept — we have a case of ideology dressed up in a lab coat.

    Which, plainly (note the five cases in point), is what we are seeing.

    GEM of TKI

  218. GUN:

    Could you kindly give us observational evidence of the tap-root of the Darwinian tree (reconciling the macro-scopic body plan and various molecular trees along the way), its trunk, major branches, and finely grading branching of major body plans and organ systems?

    Or is it that what we in fact observe is much as Gould summed up:

    “The absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution.” [[Stephen Jay Gould (Professor of Geology and Paleontology, Harvard University), 'Is a new and general theory of evolution emerging?' Paleobiology, vol.6(1), January 1980,p. 127.]

    “All paleontologists know that the fossil record contains precious little in the way of intermediate forms; transitions between the major groups are characteristically abrupt.” [[Stephen Jay Gould 'The return of hopeful monsters'. Natural History, vol. LXXXVI(6), June-July 1977, p. 24.]

    “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record:

    The geological record is extremely imperfect and this fact will to a large extent explain why we do not find intermediate varieties, connecting together all the extinct and existing forms of life by the finest graduated steps [[ . . . . ] He who rejects these views on the nature of the geological record will rightly reject my whole theory.[[Cf. Origin, Ch 10, "Summary of the preceding and present Chapters," also see similar remarks in Chs 6 and 9.]

    Darwin’s argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I wish only to point out that it was never “seen” in the rocks.

    Paleontologists have paid an exorbitant price for Darwin’s argument. We fancy ourselves as the only true students of life’s history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study.” [[Stephen Jay Gould 'Evolution's erratic pace'. Natural History, vol. LXXXVI95), May 1977, p.14.] [[HT: Answers.com]

    (Kindly see here for his final summary on the matter, c. 2002, as is clipped in the OP.)

    On fair comment, what we see is not a tree, but a scrubland of bushes, different for different bases of analysis, and pointing to if anything libraries of common designs with adaptations to particular cases, and blending as required, the Platypus and other mosaics — Gould seemed to put Archaeopteryx in that number of oddball organisms — being capital cases in point.

    And, while we are at it, the Csmbrian life revo has the top level variation FIRST.

    GEM of TKI

  219. 219

    Chas,

    You can always turn science on its ear if you creatively redefine the problem. It’s not my problem to explain how the space shuttle can get to Mars. It’s your problem to show what the barrier is. How very convenient.

    The fundamental process of evolution is iterative population sampling.

    It’s not genetic variation and natural selection? When did that change?

    Essentially you’re arguing that my question is unfair. That’s almost reasonable. Except that the answers to such questions are exactly what would exalt evolutionary theory to being the ‘cornerstone of biology.’

    The purpose of science is not to exercise some undue sense of fairness toward a theory that you wish to be true.

    yes, I’m sure you will self-declare victory on this one and do the Rumpelstiltskin dance. But I do not concede that it explains nothing more than minor change.

    Champignon does know me well. As a rational person I would not expect a darwinist’s inability to actually explain any of the things he says that evolutionary theory explains to cause him to re-evaluate his position. Your concession is implicit, not explicit.

    But this talk of barriers is dressed-up question-begging. Of course evolution does all that stuff. It just does! Unless I can show that it doesn’t. It’s Bizarro science.

    I don’t know what a Rumpelstiltskin dance looks like. Maybe I can find something on YouTube.

  220. 220

    More from the sharks:

    This surprising find by a team from the University of Queensland has experts speculating that the hybridization may be the result of climate change, which theoretically forced the predators to interbreed in order to better adapt to rising water temperatures.

    How exactly does a shark know that breeding with another species will help its offspring survive rising water temperatures?

    Evolutionary theory posits a constant search of the surrounding space, and differential reproduction when the search yields organism with some advantage or other unspecified reason for reproducing differentially.

    So wouldn’t evolutionary theory predict that the sharks would always interbreed, and that at some point the environmental change might render it beneficial?

    What does this mean for the speciations which would certainly be held as examples of evolution in action when they occurred? It sure looks more like sharks breeding with nearer sharks until they look different from more distant sharks and then breeding with the more distant sharks anyway. That’s rather thin gruel.

    Let me sell you my new space-age transport vehicle. It can take you anywhere on earth. It looks just like a sofa. Allow me to demonstrate by sliding it and its occupants around my living room and back to where they started. It’s your job to explain the barriers that keep it from going to the South Pole, but don’t worry, I can be very creative.

    The hybrid sharks were also found to be stronger than either of the parent species — “a literal survival of the fittest.”

    I’m stronger than either of my parents ever were. Is that survival of the fittest? It’s easy to boggle over the surreal oddity of such a statement and forget to wonder how they determined that the offspring were stronger than the parents. Because at this point anything they say is suspect.

    Simpfendorfer said the study, published late last month in Conservation Genetics, could challenge traditional ideas of how sharks had and were continuing to evolve.

    “We thought we understood how species of sharks have separated, but what this is telling us is that in reality we probably don’t fully understand the mechanisms that keep species of shark separate,” he said.

    Let me get this straight: Folks have been citing speciation such as this as examples of the cornerstone of biology at work, but the boots on the ground say they don’t really know how it works?

    I’m not surprised. And I don’t expect a darwinist to even blink at being told that no one actually understands even the weak examples of speciation they use to prop up their so-called theory. Because its position as the cornerstone of biology never depended on evidence or even making sense in the first place.

  221. Champ:

    I have a moment, so I will add.

    Kindly note that you are not just dealing with populations, but samples that give cross sections thereof.

    In this case, we notoriously have in excess of 1/4 million fossil “species,” representing millions of samples in museums, and literally billions known from the field. (E.g. My second Caribbean homeland, Barbados, is largely built on piled up coral limestone fossils; in aggregate, literally cubic miles of them.)

    Those millions of fossils in museums came from the entire depth of the fossil record, and across the whole world, after 150 years of careful and thorough investigation.

    There is no reasonable doubt that they give us a significantly representative cross section of the main outline of the patterns of life as preserved, from micro-organisms to whales and dinosaurs, with plants, birds, shark teeth etc etc etc along the way. Even, footprints.

    And, those are the fossils in aggregate that Gould has summed up: sudden appearance, stasis, disappearance [and/or continuity to the modern world]. Islands, in short. Or, if you will, a forest of little bushes.

    If the pattern of life genuinely had been gradual transitions as populations were supplanted by incrementally superior ones, we would find instead a record DOMINATED by gradual change, with incremental continuity from ancestral forms of body plans to descendants.

    That is not what we find, and so the challenge to those who hold that Darwinian and similar mechanisms explain the record, why do we see what wee see and not what we would expect to see.

    Common descent is irrelevant, there are many ways to get to that without invoking blind chance and mechanical necessity acting through chance variation and culling out of less successful populations as the sole responsible mechanism.

    What is needed is something that explains a pattern DOMINATED by suddenness and stasis.

    And, by a pattern where as we look across the domains of life we find that molecular taxonomic trees are not singing off the same hymn sheet as the traditional Darwinian Tree of Life, and indeed, they are not in mutual agreement.

    If there had been a sound, solid, well documented answer that pivots on straightforward observations, that would long since have been trumpeted. That instead we see the sort of duck, dodge and divert — then denigrate and demonise — tactics, year after year here at UD and elsewhere, speaks volumes on the actual state of the evidence.

    The evidence is, from protein fold domains to body plans to species in the fossil record and today, that life is dominated by islands with common body plans that also can adapt, often within a more or less standard pattern of adaptations (I have in mind here the astonishingly standardised body shapes and colours of the cichlids).

    That is multiplied by the Cambrian life revolution that was known in Darwin’s day and which he hoped further investigations would remove.

    What instead has happened, is that we see that the variation at the very top level of classification comes first. And, on the conventional timeline, suddenly.

    So, we have no good reason on the evidence, to see life forms as significantly exceptional to the known pattern that where we have a function based on multiple, well matched parts that work together, only a relatively few configurations out of the vast field of possibilities, will work.

    In short, islands of function.

    Mocking Sir Fred Hoyle that his challenge on a tornado building a jumbo jet in a junkyard is a “fallacy” is almost irrelevant. The problem starts with building say an indicating, D’Arsonval Galvanometer movement instrument on the panel of the cockpit by the same means. (This is not so remote, the flagellum, ATP synthase and the Kinesin walking truck are all motor movements, just to start at molecular nanotech level. I again invite you and onlookers to explore Abel’s latest paper on these sorts of things.)

    Talking points can be amassed to distract from it or bury it under a pile of fundamentally specious objections, but, in the end, when we get back tot the actual observed evidence, there it is.

    So, we must ask: what best explains FSCO/I and associated islands of function?

    Observation and analysis unbiased by a priori materialism both reply: design.

    So, if you wish to overturn this, you need to provide solid, straightforward evidence.

    Given what has happened here at UD for years now, you will understand why I will not hold my breath waiting.

    But, I will invite the interested onlooker to have a look from here on.

    GEM of TKI

  222. Chas: The fundamental process of evolution is iterative population sampling.

    Scott: It’s not genetic variation and natural selection? When did that change?

    Sometime in the mid 1960′s. With the use of stochastic, rather than deterministic, representations of the process, and subsequently with coalescence theory. NS continues to be important, but it is simply systematic bias within a more general sampling process.

    If you have any sample-and-replacement process, the genetic composition of a variant population will change, inexorably, towards fixation of one or other of the variants. Selection does not have to be involved. Try it – it’s dead easy to program, or to represent with coloured beads. This is neutral drift. If you have weak preference for one allele over another – a systematic bias – the favoured allele will be fixed more often, but the unfavoured allele can still get there an appreciable proportion of trials, thanks to drift. Turn up the differential still further, and the number of times the favoured allele wins increases.

    We may represent an ‘allele’s progress’ as commencing with a mutation and terminating with extinction or fixation. Fixation means that every locus instance in the future population descends from that original mutated sequence. Extinction means that *no* sequence descends from it.

    Suppose we could capture a 2D map of the population, with our locus of interest coloured blue. A mutation occurs – one red dot. If we capture successive images and stack them, we get a 3D representation in time. Most of the time the red may sputter for a generation or two and then be eliminated. But occasionally – one in every N mutations where N is the number of loci – a mutation will sweep to fixation. In our 3D cylinder of successive population snapshots we would see a cone of red with the mutation at its apex and fixation at its base. Fixation for one is extinction for all else.

    This is the fundamental process of evolution – a stochastic mutation-amplification/dilution process. Selection – a systematic bias in favour of a particular allele – increases both the chances that a particular mutation will fix, and steepens the slope of the descendant cone – it fixes more quickly. Selection stacks the deck. It has a dual role of dismissing poor mutations before they get anywhere, and promoting favourable ones depending on the extent to which they increase reproductive output.

    Mutation, selection and drift give rise to variant populations. Ongoing sampling amplifies or dilutes each variant. Every allele that becomes fixed means inevitable loss of something from the ancestral population’s character.

    Now, what is important about this way of looking at it is that stasis is highly improbable, and divergence of isolated lines almost inevitable. Mutation demonstrably occurs all the time. Sampling demonstrably occurs all the time – generations are not exact replicas of the composition of their parental generation.

    So, this process can drive change within a single lineage. Since there is constant loss of ‘old’ alleles and input of new ones, change is inevitable. Because mutation and fixation are stochastic, the changes in two parallel lineages are independent. Hence: divergence. Between close relatives initially, but ongoing divergence makes them less and less close. Unless … well, what?

    As a rational person I would not expect a darwinist’s inability to actually explain any of the things he says that evolutionary theory explains to cause him to re-evaluate his position. Your concession is implicit, not explicit.

    Oh, do me a favour! I explicitly deny a concession, but I’m still conceding? As I try to explain above, the evolutionary process – which you accept to occur in a ‘local’ fashion – is always dependent upon what the current population holds. As the ‘current population’ is in constant, irreversible flux, it is entirely unclear why I should concede that long-term change – including species divergence leading through higher taxonomic levels – should not flow inevitably from these lower-level fluxes. Grant me some intellectual honesty! As a rational person, if I could be shown that these micro-processes were insufficient to explain macro change, I would be happy to concede.

    But this talk of barriers is dressed-up question-begging. Of course evolution does all that stuff. It just does! Unless I can show that it doesn’t. It’s Bizarro science.

    Show me a science that does no extrapolation. Some extrapolations are unreasonable, and may be argued against. What, beyond gut feeling, precludes this extrapolation?

  223. I don’t think the reportage of this was particularly good, and some of the statements attributed to the scientists seem a little inaccurate wrt evolutionary theory. There is no teleology in evolution; nothing is ‘forced’ to do anything.

    It is frequently the case that hybrids are more ‘vigorous’ than either parent, but this effect cannot last indefinitely – it is a consequence of diploidy that will be lost if the hybrid population continues to interbreed without further input from the parental species.

    I’m stronger than either of my parents ever were. Is that survival of the fittest?

    It means ‘survival of the best fitted’, going back to Spenser. The connotations with physical fitness are an unfortunate source of confusion. Fitness means reproductive output, in biology – if one variant produces an average 2.1 offspring, and another an average 1.8, the first is ‘fitter’.

  224. K/F,

    The basic evolutionary process (detailed in my reply to Scott below) makes no particular statement about complexity. It is about change which, in your ‘search space’, equates to the accessibility of a viable point in that space from one’s current location.

    For an evolutionary process, we have to allow that a population currently exists on a viable location in search space. How it got there, set aside. Without mutation, we will sit forever at our current coordinates. With mutation, we can only change to a coordinate that is also a viable location. Do we observe that? All the time.

    The result of the allele fixation process is that, wrt a particular allele, the population starts at one coordinate and, one by one, moves to a new one. Once the whole population is at the new coordinate, its position at the old coordinate is history. Back-mutation can occur, but it is far more likely that either a new mutation, or no mutation, occurs.

    Now, as far as exploration is concerned, we have successfully moved from one viable position on the map to another. How many viable positions are there, and how are they distributed? We don’t know. The space is shrouded in total darkness. All we know is that we can move from place to place – mutations occur, they do become fixed, and our old position is lost and highly unlikely to be recolonised. Exploration does not appear to be constrained on a broad scale, even if not all possiblilities are viable locally, and specific alleles may suffer specific additional restraint. But we are talking about generality and totality – the possibility that all alleles in an ancient species were historically prevented from entering the domain we currently see occupied by another.

    Someone tells us that we are simply exploring an island – that inviable moves were inviable because they fell into the sea. Someone else tells us that the space is a honeycomb – each inviable move simply hit the empty space in a filagree of interconnectedness.

    How to tell? Assertion of islands is insufficient. I do not assert a honeycomb – I simply point out that we observe stepwise change; every current position is surrounded by accessible new positions that become the new current position, with an arrow to this motion away from the old point provided by old-allele extinction, and no clear anchor promoting one particular way of doing things.

    So, we must ask: what best explains FSCO/I and associated islands of function?

    Observation and analysis unbiased by a priori materialism both reply: design.

    Biased instead by a priori notions of extra power in Creators? The designs of which we are capable pale into insignificance beside the apparent designs in Nature. On the one hand you argue that the only way to produce such complexity is Intelligence, yet that quality is manifestly not up to the task you set it, in any instances we can access by observation and analysis.

  225. 225

    Chas,

    For an evolutionary process, we have to allow that a population currently exists on a viable location in search space. How it got there, set aside.

    If you wish to redefine evolution as how existing species vary and not how they “got there” in the first place, great. I think you’ve just joined the other team.

    Otherwise you’re ‘setting aside’ the really hard part and focusing on what was plain to the naked eye for thousands of years before Darwin.

    Biased instead by a priori notions of extra power in Creators? The designs of which we are capable pale into insignificance beside the apparent designs in Nature.

    So “it’s too complicated, it couldn’t have evolved” is bad, but “it’s too complicated, it couldn’t have been designed” is okay. If something appears to be designed but it’s very, very complicated, then the design must be illusion and it must have evolved, because… why?

    The evidence of design doesn’t go away. It just leads to more questions. Who, what, how, why? Is that a sound reason for setting aside? What precisely have we seen from evolution that makes it the default explanation for complex systems of unknown origin? (That’s semi-rhetorical. It’s been conceded that the answer is approximately nothing, so why beat a dead horse?)

  226. 226

    So fitness doesn’t lead to increased reproduction, it is increased reproduction. Why use the word at all, since as you pointed out it gives the misleading impression that it’s not just differential reproduction? And what does “survival” mean in this context? Everything survives, but those that reproduce more are fitter. So the fittest does not survive, rather, everything that doesn’t go extinct survives.

    If you go by the common understanding of the words it’s tautological. If you go by the technical meaning, it’s not saying anything anyway. Explain to me why we need evolutionary theory to invent multiple terms for an observed phenomenon? Apparently it’s so that we can pretend that the use of the terms explains something when in fact they are nothing but interchangeable definitions. Making up a new word for something or recycling an existing word with a new meaning doesn’t explain anything. It’s just moving furniture around.

  227. 227

    I’ll reduce this for simplicity.
    Fitness is relative – it is differential reproduction. That which reproduces more is more fit than that which reproduces less. (Sorry, but the use of that word seems deliberately misleading.)

    Survival is defined as a rate of reproduction greater than zero. If one shark reproduces more (is more fit) than another, to call it survival of the fittest is meaningless because the less fit also survives.

    Extinction is a reproductive rate of zero (assuming that the existing specimens are not immortal.) Everything that does not go extinct survives.

    So all that matters is reproduction. Fitness, survival, and extinction all describe or quantify it.

    Survival of the fittest is actually more of a tautology than it was before. The fittest survive. The fittest reproduce. The survivors reproduce. The reproducers survive. The fittest survivors survive, and so do the less fit survivors with the exception of those that don’t survive.

    In all of this there are but two concrete observations: that things reproduce, and that some reproduce more or less than others.

    At best this leads to an exploration of why some reproduce more or less than others. But where the things that reproduce come from? You can’t get there from here.

    (Okay, that wasn’t exactly a reduction.)

  228. 228

    Sometime in the mid 1960?s. With the use of stochastic, rather than deterministic, representations of the process, and subsequently with coalescence theory. NS continues to be important, but it is simply systematic bias within a more general sampling process.

    Evolution is not sampling. That did not change in the 1960s. Evolution is genetic variations and selection.

    It should be obvious that you cannot examine the process of evolution using samples. How do you observe selection? It’s impossible, unless you tautologically assume that it was selected because it’s there.

    No selection, no evolution. How does evolution explain anything if you take away natural selection?

    Oh, do me a favour! I explicitly deny a concession, but I’m still conceding?

    Yes, that’s it.

    As the ‘current population’ is in constant, irreversible flux, it is entirely unclear why I should concede that long-term change – including species divergence leading through higher taxonomic levels – should not flow inevitably from these lower-level fluxes.

    You’re free to think that “lower level fluxes” lead to taxonomic diversity. You don’t have to concede it that it isn’t true.

    But while reaffirming your opinion, you are implicitly conceding that it is unsupported by empirical evidence. (You do that by not supporting it with empirical evidence.)

    In other words, you’re telling me what you think. Thanks, but I already knew that many posts ago. But so far the only reasons you’ve given me to share your opinion are “why not?” and it’s ‘inevitable.’

    Okay, so we’ll upgrade it from your opinion to your strongly-held opinion. And we’ll leave it there unless you can come up with something more persuasive than just reasserting it.

  229. So fitness doesn’t lead to increased reproduction, it is increased reproduction. Why use the word at all, since as you pointed out it gives the misleading impression that it’s not just differential reproduction?

    Sorry, but I’m not an apoologist for 19th-century semantics. Spenser said “best fitted”; Darwin rephrased. Take it up with them! I’m not sure whether physical fitness was even a usage back then. To further muddy the waters, a ‘fit’ male or female in my neck of the woods is an attractive one. Yawn. One can play semantic games, or one can attempt to understand what people are trying to convey.

    If you go by the common understanding of the words it’s tautological.

    Meh. It isn’t, but even if it was: so what? Unless tautologous means “wrong”. 1 + 1 = 2 is a tautology.

    Explain to me why we need evolutionary theory to invent multiple terms for an observed phenomenon?

    Yessir Scott sir rightaway sir! :0) We can either invent new words and confuse everyone – including ourselves – in a morass of geschmaltimpenetechnibabble. Or we can add a meaning to an existing word and spend hours on the internet arguing with people about the other uses of the word. Either approach has its pros and cons.

    The central point of ‘fitness’ (mean reproductive output of types) is that, if you have a finite population of variant replicators, and a consistent differential between them in the average number of times each gets copied, then they each have a different exponent – a different inherent rate of increase. Increase is capped, both by the overall limit, and by the presence of the other potentially increasing element. So if you have such a capped ‘contest’ between two replicators potentially increasing at different rates, which will win? The one with the greater average number of offspring? You are correct! Is that tautologous? Kinda – if you say “the one that increases at the greater rate will increase at the greater rate”. It is also kinda true.

    (And bear in mind that we are not talking about individual sharks, but about individual ‘types’ of shark within a population. Any one shark, regardless of how genetically equipped, can produce none, one, two, three … selection (or its absence) refers to the effect of average reproductive differentials during multiple lives of the two types – bearers of variant alleles at the same locus.)

  230. 230

    Chas,

    You misunderstand me. I don’t have a problem with any of the terms. It’s that they are just varied ways of describing the observation that some things reproduce more or less than others, or more or less than they used to.

    That’s fine. But put together all of them tell us what we already know. They describe what we see. They tell us nothing at all of how or why it is the way it is.

    If I ask you why I used to have five oranges but now I have four, you can respond that it’s because my number of oranges has decreased by one. You can invent numerous new terms to elaborate on this. But you’re still just telling me what I already knew.

    Same here. All these terms restate the obvious. Evolution is supposed to be a theory of why and how, not restating the obvious. It’s tautological and it’s accurate. But what does it tell us?

  231. 231

    Let’s add a real-world example.

    I used to see more gulls with grey wings. Now I see more gulls with black wings. Evolutionary theory, please tell me why?

    Well, it’s because the gulls with black wings reproduced more than the ones with grey wings. There are more of them now. We could also say that the ones with black wings are fitter. They survived more.

    Gee, thanks. That really clears things up. Thanks for restating the observation in a manner that adds no explanation whatsoever.

  232. A tornado formed south of town. There were no tornados north of town. Meteorology, please tell me why?

    Well, the conditions were right for tornados south of town. North of town, not so much.

    Gee, thanks. That really clears things up.

    I guess meterology is a tautology, just like evolutionary theory.

  233. Evolution is not sampling. That did not change in the 1960s. Evolution is genetic variations and selection.

    No, it isn’t. It isn’t sampling either: I specifically said that sampling is the fundamental process of evolution, not that sampling is evolution.

    Evolution is descent with modification. Or, as Wikipedia has it:

    “Evolution is any change across successive generations in the heritable characteristics of biological populations.” (my emphasis).

    Variation is necessary (otherwise there is nothing to change) but selection is not. The central cause of allele frequency change (leading inexorably to fixation for one variant or another) is iterative sampling, with (Selection + Drift) or without (Drift alone) a bias for or against a particular allele.

    See the neutral theory of Kimura, first published in 1968, and now almost universally accepted by evolutionary theorists as the background process against which “Darwinian” selection occurs when there is a differential.

    There is not much point grumbling about those pesky evolutionists failing to address your misapprehensions about their area of expertise. “RM + NS” is NOT the totality of causes of evolution. The missing bit – chance – drives diversity, even where NS is absent.

    You’re free to think that “lower level fluxes” lead to taxonomic diversity.

    Why, thanks! But what would persuade me to think otherwise? That is, mutation does occur; population sampling fixes alleles in multiple demonstrations mathematical, computational and empirical both in the lab and in the wild. You agree they lead to diversity between related species. So what is it that requires specific empirical support, beyond what we can gain from the available living organisms? Evolution of a new genus? How very convenient! Something that requires a million years’ worth of data – that is what I want to see demonstrated. Till then, evolution is just shallow “ideology in a lab coat”, all the above notwithstanding. Evolutionary theory explains everything you can’t deny with a straight face.

    But while reaffirming your opinion, you are implicitly conceding that it is unsupported by empirical evidence. (You do that by not supporting it with empirical evidence.)

    In other words, you’re telling me what you think. Thanks, but I already knew that many posts ago. But so far the only reasons you’ve given me to share your opinion are “why not?” and it’s ‘inevitable.’

    I don’t kid myself that you are looking for reasons to share my opinion!

    Nonetheless, it (iterative mutation-fixation with or without selection) is demonstrably inevitable! It falls out from observable processes, and can be analysed probabilistically to demonstrate that alternatives (indefinite birth-death in a finite population that does not lead to fixation) are vanishingly improbable.

  234. 234

    Champignon,

    This is really coming into focus now. Do you actually think that meteorology is the practice of observing any weather phenomenon and stating that the conditions were right for it?

    Clearly your expectations of science are very, very low, which is why evolutionary theory impresses you.

  235. Why does a loudspeaker produce lots of noise when you point the mic at it?

    Maybe it has something to do with the noise the loudspeaker is making – the more noise it makes, the louder it gets!

    An explanation of a feedback loop can sound like a tautology but it isn’t. Differential survival based on heritable traits and random variation involves feedback loops.

    I used to see more gulls with grey wings. Now I see more gulls with black wings. Intelligent Design theory, please tell me why?

  236. 236

    No, it isn’t. It isn’t sampling either: I specifically said that sampling is the fundamental process of evolution, not that sampling is evolution.

    Sampling is not “the fundamental process of evolution.” Variation and selection are. You’re not making any sense.

    That is, mutation does occur; population sampling fixes alleles in multiple demonstrations mathematical, computational and empirical both in the lab and in the wild. You agree they lead to diversity between related species. So what is it that requires specific empirical support, beyond what we can gain from the available living organisms? Evolution of a new genus? How very convenient! Something that requires a million years’ worth of data – that is what I want to see demonstrated.

    You can sample all you want, and document as many variations as you want. Evolution is variation and selection. Even if we assumed that the process is made of individual variations, are we also to assume the selection part? What part of the process is left that we are not assuming?

    Evolution is variation and selection. You cannot say that variations were selected without identifying variations and selections.

    I agree that millions of years of carefully documented observations is an unreasonable expectation. If you wish to confirm your opinions with empirical evidence you’ll have to find another way. In what other field of science do we give a theory credit for accuracy because it’s just too darned hard to gather the data? Isn’t that what you’re asking me to do?

    Nonetheless, it (iterative mutation-fixation with or without selection) is demonstrably inevitable!

    That appears to be the case, as demonstrated by species of sharks that vary, separate, and then mix back together again. The evidence you have is the evidence you have.

    Evolutionary theory explains everything you can’t deny with a straight face.

    And yet I’ve asked repeatedly for it to explain something, which I believe is a subset of everything. No reply. That is your implicit concession. Now I have to go find that dance on YouTube.

  237. Scott,

    I guess the problem is that evolution really does boil down to a set of statements of the obvious. But that’s how many explanations work – IF there is differential reproduction in a variant population, THEN blah de blah de blah. Whether these apparently axiomatic phenomena occur in reality needs to be investigated, of course. They weren’t all that obvious, once, and they remain non-obvious to a lot of people now. But we are stuck with the materials we are stuck with. Living and recently-dead DNA is all the DNA we have to work with. As far as population dynamics are concerned, living populations are all we can look at. So then we get out our slide rules and our computer models, our logical argumentation toolkit and so on. And that’s where the fun starts! :0)

  238. 238

    Exactly. That brings us back to the search for answers that are not obvious, such as where all these cool plants and animals came from, as well as ourselves. Apparently we need to keep looking.

  239. 239

    GCUGreyArea,

    You’re holding up something very simple and suggesting that it can demonstrate something very complex. That’s just another way of begging the question, restating the assertion that the evolution of biological diversity is as simple as feedback from a mic and speakers. It isn’t. So what good is the illustration?

    used to see more gulls with grey wings. Now I see more gulls with black wings. Intelligent Design theory, please tell me why?

    If I were you I’d also want to change the subject. As I told Elizabeth, that question makes as much sense as “When did you stop beating your wife?” What do you think you accomplish by formulating an illogical question that includes the term “ID?”

  240. GCUGA:

    Barkhausen criterion feedback oscillations on phase shifts and gains around a loop are not after the fact tautologies. They explain on dynamics at work, which may be observed and measured, indeed gain and loop margin are important issues in system design.

    To define fitness on differential reproduction easily falls into a tautologous loop. Yes there are ways to avert that, but it is important to identify what is going on, how.

    So far as I can see, the key point is that non foresighted chance variations are where any possibility of info gets injected into a pop. Then, in partial dependence on environmental opportunities and threats — there are a lot of random variable effects at work here too — we have culling out of the less well matched and/or the unlucky.

    The net pop drifts or is stuck back at starting point, depending.

    But, the selection filter has not solved the problem of origin of complex, functionally specific organisation and linked info. It does not have anything material to say to that subject.

    WE ARE BACK AT THE KEY ID POINT: FSCO/I IS PER OBSERVATION AND ANALYSIS LIKELY TO COME AS ISLANDS THAT ARE DEEPLY ISOLATED IN THE FIELD OF POSSIBILITIES, AND THE BEST, EMPIRICALLY WARRANTED CAUSAL EXPLANATION FOR SUCH IS DESIGN.

    GEM of TKI

  241. Scott,

    Do you actually think that meteorology is the practice of observing any weather phenomenon and stating that the conditions were right for it?

    Of course not. That would be a grotesque misrepresentation of the field. Meteorologists aren’t stupid enough to overlook such obvious tautological reasoning.

    On the other hand, 99+ percent of biologists are stupid enough to overlook that, according to you. Why are biologists so much stupider than meteorologists? Who knows? I guess the designer made them that way.

  242. Barkhausen criterion feedback oscillations on phase shifts and gains around a loop are not after the fact tautologies.

    Spewing long words does not impress me.

    That inherited traits which increase reproductive frequency lead to an increase in the frequency of those traits within successive populations is a feedback system, not a tautology. It is also something that is observed, and is modeled and studied by real scientists in a genuine attempt to understand it.

    But, the selection filter has not solved the problem of origin of complex, functionally specific organisation and linked info. It does not have anything material to say to that subject.

    Well that is barely comprehensible, but I’ll try … The observation that placing a mic near a speaker causes a feedback loop whereby sound volume causes an increase in sound volume does not explain where the microphone came from. That does not mean that the feedback loop does not exist, or that an explanation of its dynamics is wrong.

    If you want to discuss the origin of life then please start a new thread to discuss it, don’t try and hijack this one, which is about evolution.

  243. 243

    Champignon,

    Of course not. That would be a grotesque misrepresentation of the field. Meteorologists aren’t stupid enough to overlook such obvious tautological reasoning.

    I’m sorry, that was your illustration. Don’t blame me because it doesn’t fit.

    Have I not practically begged for an example of an evolutionary explanation deeper than ‘something varied and it was evidently beneficial because it was evidently selected, times 10,000?’ Faced with that vacuum, you’d rather throw stones at the messenger. I’d be more interested in getting my biology tuition back.

    This is not Dentyne. It doesn’t matter if 99 of 100 biologists recommend it. Why do you think the term “group think” was invented, or the story of the Emperor’s New Clothes? Do you have any idea how many times I’ve read a biologist saying that his particular field is problematic for evolution, or that something he’s found may change our way of thinking? But they all the think the other 99% know something they don’t and they’re afraid of getting laughed at or fired.

  244. 244

    That inherited traits which increase reproductive frequency lead to an increase in the frequency of those traits within successive populations is a feedback system, not a tautology. It is also something that is observed, and is modeled and studied by real scientists in a genuine attempt to understand it.

    What is observed and modeled is not a tautology. There are solid reasons why a population of grey-winged herring gulls may geographically separate into a newer population with black wings. Natural selection may explain why finch beaks and change back.

    Picking up a fossil or even a living organism and asserting that its present state is evidently the result of iterations and natural selection simply because it exists is quite circular.

    No one should be fooled by this sleight of hand. The behaviors of variation observed and modeled by biologists aren’t even close to representative of the behaviors they attribute to it.

    As seen in previous comments, the evidence that the same processes which alter finch beaks also produce finches and beaks amounts, in its entirety, to ‘Why not? Prove that it doesn’t. Of course it does. Don’t you see it?’

    That’s really it. The cornerstone of biology is styrofoam laminated with formica.

  245. 245

    BTW, as soon as you get a feedback system that grows a membrane, flagellum, light-sensitive spots, an immune system, echolocation, or develops nuclear weapons to keep itself from being interrupted and plays the guitar for fun during downtime, then we can talk about feedback systems.

    It’s question-begging. You’re taking a simple observed process like a feedback system and asserting, with no evidence, that the vast diversity of life is no different. It’s exactly the same fallacy as looking at changing finch beaks and asserting, with no evidence, that the vast diversity of life is no different. When push comes to shove the mountain of evidence balances on, ‘Why wouldn’t it be the same? It makes perfect sense to me that it should be the same.’ Fine. Fill us in when you get somewhere with that.

  246. GCU:

    I am sorry, but you just went into a bit of an exercise in unintended irony.

    First, I think you should look again at just who started the thread and the focus I set in so doing: the issue of islands vs continents of complex, specific function and the related question of arriving at shores of such zones of function. (It is right there in the title of the thread . . . ;-) )

    Which relates to the difference between adapting a body plan and getting to one, i.e. to both OOL and Macro vs micro evo.

    Calling a thread back to reflecting on that is not hijacking it, FYI.

    Next, the criterion that makes an amp go into feedback oscillations is the Barkhausen criterion, which acts exactly as I described. That is, in raising “feedback” in the context of loudspeaker howls, you are speaking to a very specific issue. I am taking you up, and am not merely spewing forth obnoxious substances or sounds as you seem to irritably assume. (Please, stop listening to and enabling the sort of venom spat out by those who set up hate sites and can only resort to abuse. Discussing the Barkhausen criterion — which happens to be a specific point of knowledge in systems — is not at all to be confused with vomiting or the like.)

    Namely, assuming a phase inversion already in the amp:

    B*A = -1, in phase and amplitude

    [we are by implication dealing with complex numbers here, and to get oscillations the fed back signal must reinforce the original excitation in amplitude and phase; inversion of a sinusoid being a pi radian/180 degree phase shift; frequency-sensitive phase shifts coming from the action of components that cause lags and/or storage of energy acting with dissipative components],

    B being the feedback fraction, and A the forward path gain.

    Consequently where oscillations are undesirable, one watches the margins to reach there.

    You raised the idea of oscillatory feedback in a previous comment, and I responded to it. In responding, I pointed out that the reason that the Barkhausen approach is not tautologous, is that there are specific dynamics and processes at work.

    In other words, I AGREED WITH YOU THAT FAR.

    I then raised the issue of the dynamics at work in:

    CHANCE VARIATION + NATURAL SELECTION –> DESCENT WITH MODIFICATION, AKA EVOLUTION

    I noted that the culling out part SUBTRACTS varieties from the pop, i.e. it removes and does not add info.

    That points straight back to the chance variations as the supposed means of gaining info, there is nowhere else to go; however things may find to vary by chance — Mr MacNeill’s list was nearly 50 items long, the variation is uncorrelated with the function and non foresighted. Which leads right back to the problem of FSCO/I, i.e arriving at shores of function on a random walk, rather than to adapting already functioning body plans, including of course in the end the first body plan. In both cases, on the evidence of DNA complement, we are well past the thresholds of required fresh info to credibly come from chance based variations, 500 – 1,000 bits.

    That is, a major missing dynamic is highlighted: there is no credible engine of biofunctional info, for novel body plans etc, starting with the very first one, but also extending to the major plans and to specialisations, such as the one way flow bird lung as discussed above in-thread, the avian wing and control system, sonar systems in bats and whales, the eye — said to have evolved 40 distinct times — and more.

    So, my point is that I understand and use feedback in oscillator design and in preventing undesired oscillations. There is a specific dynamic, a how-why chain of influence at work, so we are not just saying the same thing in different words.

    By contrast, once we correctly explain the NS part, i5t drops out of addressing he question of where the required FSCO/I comes from, as it is a subtractor, not an adder of information.

    So, we are right back at needing to explain how a random walk can reasonably find shorelines of function that are deeply isolated in vast config spaces, for first cell based life and for major body plans and special organs. For, complex function is critically dependent on the C1 – 5 factors described at point 6 in the OP, i.e specific matching, proper alignment at the required time, no missing parts, etc. And, recall, something like ATP synthase, or kinesin or the flagellum are motors so this is not mere analogy. A bird lung or a bird wing depend crucially on multipart integration, and so forth.

    (And BTW, the criterion of additionality, where reproductive replication is critically dependent on stored code driven self replication in cells, means that we are ADDING complexity to be explained, not getting rid of it.)

    There is but one observationally, empirically grounded causal explanation for such FSCO/I, design.

    GEM of TKI

  247. F/N: The astute onlooker will observe how, after a full week, 3,000+ visits and 246 comments to date, darwinist objectors simply have not been able to show on observation and analysis that:

    (i) in general, complex, specific multi-part function can be had without requiring sharp constraint to a narrow zone T in the space of possible configs W, or else

    (ii) life forms are a major class of exception such that one may “easily” access the first life form in Darwin’s warm little electrified pond of chemicals and/or the equivalent or having somehow got to the first living cell, gradually and incrementally adapt it to form the panoply of diverse body plans in the fossil record and the world around us.

    In short, we have every epistemic right to infer that the naturally expected, well observed pattern whereby multi-part, specific and complex functions sharply confine the set of acceptable configs from the set of possible configs, holds in the pre-biotic and biological realms also.

    In particular, we should observe how both the root and the incremental, gradualistic trunk and branching patterns of the Darwinian tree of life are consistently conjectural rather than observed. In short, what we have evidence of is that body plans appear, and may be adapted, but we have no good reason on empirical warrant, to infer from observation, that this traces to a process of gradualistic, incremental development from one or a few original forms; driven by chance-driven variation of existing forms and culling out of less successful variants by differential reproductive success in environmental niches leading to descent with modifications all the way up to body-plan level branching.

    Instead, we have the observational and analytical grounds to see that once we require multi-part complex and specific function, the best empirically warranted causal explanation is design. Which is of course the core design inference.

    So, we may find it useful to now ponder Rabbi Moshe Averick’s remarks:

    The entire plot of the classic film, 2001: A Space Odyssey is based on . . . [an] obvious principle. At a dramatic moment in the film, when a rectangular monolith is discovered buried on the moon, it is clear to those who discover it (and accepted as absolutely logical and reasonable by everyone watching the movie) that this is unmistakable proof of alien life. After all, a precisely measured monolith couldn’t possibly have made itself or “evolved naturally”. . . . The human body is an incredible piece of machinery; who put it together? It certainly required a great deal more sophistication to build a human being than to construct a rectangular monolith [[or a Jumbo Jet, or a calculator] . . . .

    As it turns out, Darwinian evolution is not, as the skeptic would have us believe, a testimony to what can emerge from undirected processes; it is a testimony to the unimaginably awesome capabilities and potential contained in the first living cell and its genetic code. A paradigm-shifting insight emerges from all this: Contrary to popular belief, not only is Darwinian evolution not the cause or explanation of the staggering complexity of life on this planet; Darwinian evolution itself is a process which is the result of the staggering complexity of life on this planet . . . All existing life is nothing more than a variation on a theme. All the “organized complexity” of life is a variation on the “organized complexity” of the first living organism . . . .

    [[I]f it is statistically improbable that a 747 [[as Sir Fred Hoyle suggested and as prof Dawkins wishes to rebut by his infinite regress of complexities argument] could have originated by chance, then it is an even greater statistical improbability that the designer of the 747 originated by chance. I agree wholeheartedly. Both the 747 and the human creators of the 747 are here not by chance, but by design! . . . .

    The philosophical problem that must be addressed is the following: How do we escape from the dilemma of the infinitely regressing series of creators (i.e., whoever created me would have to be at least as complex and sophisticated as I am, and therefore he would also need someone to create him, and so on.)? To state this dilemma in a slightly different way: Since all agree that at one time life did not exist and now it does exist, there must be an actual beginning to the process, it cannot go back infinitely . . . .

    Properly presented, the question is as follows:

    Any functionally complex and purposefully arranged form of physical matter (i.e. a Boeing 747, a calculator, or a bacterium), must itself have a creator at least as complex as the object in question. How do we (or can we) escape an infinite regression of creators?

    That which demands and requires a preceding creator is a complex arrangement of physical matter. With this precise formulation of the question, the answer becomes obvious. At some point in the progression, we are faced with the inescapable conclusion that there must be a creator who is not physical matter at all; a creator who does not need to be created; a creator who is not subject to the limitations of cause and effect. There must be a creator who is the first, who is the beginning of it all. There must be a creator who is outside of the physical universe. A creator who is outside of the physical universe, not existing in time and space, and composed of neither matter nor energy, does not require a preceding creator. There is nothing that came before him. He created time, he does not exist in time; there is no “before”. (“What happened before the big bang? The answer is there was no ‘before.’ Time itself began at the big bang.” 16 Physicist, Dr. Paul Davies) We are created; along with time, space, matter, and energy. We are subject to the limitations of a time/space bound series of causes and effects. The creator simply is. [[Rabbi Moshe Averick, "Turns out Richard Dawkins' watchmaker has 20/20 vision after all," Aish.com, Feb. 5, 2011. Well worth reading in toto, here.]

    Looks like the watchmaker is not so blind, after all; even if one is willing to concede the whole panoply of Darwinian evolution from an initial cell. And, when we insist on springing the catch and looking under the bonnet ["hood" for you Americans], the same principle of the implications of FSCO/I point to design of body plans of major life forms, from the first body plan.

    I think we can provocatively suggest that, if we follow the evidence and analysis, the real issue is over how design was carried out, not whether living and fossil life forms show strong signs of design.

    GEM of TKI

  248. Chas : For an evolutionary process, we have to allow that a population currently exists on a viable location in search space. How it got there, set aside.

    Scott: If you wish to redefine evolution as how existing species vary and not how they “got there” in the first place, great. I think you’ve just joined the other team.

    You misunderstand. I was trying to illustrate, within the metaphor of the “search space”, what a single step equates to. Once a population has moved from one coordinate to another, ALL of its prior history has been wiped out – for it was only contained within the bodies of its living members. So to take any population at any time we can access (ie, the present), we can only define an evolutionary process going forward – the next step.

    Chas: Biased instead by a priori notions of extra power in Creators? The designs of which we are capable pale into insignificance beside the apparent designs in Nature.

    Scott: So “it’s too complicated, it couldn’t have evolved” is bad, but “it’s too complicated, it couldn’t have been designed” is okay. If something appears to be designed but it’s very, very complicated, then the design must be illusion and it must have evolved, because… why?

    Well spotted! You have me skewered by the tines of logical inconsistency! And at the other end of this double-ended weapon, you too are impaled.

  249. The astute onlooker will observe how, after a full week, 3,000+ visits and 246 comments to date, darwinist objectors simply have not been able to show on observation and analysis that:

    (i) in general, complex, specific multi-part function can be had without requiring sharp constraint to a narrow zone T in the space of possible configs W, or else

    The onlooker would have to be a damn sight more astute than me to parse that one!

    (ii) life forms are a major class of exception such that one may “easily” access the first life form in Darwin’s warm little electrified pond of chemicals and/or the equivalent or having somehow got to the first living cell, gradually and incrementally adapt it to form the panoply of diverse body plans in the fossil record and the world around us.

    The astute observer will note that this amounts to a sophisticated replacement of bald assertions with more sciencey-sounding ones regarding the nature and navigability of the ‘space’ that can be constructed from some (unclear) coordinate system based upon the sequential information in organisms. Declaring “islands of function” is akin to declaring “species are virtually immutable”, allowing a bit of wiggle room for the undeniable bits. Which one may well think, so let’s boil it down: Post 1: “Yes they are”. Post 2: “No they’re not”.

  250. Chas:

    Pardon, but first of all, it does not seem to have dawned on you that the definition of “species” is fairly debatable and arbitrary; as the black tip sharks case recently discussed at UD illustrates.

    Fixity of species is a strawman — if you want a reasonable body plan/ functional info challenge threshold, try the family as a more typical level. As in dogs vs cats, etc. That’s about the level Behe targetted, and it seems more or less reasonable.

    Next, you don’t seem to be familiar with the context of say Dembski on CSI:

    NFL, p. 144: [[Specified complexity can be defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ” [where W is a symbol for the number of ways components of a system can be arranged, tracing to the Omega of statistical mechanics, e.g. in s = k log w]

    Third, if you had bothered to read the OP before commenting to object, you would have seen this:

    9 –> What is coming out ever more clearly is this:

    when a set of matching components must be arranged so they can work together to carry out a task or function, this strongly constrains both the choice of individual parts and how they must be arranged to fit together.

    A jigsaw puzzle is a good case in point.

    So is a car engine — as anyone who has had to hunt down a specific, hard to find part will know.

    So are the statements in a computer program — there was once a NASA rocket that veered off course on launch and had to be destroyed by triggering the self-destruct because of — I think it was — a misplaced comma.

    The letters and words in this paragraph are like that too.

    That’s why (at first, simple level) we can usually quite easily tell the difference between:

    A: An orderly, periodic, meaninglessly repetitive sequence: FFFFFFFFFF . . .

    B: Aperiodic, evidently random, equally meaningless text: y8ivgdfdihgdftrs . . .

    C: Aperiodic, but recognisably meaningfully organised sequences of characters: such as this sequence of letters . . .

    In short, to be meaningful or functional, a correct set of core components have to match and must be properly arranged, and while there may be some room to vary, it is not true that just any part popped in in any number of ways can fit in.

    As a direct result, in our general experience, and observation, if the functional result is complex enough, the most likely cause is intelligent choice, or design.

    This has a consequence. For, this need for choosing and correctly arranging then hooking up correct, matching parts in a specific pattern implicitly rules out the vast majority of possibilities and leads to the concept of islands of function in a vast sea of possible but meaningless and/or non-functional configurations.

    10 –> Consequently, the normal expectation is that complex, multi-part functionality will come in isolated islands. So also, those who wish to assert an “exception” for biological functions like the avian flow-through lung, will need to empirically warrant their claims. Show us, in short.

    What the astute onlooker will easily see, after the smoke of burning ad hominem-laced strawmen has cleared, will be that objectors to the design inference have no good reason for us to see living forms as material exception to the point that complex, multi-part, specific function normally tightly constrains choice and specific arrangement of parts. On pain of loss of function.

    The challenge of finding shorelines of function amidst vast seas of non-function, is very much still on the table, unanswered.

    GEM of TKI

  251. What the astute onlooker will see, after the smoke from overused and overheated metaphors has dissipated, is that you haven’t established that ‘functional space’ is dominated by isolated ‘islands of function’ (or equivalently, that the fitness landscape contains mostly peaks that are surrounded on all sides by deep valleys).

    Until you do that, the problem of arriving on “shorelines of function” is pure wishful speculation.

  252. 252

    Champignon,

    The entire premise of evolutionary theory is from the cell to the fish to you and me, all living organisms are connected to their ancestor by pathways consisting of genetic variations which were selected.

    No one has proposed anything in any instance specific enough to critically analyze or falsify. The theory itself is vaporware.

    By going above and beyond and demonstrating how preposterous the theory is, neither KF nor anyone else is assuming responsibility for demonstrating that such pathways don’t exist. That’s the default until you or someone demonstrates otherwise.

    KF is going above and beyond by attempting to refute a hypothesis that technically doesn’t even exist. It’s a clever trick. Propose a vague idea and pretend that it’s a genuine hypothesis, and then watch as others struggle to falsify what hasn’t been explicitly proposed.

    KF and many others have gone the extra mile. But the reality is that evolutionary theory hasn’t made specific claims that can be refuted. Its explanations are vague and fuzzy. Every evolutionary explanation is made of countless unspecified variations selected for countless unspecified reasons.

    No one should have to waste time arguing against such pure fluff. Numerous individuals, including yourself, have implicitly conceded that it doesn’t even attempt to explain anything specific in biology beyond gulls and sharks breeding with other gulls and sharks to produce more gulls and sharks.

    Sadly, there’s an institutional directive to bamboozle everyone from grade school onward until they agree to see what isn’t there while tax funds are directed against legislation that would even permit unbiased critical analysis. That’s why KF and others are forced to pretend that they’re addressing a serious scientific theory.

    But as you’ve conceded, it doesn’t really even exist.

  253. C:

    I note again mere rhetorical dismissiveness, not substantial argument on solid, straightforward observations. In particular, in the teeth of explanation and typical, straightforward examples on why multi-part, complex, specific function will normally come as narrow, isolated zones in a vastly larger space of configs that are possible but overwhelmingly useless, we find no good grounds and examples to accept that life forms with their embedded DNA codes — codes! — are exceptional.

    Just, more dismissals; backed up by a demand that we accept a default convenient to the evo mat view.

    (To see what is fundamentally wrong with such, onlookers, just think: did C compose the above by using random monkeys at keyboards, or intelligently? No prizes for guessing why and why it is relevant to what he is so eager to distract from, pooh pooh and dismiss.)

    In short, you just lit off another lot of laced strawmen, polarising and clouding the atmosphere.

    That’s sad, but also quite revealing.

    With the zeal and vast resources behind evo mat, if the evidence was there that would have been triumphantly trumpeted, as ever so many fatally flawed icons have been headlined.

    So, inadvertently, you imply that the balance on the merits actually lies with those who use known reliable signs to infer to design on the evidence in the world of life.

    GEM of TKI

    PS: SA, you are right, I find myself having to try to nail a shingle on a fog bank.

  254. F/N 1: let’s highlight a strawman:

    C: you haven’t established that ‘functional space’ is dominated by isolated ‘islands of function’ (or equivalently, that the fitness landscape contains mostly peaks that are surrounded on all sides by deep valleys).

    1 –> But, I did in fact show from the OP on, just how config spaces that exhibit FSCO/I do normally show the pattern of islands of function isolated in much larger seas of non-function.

    2 –> This being inconvenient, it was ignored. I suggest that C should look at the OP again, and particularly at C1 – 5.

    3 –> Then, we see also an “equivalent” that isn’t.

    4 –> The point of highlighting seas of NON-FUNCTION by contrast with islands of function, is that the real challenge is not to climb from low degrees to higher degrees of function or to niches of specialisation.

    5 –> Not at all. The challenge is to get to function in the first place, where non-functional configs dominate the space. So, there is no difference between zero function and zero function to reward by reproductive success.

    6 –> only when one happens on s shoreline of function, can we talk about moving up from the shores and valleys to higher degrees of function.

    7 –> What is the response? In the teeth of repeated emphasis on the point, it is suggested that moving around between valleys and hills is equivalent.

    8 –> So, either we are looking at gross misunderstanding in the teeth of abundant correction, or willful distortion.

    9 –> In neither case, is the substantial issue being squarely faced. But surely, C knows that gibberish will not work in place of a program, or in place of properly composed text.

    10 –> Going beyond, gibberish would not work in place of DNA protein codes. ( Start with, just under 1/20th of random codons will be stops, given three stops in 64 codes.) Not to mention inter-woven codes such as has been discovered.

    GEM of TKI

  255. I am sorry, but you just went into a bit of an exercise in unintended irony.

    First, I think you should look again at just who started the thread and the focus I set in so doing: the issue of islands vs continents of complex, specific function and the related question of arriving at shores of such zones of function. (It is right there in the title of the thread . . . ;-) )

    But as the astute onlooker will have noted – I was responding to this thread:

    I used to see more gulls with grey wings. Now I see more gulls with black wings. Evolutionary theory, please tell me why?

    Well, it’s because the gulls with black wings reproduced more than the ones with grey wings. There are more of them now. We could also say that the ones with black wings are fitter. They survived more.

    Gee, thanks. That really clears things up. Thanks for restating the observation in a manner that adds no explanation whatsoever.

    Which was, plainly as the honest onlooker will observe, about evolution.

    So, we are right back at needing to explain how a random walk can reasonably find shorelines of function that are deeply isolated in vast config spaces,

    When you can provide proper empirical evidence of this isolation then we might have something to talk about – by empirical evidence I mean more than verbal spaghetti, I mean a substantial map of the configuration space of biology, substantial enough to actually demonstrate the topology you claim – substantial enough to counter what is implied by all the other evidence from biology suggesting that this terrain is navigable and that these islands are connected. I’m afraid your personal self belief will not suffice as evidence, not will your army of jackbooted oil of ad-hom soaked straw-men manage to distract the astute onlooker ;)

  256. 256

    GCU,

    You typed the following, and even bolded the relevant text.

    When you can provide proper empirical evidence of this isolation then we might have something to talk about – by empirical evidence I mean more than verbal spaghetti, I mean a substantial map of the configuration space of biology, substantial enough to actually demonstrate the topology you claim

    Do you not realize that, with regard to evolutionary theory and the origin of species, absolutely nothing is more central to the theory than exactly what you have asked for? The existence of a topology that permits a search from one function to the next, or the lack thereof, is precisely what makes or breaks it.

    First, you have openly admitted that you are unaware of any such topology. To put it simply, you have conceded that you have no reason to think that the evolution you imagine took place is even possible. To theorize such evolution for 150 years and lack any knowledge of such a topology is like 150 years of archaeology without finding a shard of pottery or a glyph.

    In what world of bizzaro science should we assume that such a topology exists and require critics to demonstrate that it doesn’t?

    Your concession is implicit, like most others, but comes closer than most to being explicit.

  257. Do you not realize that, with regard to evolutionary theory and the origin of species, absolutely nothing is more central to the theory than exactly what you have asked for?

    Yes, kind of … On the one hand you have all the evidence from biology – The fossils, phylogenetics, molecular evolution etc, that indicate that the landscape is navigable without the need for giant leaps guided by an intentional force. Sure, the topology has not been mapped out but, as per an inference to the best explanation, all the evidence biologists and palaeontologists have gathered infers just such a connected landscape.

    On the other hand you have KF claiming that the topology consists of small isolated islands, a claim that stems from, I would argue, a closed mind and a limited imagination.

    This is where ID could really score if it got its act together – if it could map the biological landscape so we can all see the topology, and it turns out to be as KF prophesied, then the issue could be largely settled.

    In what world of bizzaro science should we assume that such a topology exists and require critics to demonstrate that it doesn’t?

    For the reasons stated – the evidence strongly suggests it.

    Your concession is implicit, like most others, but comes closer than most to being explicit.

    Nothing is conceded. The evidence from biology suggests such a connected landscape, if ID-ists want to claim that there are no connections then they need an alternative explanation for the evidence – some argument as to why all this evidence doesn’t imply such a landscape.

    You can’t just ignore evidence because you don’t like what it implies ;)

  258. The entire premise of evolutionary theory is from the cell to the fish to you and me, all living organisms are connected to their ancestor by pathways consisting of genetic variations which were selected.

    Nope. Why do they all have to be selected? A better way to put it would be that the evidence implies that all living organisms have descended from a population of simple universal ancestors, and that those that are alive today are the descendants of creatures that reproduced.

    You keep forgetting, as does KF and others, that there is an overwhelming amount of evidence supporting the general hypothesis of universal common descent. The pathways that connect all extant life back through history to the LUCA are strongly indicated by multiple lines of evidence, it was not conjured up as an idea in order to make evolution sound plausible.

    It is up to ID-ists to come up with an argument as to why all this evidence does not imply what scientists argue that it does imply.

  259. 259

    GCU,

    The fossils, phylogenetics

    How is this evidence? How can you demonstrate that you can build a function from genetic variations and natural selection using evidence that can never, ever show the natural selection of individual genetic variations?

    You are proposing evidence of darwinian evolution that is missing the evolution.

    What if the evidence does support a connected landscape? A hierarchy of vehicles or computers or writing utensils supports a connected landscape. Evolution is a theory of what connects them. To observe the existence of things which may be connected and assume what connects them is begging the question.

    You may remind me that vehicles and computers cannot evolve in such a manner because they do not reproduce with variation. Many have made this obvious point, as if pointing out that such things cannot evolve in that manner is itself evidence that other things can. It is not.

    How many times must I explain that you cannot have evidence of evolution by genetic variation and natural selection that omits the individual genetic variations and their selection?

    Having established that the evidence you cite is not evidence, that leaves you with the possibility that functions in biology are connected by pathways of genetic variation and natural selection. You have stated outright that you have no knowledge of such a topology. Astoundingly, you have suggested that the burden lies with someone other than proponents of evolutionary theory to explore such topologies and determine whether or not they support the theory. That is bizarro science. And it is an implicit concession that central premise of evolutionary theory, the existence of such pathways, is missing.

  260. How many times must I explain that you cannot have evidence of evolution by genetic variation and natural selection that omits the individual genetic variations and their selection?

    In what way does it omit genetic variation – we observe it. We can also observe how environmental pressures lead to differential survival rates.

    If you mean that there is no evidence unless each mutation and the reasons for it persisting and spreading have been documented for all life, then I would say that there is no evidence that a river valley was eroded by water – because the removal of each molecule by the water was not observed.

    Now then, where are the direct observations of the designer?

  261. 261

    In what way does it omit genetic variation – we observe it. We can also observe how environmental pressures lead to differential survival rates.

    Of course we observe it. And from both we observe that the “topology” from a finch with a shorter beak to one with a slightly longer beak can be traversed by variation and selection. “As you said, you can’t just ignore evidence because you don’t like what it implies.” And that is exactly what the evidence shows us.

    To claim that the space between no beaks and beaks or between no wings and wings is traversable by the same means is begging the question. I can stretch out a sweater. Does it follow that I can create a three-piece suit by stretching existing clothing?

    I would say that there is no evidence that a river valley was eroded by water – because the removal of each molecule by the water was not observed.

    This is another form of question-begging. You hold up something simple and assert that the evolution you propose is simple because it’s no different. You’re assuming your conclusion, that the origin of species is as simple as the erosion of molecules.

    That one thing may be reasonably determined by extrapolation does not indicate that absolutely any and all extrapolations one may imagine are also valid. The support for one extrapolation cannot be borrowed by another. Can I propose any extrapolation and cite as evidence the extrapolation that water erodes canyons? How did you hope to pull that off? That the example you cite is not even biological is yet another implicit concession that you lack evidence grounded in biology.

    Your argument amounts to “why not?” Why should I determine why or why not? To propose something and ask “why not?” is a hypothesis, not a tested scientific theory.

  262. To claim that the space between no beaks and beaks or between no wings and wings is traversable by the same means is begging the question.

    What question? – we have a fossil record that implies that these changes are possible, and an understanding of genetics to back it up. Multiple overlapping lines of evidence all implying the same thing, hence the reason and reasonableness of the extrapolation.

    That the example you cite is not even biological is yet another implicit concession that you lack evidence grounded in biology.

    Ermm, did you understand that I was not making an argument about biology there, I was using that metaphor to try and get at what you meant by this:

    you cannot have evidence of evolution by genetic variation and natural selection that omits the individual genetic variations and their selection?

    Lets try again:
    Do you mean that there is no evidence for evolution unless each mutation, and the reasons for it persisting and spreading, have been documented for all life?

  263. GCU:

    I have just a moment.

    Will you kindly look at the original post, which does summarise relevant evidence that is also quite evident to common good sense and experience, not to mention logic (think of how the parts of a motor — cf here biological motors in the cell [flagellum and ATP synthase will do for starters] — must be properly put together for it to work . . .): when we have function that depends on multiple specific, integrated organised parts, the function is going to come from a rather narrow zone relative to the many ways the same parts — or their constituent molecules or atoms — could be arranged.

    What is astonishing is how stoutly this is denied and dismissed by those who wish to force us to accept as default what they cannot show at all: that, somehow — with no observed cases in point — we must take it that biological systems are somehow so different that Mengue’s C1 – 5 are irrelevant as constraints on possible configs.

    I can only conclude that we are here up against the usual evolutionary materialist a priori and yet another of its imperious demands for our blind acknowledgement of its suzerainty.

    Sorry, I have never been in thralldom to such tyranny of the mind as Lewontin et al have so openly admitted.

    As to the theme for the thread, that, too is obvious from the original post, where I set it.

    And so, I repeat, it cannot be out of order or a hijacking — Imagine, I stand accused of hijacking my own thread, by calling attention to the focus of the OP! — to call attention back to the highly relevant material from the same original post.

    G’day,

    GEM of TKI

  264. 264

    GCU,

    What question? – we have a fossil record that implies that these changes are possible, and an understanding of genetics to back it up. Multiple overlapping lines of evidence all implying the same thing, hence the reason and reasonableness of the extrapolation.

    I’m beginning to think you don’t see it. How does the fossil record imply that the transitions between fossils are the result of genetic variations and natural selection?

    It implies no such thing. Why do you think it does?

    What in our understanding of genetic implies that such a thing is possible? You see, you can’t just toss these things out there and cite them as evidence. It is necessary to explain why they think they are evidence.

    Where have your ‘multiple overlapping lines of evidence’ gone? Apparently they were never evidence to start with.

    Do you mean that there is no evidence for evolution unless each mutation, and the reasons for it persisting and spreading, have been documented for all life?

    By “evolution” do you mean the origin of species? How is it my job to formulate a hypothesis for what you propose? Isn’t that what you’re asking me to do? You’re suggesting that formulating a hypothesis would be very difficult, and so I should either do it for you or just let it slide. How about neither?

  265. I’m beginning to think you don’t see it. How does the fossil record imply that the transitions between fossils are the result of genetic variations and natural selection?

    It implies no such thing. Why do you think it does?

    It doesn’t – not on its own. All it implies is that it is possible to get from one fossil to another by a process of gradual change.

    Darwin proposed natural selection as a mechanism that could drive and constrain those changes but he knew nothing of genetics. We do know lots about genetics – enough to begin to understand how gradual changes to a genome can cause gradual changes to a phenotype and which when viewed over a long time period add up to a large transition.

    How is it my job to formulate a hypothesis for what you propose?

    I’m beginning to thing this is not just a failure to comprehend what I wrote but actually deliberate obfuscation.

    You claimed:

    you cannot have evidence of evolution by genetic variation and natural selection that omits the individual genetic variations and their selection?

    I asked:

    Do you mean that there is no evidence for evolution unless each mutation, and the reasons for it persisting and spreading, have been documented for all life?

    You respond:

    .. How is it my job to formulate a hypothesis for what you propose? Isn’t that what you’re asking me to do?

    ?

    You see, you can’t just toss these things out there and cite them as evidence. It is necessary to explain why they think they are evidence.

    Can I suggest you take a look at some evolutionary biology textbooks to familiarise yourself with the actual theory, the evidence and the ways in which it supports the theory. It might help clear things up a bit ;)

  266. 266

    GCU,

    Might I ask why you have an interest in discussing the matter at all, if when confronted with a challenging request for specific information you simply refer me to the textbooks? The textbooks contain phylogenetic trees, fossils, and variations on the finch beak theme.

    All it implies is that it is possible to get from one fossil to another by a process of gradual change.

    Surely you realize that you can get from absolutely anything to absolutely anything else by changing it gradually if you have the means. The question is whether random genetic variation and natural selection is a means by which entirely new species and features can form. And you don’t seem able to answer it. (“Yes” does not count.)

    enough to begin to understand how gradual changes to a genome can cause gradual changes to a phenotype and which when viewed over a long time period add up to a large transition.

    Asserting that it can happen and understanding how it ‘does’ are not the same. How can one understand how something happens and not even be able to offer a hypothetical account if it happening? Does it or does it not explain something? Anything less than an example amounts to an implicit concession that it explains nothing.

    I have explained why phylogenetic trees and fossils are not evidence of change by genetic variation and selection. (You actually agreed on that one.) I have explained that a beak that grows longer and then shorter and then longer again over generations cannot be extrapolated to determine the origin of beaks or of birds.

    What have I omitted?

    If you’re fresh out and wish to refer me to the textbooks, I’ll take that as indicating that we’ve exhausted whatever evidence you’re personally acquainted with while you remain convinced that there must be more that neither one of us is aware of.

    If you’re going to remember several lines of evidence from the textbooks to share in discussion while forgetting others, why not remember the ones that actually support the theory and forget the phylogenetic trees, fossils, and finch beaks? Perhaps the ones you can’t call to mind are better.

    Oh, I almost forgot: :)

  267. Scott,

    The question is whether random genetic variation and natural selection is a means by which entirely new species and features can form.

    If that’s the question, then the answer is no.

    I would also suggest you “take a look at some evolutionary biology textbooks to familiarise yourself with the actual theory” as CGU mentioned.

  268. Scott,
    There are no creation events in evolutionary theory. That’s what ID is for. For people that want to believe in creation events.

  269. 269

    LYO,

    Who mentioned a creation event? If you can’t answer, don’t. But please don’t trifle over my choice of words.

  270. Whilst I have a few moments

    The question is whether random genetic variation and natural selection is a means by which entirely new species and features can form.

    Which is why I suggested you read up on some of the research on the topic – that is where all the evidence is documented and analysed. Start with the textbooks, then you might be in a position to move on (and up) to the published research that the textbooks are based on.

    On the topic of research, a new paper out in PLoS Biology explores the evolution of molecular machinery: Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand-Dependent Ancestor

    With a write up on natures blog here:

    And an excerpt from the end of the blog writeup:

    And to intelligent-design proponents, Thornton adds, the results say that “complexity can appear through a very simple stepwise process — there is no supernatural process required to create them.” Still, evolution of a three-protein machine is unlikely to silence those proponents — there are many far more complicated biological machines with far more protein parts and intricate internal mechanisms. Thornton says that his and other groups will now probably use the same tools to dissect the evolution of more complex molecular machines.

    Rather than waving their arms and making grand claims, these people are actually doing research!

    Perhaps the ID community should follow their example, or would that be too risky? ;)

  271. GCUGreyArea,

    Rather than waving their arms and making grand claims, these people are actually doing research!

    Perhaps the ID community should follow their example, or would that be too risky?

    Scott is quite risk-averse. That is why he is ‘neither defending nor championing ID in this discussion.

    LOL.

  272. Research into protein evolution is a Thornton in the side of ID.

  273. Pardon, but first of all, it does not seem to have dawned on you that the definition of “species” is fairly debatable and arbitrary; as the black tip sharks case recently discussed at UD illustrates.

    Sorry KF, but it ‘dawned on me’ many years ago which definitions of species are arbitrary human constructs for classification purposes and which have a genuine biological basis. Like many non-biologists, you insist that the discrete categories that satisfy us on the basis of apparent discreteness impose some kind of discrete category upon the natural world.

    It is only biological species that have relevance to evolution. They are discrete at a moment in time thanks to the specific biological mechanism of breeding – the means by which genes flow. Two diverging lines that can hybridise are not discrete biological species – genes can flow between them. They may be different enough for us to categorise them so, but the organisms themselves do not care a fig for our categories. Species are delimited by gene flow. Genes cannot physically flow from one biological species to another.

    But genes can flow within such a species, for however long as hybridisation remains a biological possibility.

    And this is absolutely key to the concept of species mutability. We are not saying that one reproductively isolated species can turn into another species existing at the same time – they are discrete. But the succession of populations that holds the genetic consensus of the species – the only place where such a ‘reference’ is kept – is continuous and can, does, and indeed, must change. It must change because each time a gene is fixed, all history is wiped out, and it is readily demonstrated mathematically and empirically that population reproduction tends inexorably to reduce variation – ie to fix alleles. The source of replacement alleles – mutation – does not regenerate the lost ones, but new ones.

    If the population only samples the genes in existence in its immediate predecessor, there is no internal anchor, restraint or lookup within the succession of populations, and no apparent barrier to indefinite fixation of novel alleles. Asserting that there must be is to make an unsubstantiated claim about the distribution of functionality within this unknown space that is simply not warranted. The viability of moves through a conceptual space is entirely dependent on the means by which viable locations are assessed, and the degree to which viable locations are connected. You cannot simply divine the structure of this space from its most basic parameters – the base system (4) and the number of digits (up to 3,000,000,000 and more) and some sideways glances at natural languages.

  274. Fixity of species is a strawman — if you want a reasonable body plan/ functional info challenge threshold, try the family as a more typical level. As in dogs vs cats, etc.

    So you are saying that we can accept evolution within the dogs (jackals, dingoes, wolves, hyenas) and within the cats (domestic, lion, tiger, jaguar) but not in the lineages leading from the common ancestor of cats and dogs.

    I do find myself continually wondering whether we are arguing about selection or about common descent. Whatever selection can or cannot do (Scott’s challenge to reconstruct an adaptive history), we appear to see common descent in lineages. The same techniques that allow cladistic analysis within family groups (and, indeed, relatedness in genuine relatives within each species) give the same signal when applied between the two clades, Cat and Dog.

    There is nothing additional separating cats/dogs, as opposed to dogs/wolves, other than time. Time for greater divergence.

    “Islands of function” implies that cats all sit in one neighbourhood, and dogs in another. I would suggest that, connecting them, is a sequence of real genomes representing their respective ancestors and converging on a point in the space representing their last common ancestor. Just the same historical convergence that we would observe between the housecat and the wildcat, except the modern organisms are a bit further apart in the cat/dog case.

  275. 275

    GCU,

    How many times – a dozen? I’ve lost count – have I pointed out the numerous examples of “evolution” that omit any explanation of the natural selection involved, leaving its role as an undefined assumption.

    Your example goes one step further, explicitly ruling out the involvement of natural selection.

    The result challenges the assumption in biology that increased biological complexity evolves because it offers some kind of selective advantage. In this case, the more complex version doesn’t seem to work better or have any other obvious advantage compared with the simpler one;

    Evolution is driven by variation and selection. I’ll leave out all of the deliberate manipulation of the process to simulate random variation. How does this support the premise of diversification through variation and selection? It explicitly does not. It expressly separates itself from that premise, unless we’re to believe that spiders over time developed the process of weaving orbital webs just for the sheer heck of it.

    In fact, it ‘challenges that assumption.’ Awesome. That makes two of us!

  276. 276

    Champignon,

    Scott is quite risk-averse. That is why he is ‘neither defending nor championing ID’ in this discussion.

    Nice of you to chime in. You were the first to disappear when I asked whether the cornerstone of biology could explain something in biology. You stopped ‘defending and championing’ evolutionary theory right about then. Unless you have something to share that you didn’t then.

    But yes, that’s exactly what I said. The validity of ID is an entirely different subject. I’m clear on that because when push comes to shove folks like to turn the tables and ask how ID explains this or that. Not only is it a misguided question, but it distracts from the fact that evolutionary theory was vacuous long before anyone thought up ID. What if ID turns out to be creationism in a cheap tuxedo? What if Expelled is full of subliminal messages to turn rational people into snake-handling fundamentalists? What good does that do evolutionary theory?

  277. How does this support the premise of diversification through variation and selection?

    Many independent lines of evidence support diversification due to variation and selection. Perhaps you are confused because selection is rather permissive, and populations can diverge through drift without one being “superior” to another.

    ID could explain everything if only you could point to the designer and identify his capabilities or mode of action or perhaps identify a specific instance of design intervention.

    You are pitting vaporware against observable processes and claiming because we don’t know everything, we don’t know anything. You have absolutely nothing. You have no designer, no process of design, no theory of how to design, no theory that would, in principle, make design possible.

    You simply have nothing.

  278. Scott,

    Nice of you to chime in. You were the first to disappear when I asked whether the cornerstone of biology could explain something in biology.

    Not only did I not disappear, I was still responding to your comments in this thread seven days later. And I answered your question with this list of biological phenomena explained by evolutionary theory:

    Elizabeth, to Scott:

    But I’m still not at all sure why you are rejecting the Galapagos finch beaks, which were actually observed evolving.

    Or the 1:1 sex ratios I mentioned in comment 25.

    Or the congruence of the nested hierarchy to 1 part in 100 trillion trillion trillion trillion.

    Or the gradual transformation of reptilian jaw bones into mammalian inner ear bones through a series of functional intermediates, as mentioned by Petrushka.

    Or the bizarre hormonal warfare between mother and fetus in gestational diabetes.

    Scott, you asked for examples of “how the cornerstone of biology explains something in biology”. Evolutionary theory explains all of these. Intelligent design explains none of them.

    Scott again:

    The validity of ID is an entirely different subject. I’m clear on that because when push comes to shove folks like to turn the tables and ask how ID explains this or that. Not only is it a misguided question, but it distracts from the fact that evolutionary theory was vacuous long before anyone thought up ID.

    Yes, how ‘misguided’ of me to bring up intelligent design on an intelligent design website, or to ask how ID compares to the theory it purports to supplant.

  279. 279

    Petrushka,

    Many independent lines of evidence support diversification due to variation and selection.

    We’ve been over this in the past dozen posts. This is accurate if you attach a very limited meaning to “diversification.” I know, I know, you think it’s all the same thing. But you can’t seem to make a case for it beyond, ‘why not?’

    You are pitting vaporware against observable processes and claiming because we don’t know everything, we don’t know anything.

    I’m sure we know quite a bit of stuff. So far we’ve got finch beaks, colored cichlid fishes, and an abundance of examples of trivial or contrived variation that explicitly exclude natural selection.

    Apparently you wish to take all that we do know and receive credit for what you’re absolutely certain we will know one day.

    What if I don’t know anything? No one knows everything. It’s not like my brain is an empty vessel because I don’t know how finches got their beaks.

    I’ve given you folks plenty of time to persuade me with your religion. The responses have alternated between gulls with grey or black wings, appeals to authority, evidence that either implicitly or explicitly does not relate to the claim, and changing the subject.

    What am I to conclude? Either the evidence to support this does not exist, or it exists and you don’t know what it is but you believe it anyway, or it exists and you know it but you won’t tell anyone until they spend $50,000 and advance to the inner circle.

    I’m sure I’ll come back and try to squeeze blood from this turnip again later. But I’m done for now.

    Oddly, I don’t entirely disagree with all of your challenges to ID. Not all of them. But I don’t see how that helps you any.

  280. 280

    Yes, how ‘misguided’ of me to bring up intelligent design on an intelligent design website, or to ask how ID compares to the theory it purports to supplant.

    Some discussions are on one subject, some on another. I see that you’d rather change this one. I would too. Have at it.

    I responded to your list by pointing out that it is devoid of genetic variation and natural selection. I’m not here to stick my thumb in a dike. I can respond to it fifty times and you can post it fifty-one. Enjoy.

  281. How many times – a dozen? I’ve lost count – have I pointed out the numerous examples of “evolution” that omit any explanation of the natural selection involved, leaving its role as an undefined assumption.

    I’m not even sure what you are demanding? What would constitute an explanation of differential survival. Can you explain a bit better what you are after? Would a bacterias ability to survive normally fatal antibiotics do?

  282. Scott,

    I responded to your list by pointing out that it is devoid of genetic variation and natural selection.

    Do you even understand the evolutionary explanations for the phenomena on my list? If you did, you wouldn’t be claiming that they are “devoid of genetic variation and natural selection.”

    GCUGreyArea had some excellent advice for you:

    Can I suggest you take a look at some evolutionary biology textbooks to familiarise yourself with the actual theory, the evidence and the ways in which it supports the theory. It might help clear things up a bit.

    And:

    Which is why I suggested you read up on some of the research on the topic – that is where all the evidence is documented and analysed. Start with the textbooks, then you might be in a position to move on (and up) to the published research that the textbooks are based on.

  283. Chas D:

    There is nothing additional separating cats/dogs, as opposed to dogs/wolves, other than time.

    Talk about question-begging, not to mention the unscientific “time” element.

    Time isn’t of any use if the changes required are not possible.

  284. Chas D:

    ‘There is nothing additional separating cats/dogs, as opposed to dogs/wolves, other than time.’

    At thet will be why we have so many transitional fossils to look at then.

    Who are you trying to kid?!

  285. GCU:

    You keep forgetting, as does KF and others, that there is an overwhelming amount of evidence supporting the general hypothesis of universal common descent.

    I can take that same “evidence” and use it to overwhelming support a common design.

    And universal common descent does not have any genetic data to support it- as in there isn’t any genetic evidence that demonstrates the transformation required (for UCD) are even possible.

    All universal common descent has are throwing time at observed changes. And that ain’t science.

  286. 286

    Do you even understand the evolutionary explanations for the phenomena on my list?

    Are you saying that there is an item on your list that can be explained through genetic variations and natural selection? I pointed out a week ago that none of them could be, and you didn’t object. Apparently nothing jumped out at you either.

    I don’t mean this in quite the bad way that it sounds, but I’m gotten bored with this. Post after post after post my question is questioned six ways from Sunday, but no one wants to offer an evolutionary explanation that includes the specific mechanics of evolution.

    I’ve made my point, and I couldn’t have done it without your participation. But I have nothing to gain from continuing the discussion. I must restate my very simple point in every single post or it will get flushed away in the tide of irrelevant and often condescending comments. (I don’t want to be a hypocrite – I’m above neither condescension nor rhetoric.)

    But I’ve taken the high road this time, and although the result is satisfying, it’s also anticlimactic. So I’ll just stop now.

  287. Are you saying that there is an item on your list that can be explained through genetic variations and natural selection?

    Yes, looks like it to me.

    I’m entirely baffled by your responses on this thread – what exactly are you looking for – what form of explanation would suffice, or are you just playing trolls?

  288. I’ve made my point, and I couldn’t have done it without your participation.

    I see no coherent point being made Scott.

  289. Time isn’t of any use if the changes required are not possible

    Good job they are possible, then… as I say, one finds oneself arguing about selection one post, and common descent the next.

    On the evidence, accumulated genetic change within the cat and dog clades – accepted by KF and others as within the scope of non-interventionist evolution – is consistent with a particular time since their respective common ancestors.

    Accumulated change between the cat and dog clades is also consistent with a common ancestor, but with a greater time since divergence than that within them. There may, or may not, have been a barrier to the divergence of a common ancestor into all-cats and all-dogs. But that there was a common ancestor is inferred by exactly the same technique used to determine relationships within cats and within dogs.

    One can deny all common ancestry data – the Designer made every species exactly as we find it today. That is certainly not supported by fossil evidence. Or, one can accept all common ancestry data as indicative of a long non-interventionist history – no ID anywhere.

    But the current proposal is inconsistent in its treatment of the data. Common ancestry data within cats is agreed to indicate true common ancestry – evolution can work around “Cat Island” and “Dog Island”, and the result is the diversity of cats and dogs.

    But the common ancestor of cats and dogs, indicated by the exact same techniques, is asserted to have lived on some other “Island”. Or, alternatively, not to have lived at all. Either the first inhabitants of Cat Island and Dog Island were each separately created de novo, or an organism inhabiting “Catdog Island” was redesigned in order to form the raw materials for the current inhabitants of Cat Island and Dog Island.

    I know what your take is on it – Common Ancestry is actually Common Design – but if natural evolutionary processes are agreed to be responsible for a clade, however restricted, then the commonality in that clade is all common ancestry, and the difference all (‘naturalistic’)evolution.

  290. 290

    I guess repeating it about 2.5 times on average in each and every post didn’t do the trick.

    For the last time, the simple and coherent point is that genetic variation and natural selection cannot be used to formulate an explanation of anything more extensive than the variations in finch beaks. Your participation consisted of numerous posts (indicating that you were not constrained by time from participating) while failing to refute it, even digging up examples that explicitly stated the direct opposite of the claim you were attempting to support. That Champignon refers to “a list” rather than any specific item demonstrates that even he is unwilling to take the risk of citing a specific example. (I commend his wise choice.)

    The term for most of your counterarguments is “special pleading.” That is, you offer reasons why this theory should be exempted or excused from the accepted standards of scientific inquiry.

    The most meaningful response has been that the minor observed variations within species can be extrapolated to explain the species themselves. Why is that a valid extrapolation? More special pleading. You – or someone – even argued that because the very concept of extrapolation is logically valid that this particular extrapolation is also valid. (That was the water erosion comment.) Support for the logical concept of extrapolation does not constitute support for your specific attempt at extrapolation.

    Your collective inability to respond to such a simple, reasonable request is my point, stated repeatedly in coherent English. And now, despite my intentions, I’ve stated it again. Now I have real work to do.

  291. Chas D:

    Good job they are possible, then… as I say, one finds oneself arguing about selection one post, and common descent the next.

    Well I can take the alleged evidence for universal common descent and use it to support a common design.

    And no, that does not mean all organisms were designed as they are today. That means all organisms of today are descended from the originals.

  292. we observe that:
    Offspring inherit a combination of parents genes.

    Offspring can also have mutations no present in their genome.

    Different combinations of genes produce different individuals.

    Mutations can alter the way cells function and the way an organism appears and operates.

    Organisms with certain traits may be more or less likely to reproduce well in a given environment.

    A slight variation in a particular trait can give an advantage or disadvantage, resulting in more or less offspring.

    Mutations happen at a certain rate.

    Mutations and other changes accumulate.

    Different species will sometimes share similar genes.

    The rate of accumulation and the genetic similarities can be used to estimate when two species shared a common ancestor.

    Examples of these ancestors in the fossil record correlate with this.

    Taxonomic classifications also correlate with the above.

    Plus a whole load of other stuff that I’m less familiar with.

    Evolutionary theory is a framework for explaining those and other observations. It fits the data exceedingly well and allows biologists to make some very good predictions – but like any theory it has plenty of rough edges.

  293. All of that is in line with baraminology and ID.

    And what predictions can be made of accumulations of random mutations? Please be specific.

  294. Here’s Scott’s algorithm:

    1. Ask a question.
    2. Ignore your opponent’s answer, or else claim that it’s trivial and demand
    3. Restate your question as if it hadn’t been answered.
    4. Comment on how reasonable you’re being.
    5. Occasionally complain that you’re being “trifled with.”
    6. Pretend that justified extrapolation is a cardinal sin.
    7. Talk about how bored you are.
    8. Repeat.

  295. #2 should read, “Ignore your opponent’s answer, or claim that it’s trivial and demand a real answer.”

  296. Everything is consistent with ID – unless you know something about the designer that places constraints on their actions.

  297. 297

    Champignon,

    I’m not responding at random. If the response is trivial I’ll say so and why. If someone attempts to distract by trifling over words I’ll point that out. I mention how reasonable I to remind onlookers that I’m asking a very, very simple question. The boredom – okay, I can keep that to myself.

    If you don’t like me stating that the answers are trivial, provide less trivial answers or argue why the answers you gave are not trivial. If you don’t want me to point out when you’re trifling, don’t trifle. Or argue why it’s not trifling.

    Who said that supported extrapolation is a cardinal sin? No one, so why say it?

    You’re telling me that you’re unhappy with my responses. That’s okay. You don’t have to be happy with them. But why do you think that summarizing them (to the extent that you do so accurately) is a useful criticism of them?

    If you don’t like the output then change the input.

  298. Wrong again, as usual.

    Newton’s First Rule applies, as does parsimony and Occam, which means the explanatory filter applies.

    And all of that tells us that if necessity/ law and/ or random events can explain it then we do not add unnecessary entities.

    So again I ask you:

    And what predictions can be made of accumulations of random mutations? Please be specific.

    Or you can continue to hide behind your strawman.

  299. Scott,

    That Champignon refers to “a list” rather than any specific item demonstrates that even he is unwilling to take the risk of citing a specific example.

    I didn’t refer to “a list”, I referred to “this list” and then provided it. You seem to be afraid of addressing it. Why?

  300. 300

    I did address it when you first posted it. It consists of items that do not specify genetic variations or the selection of such variations. That makes them poor evidence to support a process consisting of genetic variations and the natural selection of them.

    I’m just noting that when reminding me later of your list, you don’t single anything out. You just lump it all together. That suggests that either nothing on the list stands out to you or that you think that the quantity of items itself makes it more substantial – the “mountains of evidence” argument.

  301. It consists of items that do not specify genetic variations or the selection of such variations.

    What does that sentence even mean?

  302. Me:

    Everything is consistent with ID – unless you know something about the designer that places constraints on their actions.

    Joe:

    Wrong again, as usual.

    In what way – that somethings cannot be created by design, or that we know some things about the hypothesized designer that constrain their actions?

  303. Wrong again, as usual.

    GCU:

    In what way

    Newton’s First Rule applies, as does parsimony and Occam, which means the explanatory filter applies.

    And all of that tells us that if necessity/ law and/ or random events can explain it then we do not add unnecessary entities.

    Therefor not everything is consistent with design.

    So again I ask you:

    And what predictions can be made of accumulations of random mutations? Please be specific.

    Or you can continue to hide behind your strawman.

  304. Scott’s locutions become increasingly awkward as he moves the goalposts. Before he was asking for examples of “how the cornerstone of biology explains something in biology.” Unfortunately for Scott, we supplied what he requested. That put him in an awkward spot, so he had to deny that the question had been answered and change it. Now he’d like us to “specify genetic variations and the selection of such variations”, presumably identifying the base pairs involved.

  305. 305

    Champignon,

    So you thought that when I referred to the ‘cornerstone of biology’ and to ‘genetic variations and the selection of them; that I was talking about two different things. I thought I was pretty clear.

    I realize that there’s more to evolution than variation and selection. But when we’re talking about the origin of species or anything new, it’s about precisely that. Note to self: Be even more deliberately careful to use the exact same words over and over in boring repetition for fear that I’ll be accused of asking different questions.

    You haven’t supplied it. You offered a laundry list of things other than evolution by variation and selection. Some of them even explicitly had nothing to do with selection. Geographical separation, for example. It is not selection when a gull chooses to breed with nearby gulls rather than gulls 100 miles away. And if it was it would still be a poor example because if you put the two together they would breed anyway.

    I could try rephrasing. You clearly believe that there was once a wingless creature, and many generations later as a result of variation and selection, there were winged creatures that flew. (That’s an abbreviated version. I’m sure there’s more to it.) I’m sure you also believe that before geckos had feet enabling them to cling to walls, they had an ancestor that did not. You believe that before there were spiders that weaved orbital webs there were spiders that did not, and before them spiders that produced no type of silk at all. And in each case the difference was genetic changes over many generations, some of which were selected.

    Correct me if I’m wrong. I’m just summarizing.

    The question is, why do you think that? I’m not asking you to explain any one of these things specifically. (That’s me being reasonable again.) But what is explained by variation and natural selection so that you (and I) can reasonably infer that it explains such things also?

    You must realize that the only meaningful answer to that question is an explanation of something using variation and natural selection. Inference and extrapolation are fine, but they do require a basis. What is it?

  306. Scott,
    It’s comical. You’re asking for evidence for evolution, and over and over again you’re given it. Yet you are unwilling to listen.

    You remind me of Steve Martin in “The man with two brains”, asking his recently deceased wife for a sign from heaven if she dissaproves of him starting a new relationship…

    http://www.youtube.com/watch?v=lmivsA3iJw8

  307. Well I can take the alleged evidence for universal common descent and use it to support a common design.

    Well, to be clear, I was not talking about universal common descent. Somewhere in between universal descent and you being identifiably the child of your parents, there is a barrier being asserted that unguided evolution cannot cross. I am trying to ascertain where people think that barrier is actually located, within a clade of anyone’s choosing.

    KF explicitly talks of families – cat vs dog as the example. Thus unguided evolution is admitted to account for genetic differences between any two cat types (eg leopard and tiger) but not between the various cat species and the various dog species. Likewise, the genetic commonality between cat species in this ‘unguided’ clade can only be due to common descent, however it first originated.

    Under ‘unguided’ evolution, populations change due to the accumulation of changes in lineages of descent, and diverge due to branching caused by long-term isolation. Therefore, the retained similarities between such populations are due to common descent – their common genes were obtained from their common ancestors, however those ancestors got ‘em.

    So common descent is a valid inference in such a scenario. The differences between the populations are all due to evolution, while their similarities are due to common descent.

    But the same thing happens when we look at the dog/cat split. There are similarities that are indistinguishable from the correspondence that is agreed to show common descent within the cats. The only difference is that there are fewer of them, and more differences.

    So the question is really how one decides that common descent is a valid cause of the same genes being observed in different cats, but is not valid when one observes the same genes in cats and dogs.

    And no, that does not mean all organisms were designed as they are today. That means all organisms of today are descended from the originals.

    Well, yeah. From the point at which the designer stopped designing, all differences can only be due to unguided evolution. But if (when we compare leopards and tigers, say) we see similarities that are due to common descent and differences that are due to evolutionary divergence, what are we to honestly conclude when we encounter that same mix of similarities and differences between cats and dogs, differing only in the proportions ascribed to ‘similar’ and ‘different?

  308. 308

    GCU,

    Just for the sheer heck of it, let’s go through this.

    Offspring inherit a combination of parents genes.

    Yes.

    Offspring can also have mutations no present in their genome.

    Yes.

    Different combinations of genes produce different individuals.

    Yes.

    Mutations can alter the way cells function and the way an organism appears and operates.

    Yes, although the extent of this is unclear. Nearly every cited example involves loss of function. This borders on question-begging.

    Organisms with certain traits may be more or less likely to reproduce well in a given environment.

    Yes.

    A slight variation in a particular trait can give an advantage or disadvantage, resulting in more or less offspring.

    Yes. What other kind of variation is there?

    Mutations happen at a certain rate.

    Yes.

    Mutations and other changes accumulate.

    Yes. But now we’re talking about mutations and genes, not functions. Did you mean to suggest that an accumulation of mutations and other changes results in an accumulation of new functions, features, organs, and behaviors? That would be begging the question, so I’ll assume you didn’t mean that.

    Different species will sometimes share similar genes.

    Yes. This is only significant if we start with certain assumptions as explained above.

    The rate of accumulation and the genetic similarities can be used to estimate when two species shared a common ancestor.

    See the above comment. First you’re assuming that genetic similarities mean common ancestry. Not all things that share common elements have common ancestors. That certain things reproduce and have ancestors does not change that.
    Second, this assumes that the variation between species is the result of such accumulated genetic variations. It has not been established that such variations can or do produce increases in function, new organs, features, behaviors, etc. So again, this is begging the question, rephrasing the assumption.

    Examples of these ancestors in the fossil record correlate with this.

    First, that they are ancestors at all is more evident in some cases than in others.
    Second, as stated, that the difference between one specimen and the next is the result of variation and selection has not been established. Is there so much as a single instance in which a genetic variation and the selection of it can be determined from fossils?
    The fossil record is like a picture of a man in New York and then in Miami and then in L.A. It establishes where he was, not how he got there. You could say that he walked, flew, drove, or was carried and the evidence would support each equally.

    Taxonomic classifications also correlate with the above.

    See the above.

    This list consists entirely of observations of what was or is and assumptions regarding how it got that way.

    Combining relevant facts into a list to make a point can be powerful. It often works even when the facts don’t particularly add up to anything. Some people, when presented with a big list of stuff, much of which is plainly true, are easily persuaded that one follows from or supports the other. Salesmen know that if you want someone to buy something you start by asking them a bunch of questions to which they will answer “yes.”

    Now you know that I didn’t just read and dismiss. I reasoned on every point and found that it does not lead to the conclusion that diversity in biology is explained by iterations of variation and selection.

    Since none of this leads to that conclusion, what does?

    Please, let no one go back to “we sent you lots of stuff and you ignored it.” I did not, and you do not get credit for quantity of bullet points or just for bothering to make a list at all.

  309. And what predictions can be made of accumulations of random mutations? Please be specific.

    On its own, nothing. It is an observation – mutations accumulate.

    One pattern that can be predicted when you add differential reproduction rates is that only near neutral or beneficial mutations will accumulate, and the resulting generations will produce a pattern of nested hierarchies.

  310. Understood. Geneticist Giuseppe Semonti touched on this in “Why is a Fly Not a Horse?”- his main point is all we know about cats and dogs is that a cat is born when there is a successful mating of two cats (and a dog is born when there is a successful mating of two dogs)- gens control traits and neither “dog” nor “cat” (nor “human”) is a trait:

    ”The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”

    Meaning genes influence development bt do not determine it.

    Also a targeted search is not unguided evolution.

    The barrier unguided evolution can’t cross? More than two new protein-to-protein binding sites, which means you are getting to start with what needs to be explained and still can’t get much from there.

  311. Yeah mutations accumulate but the question is how was it determined mutations are random in any sense of the word?

    As for nested hierarchies, based on what, exactly? Nested hierarchy patterns are man-made constructs…

  312. 312

    ScottAndrews2,
    As you appear to be playing the advocate I’ll join in!

    Nearly every cited example involves loss of function.

    How “nearly” is nearly? It seems to me that one thing can be broken in many different ways. “Never” would be different.

    So, specifically, what does the ratio of “gain of function” mutations to “loss of function” mutations have to be to make what is being discussed impossible? 1:100? 1:10000000?

    This borders on question-begging.

    You just admitted that “nearly” every example was loss of function, therefore there were >0 gain of function.

    Indulge me. Get specific! Give me an example of such a “gain of function” that you are aware of! Give me 5!

    First you’re assuming that genetic similarities mean common ancestry.

    Common ancestry is accepted by Behe. It’s well supported. It’s not an assumption.

    Not all things that share common elements have common ancestors.

    Fer’instance?

    It has not been established that such variations can or do produce increases in function, new organs, features, behaviors, etc.

    No, not to your satisfaction. But nonetheless as a working assumption it seems to be usable and productive.

    The fossil record is like a picture of a man in New York and then in Miami and then in L.A. It establishes where he was, not how he got there. You could say that he walked, flew, drove, or was carried and the evidence would support each equally.

    What is your opinion of the evolution of mammalian auditory ossicles?

    Does hearing count as a gain of function?

  313. PeterJ,

    Chas D:

    ‘There is nothing additional separating cats/dogs, as opposed to dogs/wolves, other than time.’

    At thet will be why we have so many transitional fossils to look at then.

    I don’t even know what a transitional fossil is, any more than a ‘transitional individual’. Fossils are dead individuals, who were almost certainly closely related to both their parents and (if they had any) their offspring. But they sample discrete points in an assumed continuum of serial inheritance and occasional mutation. That continuum is inferred from the nature of modern individuals and their relationship to their parents and offspring. The sampling of this continuum by discovered fossils is patchy at best, but I am not aware of any fossils that contradict the statement that more time has elapsed since the divergence of cat/dog vs dog/wolf.

    But I guess one could turn it around. If there is a deep divide between cats and dogs, wouldn’t we expect cats and dogs from 30 million year old strata to be as diffferent from each other as are modern cats and dogs? I haven’t even looked, but my bet is that those fossils that we have that can be ascribed to ‘cat’ and ‘dog’ lineages are less definitively ‘different’ the further we go back.

    Who are you trying to kid?!

    Honestly, sincerely? No-one.

  314. Yes. But now we’re talking about mutations and genes, not functions. Did you mean to suggest that an accumulation of mutations and other changes results in an accumulation of new functions, features, organs, and behaviors? That would be begging the question, so I’ll assume you didn’t mean that.

    yes – that is exactly what is observed – if you did what I suggested and started looking though the thousands of published papers on the subject you might just encounter some of this evidence you are after.

    It has not been established that such variations can or do produce increases in function, new organs, features, behaviors, etc.

    This is precisely what has been established by researchers – go and look at the research!

    This list consists entirely of observations of what was or is and assumptions regarding how it got that way.

    It is a list of observations that, when put together form part of a process by which organisms change over time and can generate the patterns observed in the fossil record, in taxonomic classifications, genetics and molecular evolution. It is also a process which, when modeled, produces the same patterns that we see in the fossil record and in genetics.

    The fossil record is like a picture of a man in New York and then in Miami and then in L.A. It establishes where he was, not how he got there. You could say that he walked, flew, drove, or was carried and the evidence would support each equally.

    That is where genetics comes in, it confirms the pattern and is used to help make predictions that lead to new fossil discoveries. To use your metaphor, genetic evidence suggests walking is the only method of travel, if the man flew he would get there much quicker than would be expected – we don’t see these rapid jumps, we see movement consistent with what we know about the rates of change in genomes in different circumstances and for different types of creature.

    Now you know that I didn’t just read and dismiss. I reasoned on every point and found that it does not lead to the conclusion that diversity in biology is explained by iterations of variation and selection.

    Quite right, you didn’t dismiss it, you are utterly failing to understand it whilst throwing in some refuted creationist claims and misconceptions to help demonstrate your lack of knowledge!

  315. I reasoned on every point and found that it does not lead to the conclusion that diversity in biology is explained by iterations of variation and selection.

    That’s the bit I missed. The bit where the conclusion is disallowed. I agree that the conclusion is not forced, but I guess what people are looking for is a heuristic to distinguish the bits of diversity that are explained by iterations of variation/selection/drift from those that aren’t.

    We can readily conjure up artificial scenarios whose diversity is fully explained by iterations of variation and selection. Correction, by iterations of mutation-fixation (both selection and drift) IN REPRODUCTIVELY ISOLATED LINEAGES. I know that doesn’t change it for you, but it does matter.

    A simplistic scenario would be a string of meaningless text. Copy it a few times, change the odd letter, delete the copies after an arbitrary ‘lifespan’, make a few more, recombine strings that are within a few degrees of freedom of sequence identity but not those that are outside it … carry on for a few million iterations and this simple process will create diversity with all the main characteristics of biological diversity except this elusive quality of ‘complex function’.

    This population will evolve entirely neutrally – there is no ‘function’, since all points of the space are functional, and there is no selection. And yet I predict that ‘species’ will emerge – points in the space colonised by multiple ‘individuals’ clustered together by genetic commonality, and distinguished from other such strings by genetic distance.

    The recombination rule will create populations exchanging text within, but not between strings that are too ‘different’.

    Now, this isn’t biological evolution (though it is evolution).

    BUT it illustrates the point (or tries to) that diversity is not dependent upon complex function, nor selection. Diversity is about accumulated differences between, and sustained commonality within, multiple lineages subject to imperfect copying. But without retention of the history of the process, I would be at a loss to demonstrate why the process produced the strings it did. “It just did; here’s the algorithm …”. So you repeat and it does something different.

    Now it may be true that complex biological structures or entities exist that cannot be created by selection. I’m not trying to beg any questions with this illustration. But the difference between cats and dogs – that is not a ‘complex function’. A cat is complex, a dog is complex, a leopard is complex, a tiger is complex. But the cat-dog distinction does not involve more complexity than the leopard-tiger one, just more (genetic) difference.

    You seem to accept that the basic processes of evolution can proceed from the common ancestor of leopards and tigers to produce those separate forms. But it cannot progress from a common ancestor of cats and dogs to produce those. Complexity has nothing to do with this asserted circumscription.

    Of course we cannot answer your challenge to bring forth extinct genes and the selective milieu of extinct organisms in order to demonstrate the principles of evolution at work in a historical setting. No more can I tell you how big was the star in which our elements were fused. You are free, for whatever reasons, to give your designer as big a role in the history of life as you please. But to characterise every one of the thousands of scientists who have worked on this ‘fluff’ over the last 150 years as stupid, deluded, malicious, deceitful, or pushing a ‘religion’ (the only religion with an extensive mathematical basis and empirical support!) is, I think, wholly unjustified.

    You will have to take my word for it, but I argue for evolution because I find it fascinating; I ‘get’ it, and it provides an excellent fit in my mind between process and the structure of the biological world. I try to convey that fascination, perhaps with little success.

  316. 316

    It is a list of observations that, when put together form part of a process by which organisms change over time and can generate the patterns observed in the fossil record, in taxonomic classifications, genetics and molecular evolution. It is also a process which, when modeled, produces the same patterns that we see in the fossil record and in genetics.

    The process is precisely what is missing.

    You hardly need a discussion forum to tell someone to go read research. In keeping with the pattern of making assumptions as needed, you assume that I have read nothing. Why? Because surely if I read it I would be convinced. If someone doesn’t like kiwi fruit they must not have tried it.

    One flaw in your reasoning is that, when comparing expectations of the theory to empirical evidence, you consider only the confirming evidence and discard the rest. The available evidence predicts that, starting with any given species, it will vary somewhat in size, shape, and color. This would also be the expectation historically.

    The pattern you infer does not include orbital spiderwebs, for example. It actually doesn’t include just about anything at all we see in biology.

    And in many cases it doesn’t match up at all. Take for example whale evolution. It doesn’t fit the pattern at all. It requires a mutation rate quite different from what is observed, in addition to the development of novel features through mutation and selection. So what do you do? You just leave it out because it contradicts your expectations.

    That is where genetics comes in, it confirms the pattern and is used to help make predictions that lead to new fossil discoveries.

    What you seem to have trouble understanding is that no one knows whether the differences between genomes is made of mutations and selections. It’s an assumption, a leap. The observation that mutations occur and change the genome does not lead to the conclusion that differences between genomes are made of mutations.

    Not only does one not logically follow the other, but the conclusion faces enormous hurdles of contradictory evidence. Not least among them is that it forces one to attribute designs that clearly require foresight, planning, and coordination to a process that has neither goals nor the capacity nor the intent to plan for them. Given a rodent, generations of mutation and selection give you a bigger or smaller rodent. The process is not consistent with numerous coordinated variations required to add wings, echolocation, and a nervous system that can coordinate them.

    Even an unwarranted extrapolation can slide by, but not when the extrapolated result is a contradiction of the sample.

    You’ve turned the other way. First evolution explained everything in biology. Now, evolution explains nothing but rather everything in biology supports the pattern of evolution. But it doesn’t. By your own words and evidence it supports genetic change over time. It does not support genetic variation and natural selection as the source of that change.

  317. 317

    No, I get it. And I am 100% convinced that you are fascinated! :)

  318. 318

    But to characterise every one of the thousands of scientists who have worked on this ‘fluff’ over the last 150 years as stupid, deluded, malicious, deceitful, or pushing a ‘religion’ (the only religion with an extensive mathematical basis and empirical support!) is, I think, wholly unjustified.

    What you’re saying is not lost on me. At the same time, to reason that what men have believed for 150 years cannot be wrong because that would mean they were deluded or deceived seems off.

    Have scientists never been wrong? Have there not been plenty of instances in which strongly-held beliefs were held in common by most men of science, and which later turned out to be entirely wrong?

    There’s an extrapolation. If scientists in general can take a position, convincing themselves and others that it is supported by the available evidence when in fact it is not, is it not plausible that they could be likewise deluded in another matter?

    That’s far simpler and more consistent with the body of available evidence than extrapolating from mutations to every genome in every living thing on earth. If someone is willing to accept that extrapolation, why not accept the previous one which is much less of a stretch?

    Single-celled creatures to pelicans and people via mutation and selection extrapolated from instances of minor phenotypic variation? No problem.

    Scientists being led to group-think and cling to ideologically motivated conclusions extrapolated from other instances of scientists being led to group-think and clinging to ideologically motivated conclusions? That’s a stretch.

  319. http://blogs.nature.com/news/2.....olves.html

    I would like to see what those who run this site have to say about the above findings. What is the perspective from an ID point of view.

    They seem to be strangely silent on this issue?

  320. The process is precisely what is missing.

    I just described the process, albeit in a rather sparse form.

    One flaw in your reasoning is that, when comparing expectations of the theory to empirical evidence, you consider only the confirming evidence and discard the rest.

    Such as …

    The pattern you infer does not include orbital spiderwebs, for example. It actually doesn’t include just about anything at all we see in biology.

    ???

    Take for example whale evolution. It doesn’t fit the pattern at all. It requires a mutation rate quite different from what is observed, in addition to the development of novel features through mutation and selection. So what do you do? You just leave it out because it contradicts your expectations.

    WHAT? So whale evolution doesn’t fit the pattern we would expect if whales evolved. Do you really believe that all the evidence for whale evolution is ignored by biologists because it contradicts evolution?

    What you seem to have trouble understanding is that no one knows whether the differences between genomes is made of mutations and selections. It’s an assumption, a leap. The observation that mutations occur and change the genome does not lead to the conclusion that differences between genomes are made of mutations.

    I agree, even though we can see that mutations occur, and we know of multiple sources for possible mutations, and we can observe and even predict their effects, we can never know if any change in a genome is due to a mutation – it could be that god changed it. In the same way we can never know if the existance of a stalactite is due to the deposition of minerals by water, of it god sculpted it. The point is that we have a whole raft of well studied mechanisms by which variation occurs in a genome, we can make good predictions based on this knowledge and no extra entities appear to be required to produce the effects that we see.

    Not only does one not logically follow the other, but the conclusion faces enormous hurdles of contradictory evidence. Not least among them is that it forces one to attribute designs that clearly require foresight, planning, and coordination to a process that has neither goals nor the capacity nor the intent to plan for them.

    Your reasoning is based on that big assumption – that what you see in nature requires foresight. The problem is that thar the actual research indicates that foresight is not required, and that what we see in nature is more or less what we would expect from the non-foresighted process of evolution.

    Given a rodent, generations of mutation and selection give you a bigger or smaller rodent. The process is not consistent with numerous coordinated variations required to add wings, echolocation, and a nervous system that can coordinate them.

    More assumptions, driven by a lack of understanding and imagination. Variation can affect many aspects of morphology including limbs and skin folds. The nervous system for hearing already exists, as do ears, and I gather that humans can do primitive echo location with a bit of practice. Have you heard of flying squirrels?

    You’ve turned the other way. First evolution explained everything in biology. Now, evolution explains nothing but rather everything in biology supports the pattern of evolution.

    ??? Are you even reading my comments?

    But it doesn’t. By your own words and evidence it supports genetic change over time. It does not support genetic variation and natural selection as the source of that change.

    That is a hopelessly confused statement. So the evidence supports the observation of genetic change over time, but variation in the genes is not the source of that variation over time? (BTW Natural selection is not a source of change, it is just a way of saying that different traits in a given environment affect reproduction rates – something that is easy to observe)

    I think I’ll leave it there for the moment.

  321. An awkward silence … ;)

  322. 322

    If you look real hard you might read what I have to say about it elsewhere on this very page.

    It raises the question – do you people actually read this stuff? I’m not trying to be snarky, but I don’t get the impression that you critically analyze anything that suggests support for evolution.

  323. The experiment was Intelligently Designed. Yet more evidence of ID!

  324. Reading your stuff is not always illuminating. One wonders why you don’t learn something about a hundred and fifty years of argument and evidence before posting.

    There’s really nothing in your argument that wasn’t hashed out seventy five years ago.

  325. Response to champignon:
    As for the other possibility — a mechanism other than undirected evolution that explains the nested hierarchy — I am unaware of any. ID does not qualify, since it does not predict the nested hierarchy.

    Well, actually, undirected evolution isn’t the only framework that predicts a nested hierarchy. The front-loading hypothesis, an inherently teleological hypothesis, does predict a nested hierarchy.

    Furthermore, you state that “a mechanism other than undirected evolution that explains the nested hierarchy — I am unaware of any.” If genetic variation was constrained by the cellular complexity of organisms, then a nested hierarchical pattern, at the DNA level, would also result, ’cause if the amount of genetic variability a unicellular species could undergo was much more than the amount of genetic variability a multi-cellular species like homo sapiens, we would expect organisms with similar number of cell types to be less distant to each other, at the genetic level, than to organisms with a significantly different number of cell types.

    The main points:

    a. The front-loading hypothesis also explains the nested hierarchy observed in nucleic/amino acid sequences, thus it cannot be said that undirected evolution is the only framework that explains it.

    b. If cellular complexity constrains genetic variability of a species, a nested hierarchy will also result.

  326. Onlookers (and participants):

    This thread of discussion has now been going on for almost two weeks.

    Running through it to see the highlights, it is again quite clear that the advocates of the idea that small, incremental chance changes rewarded by reproductive success in ecological niches can, do, and did cumulatively account for body plans from the simple to the complex have yet to show a concrete, step by step observed case in point that the proposed mechanism to account for such vast biodiversity does occur.

    What we find instead, is a consistent pattern of extrapolation and dismissal of something we do routinely observe: when a complex functional whole depends on a properly arranged, organised and wired together set of components parts, that very information-rich functional dependence sharply constrains the number of acceptable parts and how they can be fitted together, relative to the raw number of ways that these or similar parts could be arranged without such constraints.

    In short, the phenomenon of cases in point E within “islands of function,” T, in much larger spaces of possible — but overwhelmingly non-functional arrangements, W, is a real-world, commonplace (and even dominant) observation once we deal with complex, multi-part, functionally organised systems.

    As a direct consequence of this pattern of isolated constraint, it is generally not the case that chance selection and/or arrangement or rearrangement of many parts will yield a functional whole. the reason for this can be seen from Mengue’s criteria C1 – 5, made with respect to the bacterial flagellum (a biological case), which appears in the OP at point 6, and which does not ever seem to have been seriously considered by objectors to the OP, above:

    For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met:

    C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

    C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

    C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

    C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

    C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

    ( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

    Point 9 of the OP then adds the onward issue:

    What is coming out ever more clearly is this:

    when a set of matching components must be arranged so they can work together to carry out a task or function, this strongly constrains both the choice of individual parts and how they must be arranged to fit together.

    A jigsaw puzzle is a good case in point.

    So is a car engine — as anyone who has had to hunt down a specific, hard to find part will know.

    So are the statements in a computer program — there was once a NASA rocket that veered off course on launch and had to be destroyed by triggering the self-destruct because of — I think it was — a misplaced comma.

    The letters and words in this paragraph are like that too.

    That’s why (at first, simple level) we can usually quite easily tell the difference between:

    A: An orderly, periodic, meaninglessly repetitive sequence: FFFFFFFFFF . . .

    B: Aperiodic, evidently random, equally meaningless text: y8ivgdfdihgdftrs . . .

    C: Aperiodic, but recognisably meaningfully organised sequences of characters: such as this sequence of letters . . .

    In short, to be meaningful or functional, a correct set of core components have to match and must be properly arranged, and while there may be some room to vary, it is not true that just any part popped in in any number of ways can fit in.

    As a direct result, in our general experience, and observation, if the functional result is complex enough, the most likely cause is intelligent choice, or design.

    This has a consequence. For, this need for choosing and correctly arranging then hooking up correct, matching parts in a specific pattern implicitly rules out the vast majority of possibilities and leads to the concept of islands of function in a vast sea of possible but meaningless and/or non-functional configurations.

    Point 10 then concludes:

    10 –> Consequently, the normal expectation is that complex, multi-part functionality will come in isolated islands. So also, those who wish to assert an “exception” for biological functions like the avian flow-through lung, will need to empirically warrant their claims. Show us, in short.

    You will note the invited case study of a significant body plan innovation, which was simply not seriously addressed. Here is Wiki, speaking against interest:

    Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi. The airflow through the avian lung always travels in the same direction – posterior to anterior. This is in contrast to the mammalian system, in which the direction of airflow in the lung is tidal, reversing between inhalation and exhalation. By utilizing a unidirectional flow of air, avian lungs are able to extract a greater concentration of oxygen from inhaled air. Birds are thus equipped to fly at altitudes at which mammals would succumb to hypoxia. This also allows them to sustain a higher metabolic rate than an equivalent weight mammal.[15]

    The lungs of birds are relatively small, but are connected to 8-9 air sacs that extend through much of the body, and are in turn connected to air spaces within the bones. The air sacs are smooth-walled, and do not themselves contribute much to respiration, but they do help to maintain the airflow through the lungs as air is forced through them by the movement of the ribs and flight muscles.[16]

    Because of the complexity of the system, misunderstanding is common and it is incorrectly believed that it takes two breathing cycles for air to pass entirely through a bird’s respiratory system. Air is not stored in either the posterior or anterior sacs between respiration cycles, air moves continuously from the posterior to the anterior of the lungs throughout respiration. This type of lung construction is called a circulatory lung, as distinct from the bellows lung possessed by other animals . . .

    Now, how do we move, in incremental, chance-driven mutational, non-purposeful steps that are all functional and advantageous in some ecological niche or other, from a bellows to a circulatory lung with one way flow? (In parallel with all the other “adaptations” to make a functional, flying bird?)

    Let’s see what evolution pages (per the magic of Google) has to say on the matter; as a typical example of how the arguments are actually typically made on the evidence we do see:

    The hypothesis that modern birds are the descendants of a group of small dinosaurs, called dromaeosaurs, part of a bipedal group called theropods, has become increasingly accepted by the scientific community, to the point where it is very close to being a scientific consensus . . . .

    There is, however, one aspect of bird physiology that has been a puzzle since the theory of dinosaur origins of birds was proposed. The fact is that birds have a respiratory (breathing) system unlike that of almost all other tetrapods (tetrapods include all mammals, reptiles, amphibians and birds). The puzzle centres on the fact that birds seem to have a breathing system different from all other living tetrapods without any antecedent – this is a situation that creationists have, unsurprisingly, attempted to exploit. Now, however, there is strong evidence that theropod dinosaurs that predated the emergence of birds in the record had pulmonary systems like modern bird breathing systems. This means that the flow-through lung is not unique to birds, but was present in theropod dinosaurs before the evolution and emergence of birds . . . . All tetrapods (mammals, reptiles, amphibians, crocodilians) apart from birds have a pair of lungs that operate on the bellows principle . . . .

    A recent paper in Nature (11), shows that theropod dinosaurs have vertebrae pneumatized in a way that is very similar to modern birds. The authors have investigated the well preserved fossil of a theropod dinosaur called Majungatholus atopus and have found that the vertebrae possess very close similaritiies in pneumaticity compared with an extant bird (the sarus crane) . . . .

    this recent study has shown that non-avian theropod dinosaurs had the necessary anatomy for flow-through ventilation similar to extant birds and, that in the evolution of the flow-through system, the tail end air sacs likely developed before those at the head end of the trunk . . . .

    Carl Wieland of ‘Answers in Genesis’ has written a response to this paper (13), that is generally reasonably restrained, but utterly fallacious. He correctly points out that this analysis does not, in itself, resolve the issue of the steps by which a bellows type lung evolved into the avian flow-through system. His discussion is, however fundamentally flawed in one important respect: his main objection to the evolution of an avian system from a bellows system is that he cannot see how it could happen. This of course is the old canard (a term that is peculiarly well suited to this subject!) of the argument from personal incredulity. Carl cannot conceive of a pathway by which the avian lung could evolve from a bellows arrangement, so of course, in his mind, it cannot have happened. This was the original design argument used by William Paley. It was intellectual gruel then, and it is intellectual gruel now . . . . The fact is that not only is the evidence very strong that birds evolved from theropod dinosaurs, but there is no objection ‘in principle’ to development of the avian respiratory system.

    You can’t make this up.

    Here, you have an evolutionary materialism apologist, attempting to address the origin of the avian lung system, and all he can do is point out that well, there is another set of animals that seem to have a similar lung, and those nasty Creationists are simply too skeptical, even though we have not shown the required steps.

    After, all, we can add, the only properly “scientific” way to look at the origin, is to assume that it MUST somehow have come about by “natural causes,” not “supernatural” ones. So, if we can point out another animal that maybe had a similar lung and which we can argue is ancestral, the problem can be set aside.

    Now, let us assume for a moment that the relevant dinosaurs did have flow-through lungs. Has that answered, how such lungs came to be, step by step?

    Nope.

    It has just displaced the unanswered question, and the hope is that by polarising the atmosphere by setting up and knocking over “supernaturalist” and “creationist” strawmen, and pointing to how maybe birds evolved from the dinosaurs the question that the source of complex functionally specific organisation of body plan components and of associated information can be shelved.

    But, the obvious question is whether such FSCO/I — on actual observational evidence — can most reasonably be explained on blind chance and necessity. Or, is intelligence the most plausible explanation for such FSCO/I, for many reasons as can be seen from here on.

    No wonder, the Darwinism Refuted site underscores, citing Denton:

    The important thing is that the reptile lung, with its bidirectional air flow, could not have evolved into the bird lung with its unidirectional flow, because it is not possible for there to have been an intermediate model between them. In order for a creature to live, it has to keep breathing, and a reversal of the structure of its lungs with a change of design would inevitably end in death. According to evolution, this change must happen gradually over millions of years, whereas a creature whose lungs do not work will die within a few minutes.

    Molecular biologist Michael Denton, from the University of Otago in New Zealand, states that it is impossible to give an evolutionary account of the avian lung:

    Just how such an utterly different respiratory system could have evolved gradually from the standard vertebrate design is fantastically difficult to envisage, especially bearing in mind that the maintenance of respiratory function is absolutely vital to the life of an organism to the extent that the slightest malfunction leads to death within minutes. Just as the feather cannot function as an organ of flight until the hooks and barbules are coadapted to fit together perfectly, so the avian lung cannot function as an organ of respiration until the parabronchi system which permeates it and the air sac system which guarantees the parabronchi their air supply are both highly developed and able to function together in a perfectly integrated manner.112

    In brief, the passage from a terrestrial lung to an avian lung is impossible, because an intermediate form would serve no purpose . . . .

    reptiles have a diaphragm-type respiratory system, whereas birds have an abdominal air sac system instead of a diaphragm. These different structures also make any evolution between the two lung types impossible, as John Ruben, an acknowledged authority in the field of respiratory physiology, observes in the following passage:

    The earliest stages in the derivation of the avian abdominal air sac system from a diaphragm-ventilating ancestor would have necessitated selection for a diaphragmatic hernia in taxa transitional between theropods and birds. Such a debilitating condition would have immediately compromised the entire pulmonary ventilatory apparatus and seems unlikely to have been of any selective advantage.113

    Another interesting structural design of the avian lung which defies evolution is the fact that it is never empty of air, and thus never in danger of collapse. Michael Denton explains the position:

    Just how such a different respiratory system could have evolved gradually from the standard vertebrate design without some sort of direction is, again, very difficult to envisage, especially bearing in mind that the maintenance of respiratory function is absolutely vital to the life of the organism. Moreover, the unique function and form of the avian lung necessitates a number of additional unique adaptations during avian development. As H. R. Dunker, one of the world’s authorities in this field, explains, because first, the avian lung is fixed rigidly to the body wall and cannot therefore expand in volume and, second, because of the small diameter of the lung capillaries and the resulting high surface tension of any liquid within them, the avian lung cannot be inflated out of a collapsed state as happens in all other vertebrates after birth. The air capillaries are never collapsed as are the alveoli of other vertebrate species; rather, as they grow into the lung tissue, the parabronchi are from the beginning open tubes filled with either air or fluid.114

    Parabronchial tubes, which enable air to circulate in the right direction in birds’ lungs. Each of these tubes is just 0.5 mm. in diameter.

    In other words, the passages in birds’ lungs are so narrow that the air sacs inside their lungs cannot fill with air and empty again, as with land-dwelling creatures.

    So, the precise core challenge is to find exactly the functional intermediate steps accessible to incremental chance based changes that are the very stuff of the Darwinian tree of life. And, recall, the claimed link between birds and reptiles, Archaeopteryx, was the very first headlined “found” link, in 1861.

    One thing is certain, what we are seeing here is a consistent pattern of question-begging ducking and diversion of the central issue.

    So, we need to put the point where the IOSE discussion begins [I have updated slightly to account for an observed, ridicule based dismissal attempt at Catholic Forums], up front, centre:

    In recent decades, some educators, public policy advocates — and, most importantly, some scientists — through adopting methodological naturalism, have thought and taught that science can only work properly if it is understood and defined in terms of a search for “natural causes” or “material causes.” In the words of Harvard Biology professor Richard Lewontin (to be further discussed below):

    . . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated . . . [["Billions and billions of demons," NYRB, Jan 1997.]

    That is, before facts are allowed to speak for themselves, such evolutionary materialist thinkers hold that the only acceptable origins science theories are those that by design “must” fit in with the view that undirected blindly mechanical forces of nature and chance circumstances acting on matter and energy in one form or another, triggered purposeless changes and developments across time and are adequate to explain the world of life. In many cases, they may even assert that anything that questions such a view or its assumptions “is not science.”

    Which, to such minds, is close to saying: nonsense.

    But, it should be clear that some very big assumptions are being made; assumptions that — on their face — could easily bias or even warp attempts to sincerely find out what really happened in the deep past of origins.

    And, is it not reasonable that science should seek to discover and provide good observational evidence and objectively unbiased explanations about what really happens in our world — and (so far as that is possible) about what really happened in the remote past of origins, without a priori ideological blinkers? . . .

    Failing a serious addressing of such matters, on empirical evidence, the evolutionary materialist paradigm boils down to systematically institutionalised question-begging and censorship of otherwise quite reasonable alternative candidate explanations.

    It should be obvious to all, that FSCO/I, in our common observation and experience, is a generally recognised empirically reliable sign of design. Those who wish to draw a different conclusion for cases like origin of life or body plans need a better answer than Lewontinian a priori materialism, on whatever convenient excuse.

    GEM of TKI

  327. At the same time, to reason that what men have believed for 150 years cannot be wrong because that would mean they were deluded or deceived seems off.

    That wasn’t my reasoning. Of course they could be wrong. I was defending them as people of integrity with genuine reasons to reach the consensus conclusions that they do. I understand those reasons, in some depth, and I do not think there is something they are not telling you. This consensus includes people of faith as well as atheists, right and left-wingers, fools and knaves and geniuses and …

    Scientists being led to group-think and cling to ideologically motivated conclusions extrapolated from other instances of scientists being led to group-think and clinging to ideologically motivated conclusions? That’s a stretch.

    I think you misunderstand the scientific mindset. There is no glory or intellectual interest in propping up old theories IF a better fit to data comes along. Scientists are curious about what is. They are as skeptical as hell, of any and every claim. But gradually, through that filter, a body of theory is lashed together. It can be overturned by inconvenient facts. Scientists can be wrong – take the many who believed in special creation pre-Darwin for example. But that doesn’t not mean that all scientists are always wrong, and all consensus ripe for overturning.

    This Cornelius Hunter-style tripe – “Science is a religion and it matters” or “ideologically motivated” – are just desperate attempts to find a rationalisation as to why a large group of pretty smart people who study these phenomena day in day out don’t have a problem with it, while 50% of average joes think it’s bullshit. That might sound arrogant, but it is a subject that needs to be studied before you can have a meaningful critique. That doesn’t mean you will automatically become “one of us”. I disagree on numerous aspects of biology with others. But I know why they think what they think, and I credit them as rational, not deluded. It is as likely that I am wrong as that they are, and I learn from the exchange.

    Fitting in with the consensus is not the reason papers get published. Darwin overthrew a consensus, so did Kimura, so did Peter Mitchell, so did any number of scientists. They did not do so by moaning about ideological entrenchment. They provided cogent arguments backed up by data.

  328. doesn’t not mean

    Nnnnggghhh. Read: “Does not mean”.

  329. Readers of an engineering-based persuasion may be interested in this. It may indeed have already been discussed and dismissed in these very pages. But I think it provides an excellent counter-argument to the assertive position as to what mutation and selection can and cannot do vis a vis complexity and function.

    It is not biological evolution, but the use of (some of) the principles of biological evolution to take a ‘box of parts’ (the junkyard) and generate, by directional selection (“a-bit-better” being more likely to survive than “a-bit-worse”) a complex arrangement (the ’747′) that, if one were presented with the end result, one would consider to be both designed and IC. The role of selection is not to achieve a distant goal, but to filter the current pool. Survivors from that filter get to pass on the characteristics that favoured their survival.

    There is a real path of incremental improvement, but sampling any particular state, one would be at a loss to explain how it got there, absent a full audit. In biological evolution. of course, a detail of the process (death) precludes the retention of that audit.

  330. Nice strawman with a load of question-begging thown in.

    1- I would like a reference to the IDists who says if we smash a watch, put in a box and shake, if it does not reform into a watch that proves ID

    2- Reproduction- that needs to be explained before you can use it

    3- Mutation- still waiting on how it was determined that all mutations are random in any sense of the word.

  331. ChasD:

    Ah yes; yet another distractive, inadvertently question-begging strawman that will look like a proof to the eye of Darwinist faith. Sadly fallacious from beginning to end, with an emphasis on question-begging and distractors from pivotal gaps in the chain of reasoning:

    1 –> Abiogenesis, responding to the dismissive prefatory remarks, is the basis for the tree of life, and needs to account for the origin of digital code based self-replication in cell based life, which requires a replicator joined to a source of energy and parts and an assembler, i.e. we have metabolism plus self-replication. So, without a solid, empirically warranted answer to this question, Darwinian macroevolution — not just an extrapolation from microevo with minor changes to an already functional thing — has no place to begin. First big begged lot of questions. (For just one instance, where did the required computer language and execution machinery used in the simulation come from: design.)

    2 –> The presentation just rhetorically waves this away and appeals to the prejudices that design thinkers are ignorant, stupid, insane or wicked creationists in cheap tuxedos and enemies of science.

    3 –> So, we must first account for a vNSR joined to a metabolic system that integrates with raw materials in the environment. The resulting specified complexity involves an irreducibly complex von Neumann self-replicator [known genome size of order 100,000 bits], and code that involves a metabolic entity that harvests energy and raw materials from the environment and uses it to generate components and carry out the processes of life. So, the scope of genome required, and the machines to carry out the instructions, are major begged questions.

    4 –> Observe next, the implicit intelligent control and goal-directedness of the genetic algorithm being used, and how the issues of availability of matching and appropriate parts, as well as how they are to fuse together in correct ways and not block themselves by fusing in improper ways, is begged — not to mention the issue of isolation from interference from the environment — a key reason for encapsulation of cells. (Have you ever had to deal with the question of matching gears to one another, or screw and nut threads? Or of what happens if the proverbial monkey wrench gets dropped or thrown into the works? Where do the gears — inherently 3-d objects get their central axes and concentric, precise and accurate matching gearing cut? How are they pinned to axles that are accurately parallel and just the right spacing for meshing? How do pendulums get pinned and have just the right length to oscillate to the right time? How do gears get pinned to pendulums without interference and changing timing? How is the variation of period of a pendulum with scope of swing adjusted for? What about compensating for alignment relative to gravity, and for temperature variation — thermal coefficient of linear, area and bulk expansion, and questions of internal alignment of crystals etc? Etc Etc? All of this precision engineering, manufacture, placing and alignment, spontaneously? Horology requires a LOT of precision engineering to work!)

    5 –> So, the questions in Mengue’s C1 – 5 from the OP are being comprehensively begged.

    6 –> Next, as usual ever since the original ChasD, we have artificial selection standing in for real world differential reproduction, i.e. we have intelligent not blind selection on existing function, AND we have in fact ducked the huge question Paley highlights in Ch II of his Natural Theology — the provision of mechanisms and organisation for self-replication.

    7 –> It is worth contrasting the real Paley, Ch II, to the strawman Paley that is attacked in the video:

    Suppose, in the next place, that the person who found the watch should after some time discover that, in addition to all the properties which he had hitherto observed in it, it possessed the unexpected property of producing in the course of its movement another watch like itself — the thing is conceivable; that it contained within it a mechanism, a system of parts — a mold, for instance, or a complex adjustment of lathes, baffles, and other tools — evidently and separately calculated for this purpose . . . .

    The first effect would be to increase his admiration of the contrivance, and his conviction of the consummate skill of the contriver. Whether he regarded the object of the contrivance, the distinct apparatus, the intricate, yet in many parts intelligible mechanism by which it was carried on, he would perceive in this new observation nothing but an additional reason for doing what he had already done — for referring the construction of the watch to design and to supreme art . . . . He would reflect, that though the watch before him were, in some sense, the maker of the watch, which, was fabricated in the course of its movements, yet it was in a very different sense from that in which a carpenter, for instance, is the maker of a chair — the author of its contrivance, the cause of the relation of its parts to their use . . .

    8 –> In short, the vNSR is being assumed into place by the writer of the GA, not evolving out of the provided parts.

    9 –> But, without having the function of genetic self-replication in place, evolution by variation of a genetic code is impossible.

    10 –> So, the whole simulation — an imagination world exercise not subject tot the real constraints of reality, so apt to be misleading unless empirically validated — rests on a cluster of begged questions, compounded by strawman arguments and scapegoating.

    ______________

    FAIL.

    Now, kindly answer to the challenge in the original post and as summed up again with a bit of expansion just above at 55.

    Let’s get concrete: account for the avian lung, not on just so stories and interpolations on fossils, but on empirical observation with step by step evidence.

    Or, failing that, provide a similar case in point.

    No more strawman arguments, thank you.

    GEM of TKI

  332. This seems to be your stock response to discussions over evolution – Any simulation, model or argument that demonstrates how the mechanisms of evolution can generate complexity is dismissed because it doesn’t explain the origin of the replicator.

    This is a whopping strawman KF. Evolution is not a theory on the origin of life and it never has been, which is why it is compatible with the hypothesis of intelligently created life (and why plenty of evolutionary scientists are theists)

    The video is not a strawman because it addresses questions of evolution. Your response is a strawman because it switches evolution out and swaps it for bio-genesis, and then attacks what it has created before standing astride the straw corpse declaring victory and condemning all who do not accept the victory as abusers and amoral sources of evil in society.

  333. GCU- ID is not anti-evolution.

    And if the theory of evolution can’t or doesn’t say anuything abot the origin of life tehn it has nothing to say about any subsequent evolution because the two are directly linked.

    Ya see if living organisms were designed then the inference would be they were also designed to evolve. And taht means that stochastic processes would be only a very minor player relegated to breaking things.

    OTOH if living organisms arose from non-living matter via stochastic processes then the inderence would be stochastic processes are the sole dominion of evolution.

    The video is a strawman because it never identifies the IDist who says tha about a watch.

  334. 334

    Abiogenesis and evolution are not the same thing. But the origin of life points to intelligent design. That’s the very reason you wish to keep the discussions separate.

    If life was designed by intelligent agents it makes little sense to insist on excluding them from any further developments. You wouldn’t allow an intelligent cause for bricks, beams, and nails and then insist on omitting that same cause from explanations of buildings made from those things.

    Even a die-hard believer in darwinian evolution cannot separate the process from the system required for the process to occur. It’s like claiming that the existence of computers with processors and instruction sets and the abundance of software that runs on them are a coincidence, two unrelated phenomena.

  335. GCU- ID is not anti-evolution.

    That seems to depend on who you ask.

    Ya see if living organisms were designed then the inference would be they were also designed to evolve. And taht means that stochastic processes would be only a very minor player relegated to breaking things.

    Why? When we design artificial things to evolve we don’t relegate stochastic processes to the role of breaking things because that’s not what we observe happening in nature.

    OTOH if living organisms arose from non-living matter via stochastic processes then the inderence would be stochastic processes are the sole dominion of evolution.

    Why? What if the universe was designed so that life could arise from non life and then evolve (with the aid of stochastic processes)?

  336. If life was designed by intelligent agents it makes little sense to insist on excluding them from any further developments.

    Well you would want evidence of intervention. Your argument applies to everything of course – we could accept an intelligent creator of matter, then claim that models of planet formation are worthless because god could have done it, or anything else for that matter – the same for erosion, if god created matter and energy then why exclude god from the creation of the grand canyon?

    The fact is that God can do anything, the world could have been created yesterday, but made to appear ancient, in which case all science that relates to the formation of things is wrong.

    When we deal with scientific explanations we are dealing with a methodology that attempts to explain observations in terms of things that can be observed and measured. Saying ‘but god could have done it just like that as well’ add nothing – even if it is true!

    But the origin of life points to intelligent design. That’s the very reason you wish to keep the discussions separate.

    The fact is that, as I have said before, evolutionary theory is a framework for explaining what we observe about life over generations. It is not a framework for explaining processes by which matter can form self replicating entities. Atomic theory explains atoms, not where they came from. Plate tectonic theory explains continental drift, it doesn’t explain how the planet formed, etc etc.

    Attempting to poke holes in one theory by making it out to be a different theory, then pointing out that it doesn’t explain what it is not designed to explain is the epitome of a straw man argument.

  337. GCU:

    Pardon but that is an ad hominem not a response on some rather specific and technical merits.

    Has it ever dawned on you that the GA stock darwinist talking point is inherently and deeply flawed for reasons as outlined above? So, to point out the fallacies involved will require a bit of listing of the same basic problems? Problems that you do not answer.

    I have given some rather specific reasons why the video erects strawmen and begs questions. Kindly, answer them on the merits, or stand exposed as simply trying to dismiss what you cannot answer.

    In particular, you need to account for the steps from one body plan to the next, for the reproduction issue, and for the imposition of targetting. Those aere easy to glide over and beg in a simulation, but these are real world constraints when you have to try the same or similar in reality not in make believe digital worlds.

    As well, the problem with the convenient exclusion of the first body plan from the discussion of evolution can be aptly shown by asking what happens when we cut a tree off from its root.

    So, can a tree grow without its root?

    In short, the whole theory of darwin-style macroevolution pivots on a major begged question. The same problem of accounting for information and organisation for specified complexity then comes out as we look at body plan after body plan. THE SAME QUESTION.

    I must now turn to a painful matter.

    You echo a slanderous misrepresentation that is now circulating in the penumbra of hostile sites, in the teeth of my very explicit statement — there are several further onward links at the original page, in the F/N — as follows:

    *F/N, Jan 10: For those who need documentation on the key Social Darwinism roots of Hitler’s thought, I suggest that such examine the Weikart lecture and a discussion of a key clip from Mein Kampf that demonstrated the Darwinist-Haeckelian frame of thought, that beyond reasonable doubt strongly shaped Hitler’s thinking, speech and behaviour. In addition, such may wish to look at a previous post in this blog, here, that ties in remarks by Darwin in his The Descent of man, chs 5 – 7 [yes, Darwin, too, was demonstrably a Social Darwinist . . . ], and highlights H G Wells’ warnings in his popular novel, War of the Worlds, 1897. In short, the danger should have been recognised and averted generations before the Holocaust, and — given known turnabout tactic New Atheist talking points here — no, this does not constitute putting “all the world’s ills” on Darwinist shoulders. A fairer understanding of the Christian gospel would recognise that the Christian Faith has always held that our ills largely stem from our common challenge that we are all finite, fallible, morally fallen and too often ill-willed, walking in rebellious alienation from our common Father, that then leads to alienation within our hearts and quarreling, abuse, oppression and worse between us and our brothers, sisters and cousins who were equally made in God’s image with us. Hence the gospel highlights our common need for recognition of our moral plight, repentance, forgiveness and moral-spiritual transformation through the Christ of God; which, far too often, includes those of us who name the name of Jesus on our lips but fail to walk — however stumblingly — in his way of discipleship and loving service . . .

    It should be clear that I have always pointed out that ALL of us face a common moral dilemma. But that problem gets compounded in some eras when there are dominant ideas that push people to think in terms of “might makes right,” or the equivalent, i.e. ideas that imply, invite or even outright promote radical relativism and/or amoral nihilism.

    Let me speak for record — I will not tolerate a hijacking of this thread on this matter — as a matter of well documented historical fact, eugenics and social darwinism have been such ideas that have wreaked havoc well within living memory.

    Both of these ideas saw themselves — and were widely accepted by leading scientists, medical men, lawyers and law makers, educators, statesmen and even clergymen — as “scientific,” which then led to acceptance of policies and practices that were horrendous. Not only did these ideas present themselves as scientific, they were beyond doubt rooted in darwinist, evolutionary thought. Darwin himself saw the way that Saxons [Englishmen], Irish [Celts} and Scots related historically as an expression of natural selection, he saw the conflict between the Ottomans and Europe in terms of natural selection, and he predicted that within centuries the more advanced races would wipe out the less advanced races of man, all in letters and/or in his Descent of Man chs 5 - 7. Galton, his cousin, explicitly built the eugenics movement on evolutionary foundations, and Darwin's family was associated with it for decades. You have doubtless seen the motto "Eugenics is the self-direction of human evolution."

    What happened is that in Germany, we had a perfect political and economic storm, that brought to power men who took these ideas to the "logical" conclusion, and set out to wipe out the Poles as the first inferiors to be removed, and the Jews as tending to pollute and dilute the strength of the Aryan race. So, Hitler set out as a political messiah to rescue his nation, as he saw it the hope for progress to a higher level of civilisation. And, on the premise that might indeed made right, and that subhumans as he saw it were life unworthy of living.

    All of these are directly traceable to the HISTORICAL influence of evolutionary materialism acting throughthe widespread acceptance of Darwinist theories of origins of life and man, which same philosophy/ideology is routinely imposed on origins science today.

    So, as others have seen ever since Plato in The Laws, Bk X 2350 years ago, I highlighted a key moral hazard that needs to be faced and addressed, not dismissed or ignored, lest it come back to bite us again.

    In highlighting the crucial amorality and cognitive incoherence of the worldview of evolutionary materialism, I have in particular pointed out how this philosophy -- which has quite plainly been imposed on origins science in our day -- is self referentially incoherent and has in it no foundational IS that can objectively ground OUGHT. Those are actually pretty well established and acknowledged points, as can be seen from Haldane and Provine:

    HALDANE, 1927:"It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms." [["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.]

    PROVINE, 1998: Naturalistic evolution has clear consequences that Charles Darwin understood perfectly. 1) No gods worth having exist; 2) no life after death exists; 3) no ultimate foundation for ethics exists; 4) no ultimate meaning in life exists; and 5) human free will is nonexistent . . . . [U Tenn Darwin Day address]

    If you don’t like the logical and moral consequences of evolutionary materialism as acknowledged by these two darwinists, then maybe you should reconsider its privileged status in today’s world of thought.

    I think you need to go back to the slander and smear sites that are spreading a polarising and smearing misrepresentation and correct. If you have any regard to truth or fairness.

    But, all of this is tangential.

    The focus for this thread is the question of FSCO/I and islands or continents of function. A very specific challenge is on the table at 55 just above — the origin of the avian lung as an illustration of how in the biological world we supposedly have continents of function that can be arrived at incrementally.

    Kindly answer it. Fair is fair, someone proposed a counter and I have promptly answered it.

    GEM of TKI

  338. F/N: Let us all remember that in the end, cellular machines and components are in the main built out of proteins, which are assembled step by step based on coded digital instructions as strings. These then fold and fit key-lock style to do the work of the cell. All of the gears, rods, backing plates, connectors, axles etc in the simulation would have to come through that process.

    That of course poses enormous challenges for the initialisation of a first self-replicating metabolic entity that can do that.

    But also — I here answer yet another strawman, this challenge holds for novel structures and systems to move to more and more involved multi-part functionally specific complex entities, the problem of step by step building a string on algorithmic, prescriptive coded information that then folds and knots itself to make the right set of matching components that self assemble to give machinery, is a huge and unanswered question.

    More questions for those touting the video to un-beg for us. KF

  339. H’mm: could darwinist responders unbeg the questions in the context of say the origin of the avian lung (or if you insist on a reptilian ancestor, in that case), with empirical data in play. KF

    PS: As Joe repeatedly highlights, Design Theory does not reject evolution, common descent or even universal common descent, the question is where did the functional info and organisation come from, in light of what we know empirically and analytically about the source of such FSCO/I.

  340. 340

    Attempting to poke holes in one theory by making it out to be a different theory, then pointing out that it doesn’t explain what it is not designed to explain is the epitome of a straw man argument.

    Excellent. So you’ll never ask how ID explains the formation of this that or the other thing again, right? And if someone else does I’ll quote you.

  341. Scott, if ID is not designed to explain anything, how can it be a theory?

  342. Interesting, if predictable, responses.

    “ID is not anti-evolution”; the video illustrates an aspect of said evolution, yet it is somehow strawmannish, or misdirection, or a response to a challenge that was not raised, or it’s about smashed clocks and no-one-ever-said-smashed-clocks or otherwise Just Plain Wrong.

    Ho hum. It demonstrates an example of functional complexity arising by navigating a ‘space’ by random mutation and directional selection. That is directly pertinent to the ‘islands of function’ challenge. It addresses only the issue it addresses – not body plans or lungs or wings or abiogenesis or anything else. Anyone who doubts the random nature of the mutation process is free to download the code. If it turns out not to be random, they are free to amend it to be so.

    What is the ‘FSCO/I’ profile of this system – one we can examine and digitise – rather than the sequence of evolution of one we cannot – such as the avian lung? Why – preferably in a short response not peppered with irrelevancies about Plato and the horrors of materialism – is it not a valid example of incremental increase in both complexity and the appearance of purposeful design and IC, using only the ID-conceded functions of mutation and selection?

  343. F/N (as they say around here) the distinction between origins and evolution is absolutely vital. Evolution (the thing ID is not anti, remember) is about changes in populations of replicators. How replicators arose is irrelevant to evolution. The fact that these replicators are doing their business inside a designed computer is irrelevant, as is the fact that this is not biological material. The processes operating upon them are fair simulations of birth, death, mutation and selection.

    The scope of these processes in nature cannot be proven categorically, but the OP uses the metaphor of ‘search space’, and another analogy from ‘hard engineering’. Yet my link is irrelevant because it addresses complexity in precisely such non-biological space?

  344. GCU:

    Pardon, but again you are pummelling strawmen.

    The video in effect claimed that FSCO/I and thus complex specifically functional multi-part body plans, can arise by UNINTELLIGENT processes of chance variation and “natural” selection.

    We therefore showed how the video in fact — inadvertently — demonstrated processes of intelligent design and goal-directed intelligent selection, as an instance of an intelligently designed Genetic Algorithm.

    Over the years, we have seen many claimed cases of the one that in fact turn out to be the other.

    Instead of playing with imaginary software worlds, why not show us, on empirical evidence how the avian lung — a good example of FSCO/I and arguably IC –came to be as a matter of fact, or at least with good empirically evidenced models to support it realistically.

    If not that case, why not propose and discuss something comparable, maybe origin of flight in bats or the echolocation system of bats and whales — kindly include how there are such close genetic parallels involved — or the like.

    You will see this is not OOL, and it is not minor adaptation of an existing body plan. it is a claimed case of an island of specific and complex functional organisation.

    Our point is that body plans, even if they originated by means of genetic variations and niche selection per superior reproductive success across generations, would enfold intelligent information injection, indeed sophisticated injection of information, whether at an initial stage or incrementally makes but little difference.

    If Darwinian macroevo on chance variations and blind natural selection is the best and best evidenced explanation of the origin of body plans, kindly provide cases in point. Not of finch beak length variation or cichlid colour schemes and body shapes, or moth colouration or variation across species borders similar to circumpolar gulls etc, but of origin of significant and unprecedented novel body structures.

    Incremental adaptation of an existing functional body plan is one thing, origin of a body plan de novo is another, once we look at the requisites of complex, integrated multipart functional structures.

    The video did show that [within limits and constraints on implied features that would have to be done in a real world case . . . ], but turned out to be a case of unrecognised intelligent design.

    Kindly, show us more than that.

    Surely, you did not intend to substantiate the point that he only empirically warranted source of such structures is intelligent design?

    Supposedly, that is our point, not yours.

    Or, did your side score an own goal, again?

    GEM of TKI

  345. 345

    Scott, if ID is not designed to explain anything, how can it be a theory?

    Perhaps you should read the FAQ. I had simply assumed from your participation in so many discussions that you were better acquainted with it.

  346. First things first:

    Intelligent Design is Not anti-evolution

    Ya see if living organisms were designed then the inference would be they were also designed to evolve. And taht means that stochastic processes would be only a very minor player relegated to breaking things.

    Why? When we design artificial things to evolve we don’t relegate stochastic processes to the role of breaking things because that’s not what we observe happening in nature.

    When we design artificial things to evolve they evolve by design, not via stochastic processes. And yes we observe stochastic processes breaking things in nature.

    Whe we design a car the car operates as it is designed to operate.

    OTOH if living organisms arose from non-living matter via stochastic processes then the inderence would be stochastic processes are the sole dominion of evolution.

    Why? What if the universe was designed so that life could arise from non life and then evolve (with the aid of stochastic processes)?

    That is not related to what I said.

  347. Genomicus,

    The front-loading hypothesis also explains the nested hierarchy observed in nucleic/amino acid sequences, thus it cannot be said that undirected evolution is the only framework that explains it.

    Not true. Front-loading fails to explain the nested hierarchy, for two main reasons:

    1. Unlike evolution, front-loading is not restricted to gradual changes. If massive changes occur (which is possible under front-loading), then the pattern of the nested hierarchy will be destroyed. The nested hierarchy is not merely an indicator of descent with modification; it’s an indicator of descent with gradual modification.

    2. Under front-loading, nothing prevents major identical changes from happening in unrelated species. This will also destroy the nested hierarchy.

    In a nutshell, front-loading has the same problem as common design: It is compatible with the nested hierarchy only if you make the additional ad hoc assumption that the designer acts in a way that is indistinguishable from evolution.

    Anyway, front-loading is a non-starter because it cannot explain how unexpressed genetic information is protected from mutation for eons until the moment comes when it is finally “turned on”.

  348. Genomicus,

    My reply is here.

  349. Scott,

    The FAQ lists two “predictions” of ID, neither of which is actually entailed by ID, and neither of which falsifies evolutionary theory.

    Meanwhile, the nested hierarchy by itself confirms evolutionary theory to an astounding degree of precision, not to mention the other predictions made by the theory.

    ID is pretty thin gruel.

  350. The nested hierarchy observed is not an expected outcome of accumulations of random mutations. Gradual modifications would produce a blending of defining characteristics and nested hierarchies cannot have that.

    The only nested hierarchy the ToE expects is one based on something called “all life”- see Eric B Knox, “The use of hierarchies as organizational models
    in systematics”, Biological Journal of the Linnean Society (1998), 63: 1–49

    Also front-loading does not require unexpressed genetic information.

  351. CCU:

    Well you would want evidence of intervention. Your argument applies to everything of course – we could accept an intelligent creator of matter, then claim that models of planet formation are worthless because god could have done it, or anything else for that matter – the same for erosion, if god created matter and energy then why exclude god from the creation of the grand canyon?

    I think you have caught, even if in denial, the essence of ID here. ID is all about evidence of intervention.

    The same evidence that applies to OOL applies to further evolution. It’s as simple as that.

    Look at the fundamental argument of the origin of protein domains: half of them were generated in the very first phases of life, being present in LUCA. As there is no evidence of any precursor of LUCA, those domains can well have been generated at OOL.

    But the other half was generated after. In the course of natural history of evolution. Up to very recent evolutionary times.

    So, if the same informational problem has to be solved for protein domains (and other functional information) at OOL, and after, then if a valid explanation is proposed (sich as ID), then it applies both to OOL and to further evolution.

    Again, it’s a simple as that.

  352. 352

    Champignon,

    This is why these debates become a waste of time. You can say something a thousand times and someone will pretend you didn’t.

    Evolution is variation and natural selection.

    Meanwhile, the nested hierarchy by itself confirms evolutionary theory to an astounding degree of precision

    It is impossible to derive so much as a single case of variation and selection from a nested hierarchy. You cannot confirm variation and selection without variation and selection. If someone told you different, I hope you didn’t pay them for it. Now that I’ve corrected you, why do you keep repeating it?

  353. GP: Very well put, as usual! KF

  354. There is no informational problem regarding the origin of protein domains. You have created a science fiction fantasy out out of missing history.

    There is no scientific mystery about missing history. It is quite obvious that protein evolution will tend to fix the most useful variants very quickly, resulting in the extinction of cousin variants. This will happen because unlike small differences in size and shape, differences in proteins will affect metabolism. Any allele that provides an advantage will fix quickly in a population.

    Which goes some way to explaining why variations on modern proteins are unlikely to be as functional as wild proteins.

  355. Scott,

    Your demand that we derive cases of variation and selection from the nested hierarchy is bogus. It’s like saying to a physicist, “If you can’t derive quantum mechanics solely from the spectra of elements and compounds, then those spectra — and the fact that they match the predictions of the theory — do not in any way confirm the theory.”

    The double standard is glaring. You set the bar much higher for evolutionary theory than for other sciences that don’t challenge your religious preconceptions.

    Science is about coming up with theories to explain and predict our observations.

    We know that:

    1. Natural selection and drift occur.

    2. They predict the nested hierarchy.

    3. The prediction is confirmed to better than one part in a trillion trillion trillion trillion.

    4. No other theory predicts the nested hierarchy, including common design, front-loading, and ID generally.

    5. This confirmation of a distinctive prediction is strong evidence in support of evolutionary theory.

    ID’s lack of confirmed observations, by contrast, is embarrassing.

  356. We therefore showed how the video in fact — inadvertently — demonstrated processes of intelligent design and goal-directed intelligent selection, as an instance of an intelligently designed Genetic Algorithm.

    No, KF. No, no, no, NO. I thought you might be above that hollow sophistry. The algorithm was intelligently designed. Its result was not, except inasmuch as its designer knew – from observation of natural processes – how nature operates on genes and phenotypes, and so knew how to mimic those processes.

    It used only mutation and selection. The end result was apparent design and complexity, by incremental selection without a particular design in mind.

    Hey ho. I don’t doubt that both sides will retain their prejudices intact. An ‘own goal’? What do you think my goal actually was? To convert souls for Darwinism? Or simply to discuss an interesting scientific and philosophical point wrt design, complexity and the limitations of mutation/selection? Your agenda may be political; mine is not (but then, that’s exactly what a crypto-political darwinist would say).

    I will leave it to your ‘astute onlookers’ to determine their own take on the matter.

  357. Perhaps you should read the FAQ. I had simply assumed from your participation in so many discussions that you were better acquainted with it.

    I have, and going by the FAQ it is not a theory in the sense that the theory of evolution is a theory.

    But you were treating it as though it symmetry with the theory of evolution.

    You can’t have it both ways!

    If ID isn’t a theory in the sense of explaining anything, then it’s not comparable with a theory that is.

    If it is a theory in the sense of explaining things, then clearly it needs to do some explaining.

    But whenever we ask for an ID explanation of something, we are told to read the FAQ. And then whenever we explain something in terms of the theory of evolution, we are told that the explanation is a “just-so story”.

    It’s heads you win, tails we lose! And the reason for that is equivocation with the word “theory”. ID is not a “theory” in a scientific sense (which is not to say it isn’t science) of a postulated explanation. It’s a default conclusion in the absence of an explanatory theory which IDists find persuasive.

    That’s why, IMO, it is bad science.

  358. Petrushka:

    Thank you for the usual cathechism. It is always good to be remembered of the “cognitive strength” of the darwinian position…

  359. 359

    Champignon,

    Are you sure you’re thinking this through?

    1. Natural selection and drift occur.

    OK.M

    2. They predict the nested hierarchy.

    Of course they don’t. They predict a nested hierarchy. Does the nested hierarchy they predict bats and spiders and humans and sea cucumbers? Not at all. Assuming that the starting point is a reproducing cell, they predict an assortment of varied cells. There is no observation relevant to drift or natural selection leading to a prediction that they would produce the variety of multicelled organisms that form the hierarchy. Those organisms cannot be explained by drift and selection, so how can drift and selection predict them?

    3. The prediction is confirmed to better than one part in a trillion trillion trillion trillion.

    See the above. That’s some fantastic imagination. The way you’re blowing through these talking points suggests that you’re repeating something you heard but clearly never thought through.

    4. No other theory predicts the nested hierarchy, including common design, front-loading, and ID generally.

    So what? Not everything needs to be a prediction. There is no logical inconsistency between any of these things and nested hierarchies. And, as pointed out, nothing at all, period explains the nested hierarchy.

    5. This confirmation of a distinctive prediction is strong evidence in support of evolutionary theory.

    As I’ve pointed out, the diversity in biology is consistent with some expectations of evolutionary theory (nested hierarchies for example) but inconsistent with others (such as the specifics of the organisms that make up the hierarchy.)

    The theory that the sun revolves around the earth predicts that I’ll see the sun cross the sky every day.

    Sure, some evidence harmonizes with evolutionary theory. Lots of evidence contradicts it, and lots can’t be explained by it. For one thing, all of your evidence omits natural selection. You include just about every living thing on earth as evidence of selection and yet you cannot cite the selection of so much as a single variation. You cannot explain A using B and C while omitting either B or C.
    It’s so mind-numbingly simple that I can’t believe I have to put it into words once, let alone make the point over and over.

  360. Scott,

    Are you sure you’re thinking this through?

    Yes. Are you?

    1. You’ve conceded that evolutionary theory predicts a single nested hierarchy.

    2. You’ve conceded that the prediction is confirmed: we observe a single nested hierarchy, to an astounding degree of precision.

    3. You’ve conceded that no other theory predicts a single nested hierarchy.

    Your only argument seems to be this: “What if there’s some invisible, magical barrier to evolution that stops it in its tracks after a certain amount of ‘microevolution’? If that were true, then evolution wouldn’t explain the nested hierarchy we see!”

    Well, yes. And if there is an invisible, magical barrier around the solar system, and if the laws of physics are completely different on the other side of the barrier, then physics no longer predicts the spectra we see from distant stars and galaxies!

    I guess we’ll have to ditch both physics and evolutionary theory.

  361. 361

    I have, and going by the FAQ it is not a theory in the sense that the theory of evolution is a theory.

    There has been enough equivocation with the word that it’s pointless to split hairs over it. You pick the word you like and maybe I’ll use it. I don’t think nitpicking over the word is relevant.

    But you were treating it as though it symmetry with the theory of evolution.

    You can’t have it both ways!

    If ID isn’t a theory in the sense of explaining anything, then it’s not comparable with a theory that is.

    Just now, after a thousand people have asked how ID explains this or that and a thousand responses explain that’s not what ID is, just now you’re noticing that ID is not an explanation of how something is designed, created, or formed?

    Perhaps you should run through the FAQ one more time.

    Detecting a thing and explaining it are not the same. When one observes that a small amount of mercury has expanded or contracted within a thermometer they infer that its volume reflects, among other factors, its current temperature. This detection is based upon sound science. What does it explain? Does it tell you where mercury came from? Does it tell you where the heat is coming from, or where it went?

    But now that you’ve discovered, after all this time, that ID has no symmetry with evolutionary theory and is not an opposing explanation of origins, I’ll leave you with some time to absorb that. I do wonder what other misconceptions have been weighing you down.

  362. 362

    Champignon,

    I’m going to bookmark this exchange because of what it demonstrates. Even as I respond to you conceding certain obvious points and disputing others, you apparently only see the former and don’t even notice that the body of my post disagreed with you.

    If you can debate a point with someone and completely filter someone’s words so that you only observe the parts where they agree with you and discard the rest as if they never happened, even when you know the person disagrees with you, that speaks volumes to your perception of other evidence. Apparently you apply this filter to absolutely everything.

  363. The nested hierarchy observed is not an expected outcome of accumulations of random mutations. Gradual modifications would produce a blending of defining characteristics and nested hierarchies cannot have that.

    You miss a central result of evolution – fixation in populations. The ‘gradual modifications’ commence as single mutations and then some, through selection and drift, become the sole allele at their locus, population-wide. Then, the ‘gradual modification’ of the entire population has moved on one allele, and all descendants must descend from the originally mutated sequence at that locus. There is no blending at that locus; there is just one sequence.

    There are, of course, more subtle issues of intervening mutation before fixation and multiple loci, but best get your head around that one first.

  364. Response to champignon:

    Unlike evolution, front-loading is not restricted to gradual changes. If massive changes occur (which is possible under front-loading), then the pattern of the nested hierarchy will be destroyed. The nested hierarchy is not merely an indicator of descent with modification; it’s an indicator of descent with gradual modification.

    Front-loading is not restricted to gradual change, but nor is undirected, non-teleological evolution directed to gradual change. E.g., the endosymbiotic theory of the origin of eukaryotic cells is entirely non-gradual. It involves a primitive eukaryote engulfing a bacterium belonging to alpha-Proteobacteria, resulting in cells with mitochondria. That’s not gradual evolution. It’s incorporating a considerably different genome into an organism with significantly different characteristics. Then, of course, there are instances of lateral gene transfer whereby molecular machinery belonging to one species can be transferred “over night” to another species. This can hardly be considered “gradual evolution.”

    Further, the front-loading hypothesis, is pretty restricted when it comes to unfolding biological states that were front-loaded. For example, if the cilium was front-loaded, the front-loading designers would have to design the initial cells on earth with homologs of the ciliary proteins in order to make such an evolution plausible. So, when we find prokaryotic homologs of ciliary components, a nested hierarchy will result even if the cilium was front-loaded. Front-loading involves gradual evolution to a very large extent, thus a nested hierarchy is expected.

    In summary,

    a. Non-teleological evolution is not restricted to gradual change, as evidenced by the endosymbiotic theory for the origin of modern eukaryotes and by the lateral transfer of molecular machines from one species to another.

    b. As the front-loading hypothesis incorporates gradual evolution to a large extent, nested hierarchies are expected for many protein families.

  365. The same evidence that applies to OOL applies to further evolution. It’s as simple as that.

    No it isn’t. The process of evolution continues today; the process of “OOL” does not. If you take any current population, it will, according to some very concrete mathematical, empirical, computational and theoretical work, evolve. Blindly, by natural means. We do not need to insert a designer to keep this process ticking over; it happens all by itself. You have to interfere to stop it.

    So you are segregating out the unavoidable, natural process of evolution through mutation and selection/drift (as I find myself repeating, the thing ID is not anti), and asserting that there was historic interference with it, even though a ‘blind’ process of evolution can and does occur all by itself. We can argue about what it can create, but essentially, left to its own devices, a population experiencing birth and death will evolve, inexorably. Mutations will become fixed, and there is no going back.

    So when you talk of ‘further evolution’, you have to offer some means to distinguish that which can occur naturally from the interference. IC is one such attempt. But it remains entirely in accord with the ID inference, as stated, to allow for an ID OOL, and then NO further interference. The two are not subject to identical considerations.

  366. Another response to champignon:

    Under front-loading, nothing prevents major identical changes from happening in unrelated species. This will also destroy the nested hierarchy.

    Methinks that someone on this thread doesn’t know what front-loading is o.o

    Please elaborate on the above point.

    Anyway, front-loading is a non-starter because it cannot explain how unexpressed genetic information is protected from mutation for eons until the moment comes when it is finally “turned on”.

    Yup. I thought so. You don’t know what the front-loading hypothesis posits. The front-loading hypothesis simply posits that the earth was seeded with life forms which contained the necessary genomic information such that future evolution could be shaped and constrained. Nowhere does the front-loading hypothesis suggest that genes were simply turned off, not performing any function, and then suddenly, these genes are expressed resulting in a host of complex systems.

  367. But now that you’ve discovered, after all this time, that ID has no symmetry with evolutionary theory and is not an opposing explanation of origins, I’ll leave you with some time to absorb that. I do wonder what other misconceptions have been weighing you down.

    “Discovered” it, Scott?????

    It’s the point that some of us have been making for years!

  368. Another response to champignon:

    Under front-loading, nothing prevents major identical changes from happening in unrelated species. This will also destroy the nested hierarchy.

    Methinks that someone on this thread doesn’t know what front-loading is o.o

    Please elaborate on the above point.

    Anyway, front-loading is a non-starter because it cannot explain how unexpressed genetic information is protected from mutation for eons until the moment comes when it is finally “turned on”.

    Yup. I thought so. You don’t know what the front-loading hypothesis posits. The front-loading hypothesis simply posits that the earth was seeded with life forms which contained the necessary genomic information such that future evolution could be shaped and constrained. Nowhere does the front-loading hypothesis suggest that genes were simply turned off, not performing any function, and then suddenly, these genes are expressed resulting in a host of complex systems.

    BTW, I would like to point out that you didn’t even try to answer my point about organism complexity also resulting in a nested hierarchy. Just saying.

  369. Woops. Double post. Apologies.

  370. Scott says:

    But now that you’ve discovered, after all this time, that ID has no symmetry with evolutionary theory and is not an opposing explanation of origins, I’ll leave you with some time to absorb that.

    The Discovery Institute says:

    The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

    “Not an opposing explanation of origins,” Scott? LOL.

  371. Scott,

    I’m going to bookmark this exchange because of what it demonstrates.

    Please do. I hope you’ll refer to it often, until it starts to sink in.

    If you can debate a point with someone and completely filter someone’s words so that you only observe the parts where they agree with you and discard the rest as if they never happened, even when you know the person disagrees with you, that speaks volumes to your perception of other evidence.

    Don’t pretend that I haven’t directly addressed our points of disagreement. You claimed that the nested hierarchy doesn’t confirm evolution if we can’t “derive” specific instances of genetic variations from it and demonstrate why they were selected. I responded:

    It’s like saying to a physicist, “If you can’t derive quantum mechanics solely from the spectra of elements and compounds, then those spectra — and the fact that they match the predictions of the theory — do not in any way confirm the theory.”

    Or like saying to Einstein, “If you can’t derive general relativity from gravitational lensing and the precession of Mercury’s orbit, then those are not confirmatory — even if they exactly match the predictions of the theory.” It’s ludicrous.

    I also responded directly to your assertion that evolutionary theory can explain the existence of “varied cells” but not “the variety of multicelled organisms that form the hierarchy”:

    Your only argument seems to be this: “What if there’s some invisible, magical barrier to evolution that stops it in its tracks after a certain amount of ‘microevolution’? If that were true, then evolution wouldn’t explain the nested hierarchy we see!”

    Well, yes. And if there is an invisible, magical barrier around the solar system, and if the laws of physics are completely different on the other side of the barrier, then physics no longer predicts the spectra we see from distant stars and galaxies!

  372. Chas D:

    You miss a central result of evolution – fixation in populations.

    How did I miss it and when has it been observed?

    BTW there isn’t anything that latches a nucleotide so one that has mutaed can mutate again and even back to the original.

  373. How did I miss it and when has it been observed?

    If you think that “gradual modifications would produce a blending of defining characteristics”, then you missed it – it is the reason that is not the case. In fact, you may have missed the whole thing about Mendelian genetics. Start in 1902 or thereabouts. Bateson. Certainly cleared the ‘blending’ thing up for early critics.

    Remember that we are talking about molecular phylogeny – DNA. Fixation is observed whenever a rare allele becomes extinct, and only one allele remains in the population. The remaining allele is de facto fixed. An allele, in this instance, being one variant of the set of DNA sequences occupying the same location on the set of chromosome copies in a population. Where do rare alleles come from? Common alleles whose day is past, or new alleles in their early stages. Once a particular variant is fixed, all descendants of that population will have that same variant at that locus – including branched species – barring further mutation.

    BTW there isn’t anything that latches a nucleotide so one that has mutaed can mutate again and even back to the original.

    Not sure I fully comprehend. But if a nucleotide can mutate once, that is proof enough that it can mutate. All it is is a point error. There is nothing to stop it mutating again. Nothing ‘latches nucleotides’. There are many reasons why mutations occur. I hate to say it, but your grasp of basic biology – the stuff you need to know to make a sensible critique – could do with a brush-up.

  374. Genomicus,

    Methinks that someone on this thread doesn’t know what front-loading is.

    Methinks someone doesn’t realize that his preferred front-loading hypothesis isn’t the only one.

    The front-loading hypothesis simply posits that the earth was seeded with life forms which contained the necessary genomic information such that future evolution could be shaped and constrained.

    Are you aware that the monophyly of life on earth has been established to odds of better than 10^2680 to 1, and that all of the front-loaded genetic information you’re referring to would have to have been crammed into the single UCA?

    BTW, I would like to point out that you didn’t even try to answer my point about organism complexity also resulting in a nested hierarchy.

    That’s because I didn’t understand what you were trying to say. Could you try again?

  375. Chas D:

    If you think that “gradual modifications would produce a blending of defining characteristics”, then you missed it – it is the reason that is not the case.

    LoL! Defining characteristics means phenotypic traits. And Mendell was a creationist.

    Fixation is observed whenever a rare allele becomes extinct, and only one allele remains in the population.

    So we have never observed it.

    And strange taht you agree that a nucleotide can mutate more than once and then say I need a brush-up. Obviously you don’t undertsand the implication, which is there isn’t any expected pattern.

  376. P: And when have we observed 500 or more bits of functionally specific complex information actually originating by blind chance and equally blind mechanical necessity, as opposed to by intelligent action? Why is that so, per the accessible quantum state resources of the 10^57 or so atoms of our solar system across say 10^17 s, and the number of possible configs of 500 bits? KF

  377. ChasD: And when have we observed 500 or more bits of functionally specific complex information actually originating by blind chance and equally blind mechanical necessity, as opposed to by intelligent action? Why is that so, per the accessible quantum state resources of the 10^57 or so atoms of our solar system across say 10^17 s, and the number of possible configs of 500 bits? KF

  378. Genomicus,

    Welcome aboard.

    Some rather interesting points.

    I observe how repeatedly, the focal issue that functional specificity and complexity point to tight constraints on possible configs in the space of possibilities, and how the sort of increments you highlight raise questions about built-in capabilities.

    Like for instance, if Eukaryotes enfold mitochondria, how do mitochondria get coded for in making a new cell? How does such a mechanism originate by chance plus necessity in a lucky case where one unicellular organism engulfs another?

    Or are we looking at intentional modularity here?

    KF

  379. KF: Beside the point. What you decide that evolution, or abiogenetic chemistry, historically did and did not achieve all by their little selves, they remain two separate phenomena. When a replicating process is set in train, however caused, then whenever designers stop interfering, the natural process rolls on, and has consequences – intentional or not. These consequences are investigated by the discipline known as evolutionary theory.

  380. Chas D

    ‘When a replicating process is set in train, however caused, then whenever designers stop interfering, the natural process rolls on, and has consequences – intentional or not’

    Perhaps. But with massive limitations. As the fossil record clearly shows.

  381. Chas D:

    If you think that “gradual modifications would produce a blending of defining characteristics”, then you missed it – it is the reason that is not the case.

    Joe: LoL! Defining characteristics means phenotypic traits.

    Double Lol! You are aware that the central displine in cladistics these days is molecular phylogenetics – DNA? That is, genotype, not phenotype? Non-blending. Hierarchies in DNA are what I refer to throughout my posts. Morphology is used as well, but molecular phylogenies are the standard.

    And Mendell was a creationist.

    So bleeding what?

    ChasD: Fixation is observed whenever a rare allele becomes extinct, and only one allele remains in the population.

    Joe: So we have never observed it.

    You are a strange, strange man. I guess a species has never been observed to go extinct, either. You think you saw the last die, but you don’t KNOW that there isn’t another one somewhere. Fixation of one allele or another is inevitable in any finite population of replicators, unless selection intervenes to prevent it. I could demonstrate the principle mathematically, or observe it in a lab population, or in a simulation using a bag of M&Ms … but no: observe it. In the wild. Capture every individual of the species, gene-sequence them and then watch the last X die. “Hey Joe, over here, I observed it!”. “Really? Show me.”. The Prince of Denial. ID is not anti-evolution, but you deny every single aspect of it. You sure you’re not a creationist?

    And strange taht you agree that a nucleotide can mutate more than once and then say I need a brush-up. Obviously you don’t undertsand the implication, which is there isn’t any expected pattern.

    Ah, now I get your point. Yes, multiple serial substitutions can occur. Surprisingly, molecular systematists are one step ahead of you on this one – they have already appreciated the point. Honestly, you think people who work on this are unaware of such things? That is one reason why recovered trees, particularly on SNPs, are not always fully congruent. Fortunately, there are many, many different kinds of marker one can use. Mutation is more than SNPs.

    1. History is bunk.
    2. Historf is bunk. (substitution)
    3. Historo is bunk bunk. (duplication)
    4. Histori is blunk bunk. (insertion)
    5. Historg is blunk nk. (deletion)
    6. Histort bluisnk nk. (transposition)
    7. History biulsnk nk. (inversion)

    During this genuine lineage of copying and mutation, the last letter of “history” undergoes multiple SNP mutation back to y, which obscures the intermediates. But there is information elsewhere in the ‘genome’ that can help resolve this source of incongruence. The insertion at 3 has been quite degraded by the time you get to 7, but that is because I had several mutations to get into the illustration. It does not demonstrate a universal issue for all phylogenies. Your expectation (hope) is that, because of the phenomena of multiple serial substitutions, and degradation, ALL molecular phylogenies are useless. That does not follow.

  382. Response to champignon:

    Are you aware that the monophyly of life on earth has been established to odds of better than 10^2680 to 1, and that all of the front-loaded genetic information you’re referring to would have to have been crammed into the single UCA?

    Well, actually, if eukaryotes and archaea arose from a pool of early bacteria, the genetic data couldn’t really tell if eukaryotes and archaea arose from a single cell or from a population of cells, if that population is homogenous.

    There wouldn’t be any cramming of genetic information either. I’m not suggesting that every single gene found in life forms was placed into the initial cells. I am suggesting that major genes that would shape future evolution were designed into the initial cells. You can get a lot from a single gene, especially if overlapping genes are used.

    By the way, I’d like to point out that you just changed the topic on me. We were originally discussing if front-loading predicts a nested hierarchy as much as non-telic evolution. Kindly respond to my points on (a) endosymbiosis and the origin of modern eukaryotes, and (b) lateral gene transfer.

    Also, you said:

    Under front-loading, nothing prevents major identical changes from happening in unrelated species. This will also destroy the nested hierarchy.

    Similarly, nothing is preventing major identical changes from happening in unrelated species under non-telic evolution. Why? Lateral gene transfer can cause a “major identical change” in unrelated species.

  383. Thanks, kairosfocus.

    Under the teleological hypothesis of front-loading, the endosymbiosis explanation for the origin of eukaryotic cells isn’t that problematic, but it is problematic for non-telic explanations.

    Also, on a side note, earlier on this thread someone was asking for some evidence that functional space consist of islands, instead of, well, continents. While digging up some references for a response to Nick Matzke on the thread “Mike Behe: A Blind Man Carrying a Legless Man Can Safely Cross the Street,” I came across the paper “Adaptive molecular convergence,” and found this bit:

    “We had also shown in another study that some of the same mitochondrial proteins had endured remarkably strong selection for radical changes at otherwise highly conserved sites early in snake evolution. This makes sense if the protein adaptive landscape is narrow rather than vast, with only one or a few pathways to reach a neighboring adaptive peak…” (emphasis added)

  384. Dude,

    Until you have evidence that the transformatons required are even possible you have no idea if common descent can cause the genetic pattern you describe.

    Mike Shermer calls it “patternicity”- that is people find patterns and then try to make something of it-> something that isn’t there.

  385. PeterJ

    Chas D

    ‘When a replicating process is set in train, however caused, then whenever designers stop interfering, the natural process rolls on, and has consequences – intentional or not’

    Perhaps. But with massive limitations. As the fossil record clearly shows.

    The fossil record shows nothing of the limitations of any process (except, perhaps, the fossilisation, preservation and discovery processes). It samples individuals. How they came to be born, the genes they had, all the ‘offstage’ activity marked by their ancestors (if any) and their descendants (if any), the fossil record does not record. Their DNA, their soft parts – (mostly) gone. They are blurry 3D ‘photographs’ of individuals and you can no more tell the limitations of the process that impinged upon their existence than you could determine the limitations upon your father’s passage through spacetime from the family album – that goes for design theories too. You can’t just assert unseen limitations in order to give unseen designers something to do.

    Fossils yield a lot of information, but little about genetic mechanism or its limitations.

  386. Dude,

    Until you have evidence that the transformatons required are even possible you have no idea if common descent can cause the genetic pattern you describe.

    That’s not sufficient cause to exclude the hypothesis. We are presented with a dataset (gene sequences) and we have no idea how they came to exist. Whimsical designer, purposeful designer, common descent, puffed into existence by encoding vital passages from the OOS … who knows?

    But IF the explanation is common descent, we would expect to see a pattern derived from the known iterative branching that common descent processes actually display. Have a look at a tree sometime. So we adopt that hypothesis. We perform the analysis and – my god! It supports the hypothesis of common descent! So we look at another sequence and it doesn’t. OK, strike one. Then we look at another sequence and it does. Gradually, we build up a dataset. All these sequences support this phylogeny; there are a few anomalies, but the overall signal we are getting is a tree. We don’t just brush the rest under the carpet; we look for explanations for the disconformities. It can be just as interesting as the conformity.

    Based upon the dataset alone, we have no idea if these organisms can have practically descended from a common ancestor, but all the analyses we can muster are consistent with them having done so. What are we to conclude? Either they did descend, or the sequences were made to look like they did – both functional and nonfunctional.

    There are special causes and there are deceitful special causes! The clearest signals are the digital ones – discontinuities in DNA: transpositions, insertions, deletions and inversions. If you can delete a particular insertion with no ill-effect, it is clearly not functional. And yet we find such things following the phylogenetic signal recovered from assumed-functional data. Deceit or common descent, take your pick. (Common design: Intention of (1) an individual to commit two or more crimes, or (2) two or more individuals to commit a crime together.)

    Mike Shermer calls it “patternicity”- that is people find patterns and then try to make something of it-> something that isn’t there.

    A fair description of ID. There comes a point when refusing to see the pattern becomes plain perverse. Experienced systematists are well aware of the pitfalls, and construct statistical methods to try and impose objective standards and remove artefacts. Oh, hang on – they ‘smuggle in’ the result. Of course.


  387. Until you have evidence that the transformatons required are even possible you have no idea if common descent can cause the genetic pattern you describe.

    That’s not sufficient cause to exclude the hypothesis.

    It means it is an untestable hypothesis. And science tends to exclude those.

    But IF the explanation is common descent, we would expect to see a pattern derived from the known iterative branching that common descent processes actually display.

    But we have no idea what pattern common descent would produce.

    Either they did descend, or the sequences were made to look like they did – both functional and nonfunctional.

    Yet they only look like they did to people who want/ need them to look like that.

    The problem is you do not know what pattern common descent would produce so you assume it produced the pattern you see. Yet your whole thing is untestable. And taht is a problem for science.

  388. Ge:

    Great stuff, keep it coming!

    (You will notice a telling silence for days in response to the Avian Lung or comparable case raised in the previous page and in the original post, it is not just at molecular level.)

    I am having to deal with a violation of confidence case behind the scenes now plus the fallout from my expose of eugenics and Hitler’s Antichrist spirit, so too busy for details.

    But I most definitely will read!

    G

  389. 389

    Champignon,

    Evolutionary theory predicts a nested hierarchy. That one word, that indefinite article, is very important.

    Your argument that evolution predicts nested hierarchies is like throwing seeds into a field and predicting that something will grow. If grass grows, that’s a confirmation. If sunflowers grow, that’s a confirmation. If man-eating plants from the Little Shop of Horrors grow, or if skyscrapers grow, that’s a confirmation.

    Sure, evolution predicts a nested hierarchy. That’s fine if you’re cherry-picking evidence. The trouble is with what the nested hierarchy is made of. Evolution doesn’t predict that. Based on observation evolution predicts more of the same, perhaps bigger, faster, slower, stronger, etc. And then you can arrange those into your nested hierarchy.

    A nested hierarchy of evolutionary changes is great. A nested hierarchy of things for which there is no evolutionary explanation and which stand in stark contrast to any observed products of evolution is obviously not a confirmation of evolution. A nested hierarchy of spiders and bats and dolphins and venus flytraps and humans and earthworms and butterflies is excellent confirmation of evolution as long as you remove every part except “nested hierarchy.” The rest is contradiction, not confirmation.

    This is something that you only notice if you’re inclined to examine the idea critically. Unfortunately most peoples’ eyes seem to glaze over when they hear “nested hierarchy” and then they drink the Kool-Aid.

  390. ChasD:

    Where did I ever say that the pre-biotic situation is the same phenomenon as that of the living cell? NOWHERE.

    What I pointed out is that in both cases it is necessary to account for the spontaneous origin of functionally specific complex — often, irreducibly complex — organisation and associated information [FSCO/I] on blind chance and mechanical necessity. That is, if the darwinian evolutionary model is to be justified on observed empirical evidence orf macroevolution rather than an imposed evolutionary materialist a priori that is then illustrated with simplistic micro cases grossly extrapolated beyond the observed phenomena that will be persuasive to the eye of Darwinian faith, but which has actually failed bear the weight of the grand claims being made.

    In the case of Darwin’s warm little electrified pond or the like, I highlighted the need to explain the origin of a metabolising entity with an integral von Neumann self-replicating facility, which also implies the origin of not just machinery but also symbolic codes [thus, language], algorithms and storage media. I pointed out that on the observed evidence this credibly requires in excess of 100,000 bits of information where just 500 bits is well beyond the credible search capacity of blind chance and necessity on the gamut of our solar system, and 1,000 bits, the cosmos we observe.

    I need not underscore further, that the vNSR is also irreducibly complex. In short, the point that the need for a cluster of well matched, properly organised and oriented, hooked up parts per a wiring diagram leads to a deeply isolated island of function is on the table.

    Going on, once we have a living cell, we then face the issue of origin of major body plans and related organ systems etc. In this case, we often face the same FSCI threshold issue, with credibly 10 – 100 + million bits of information required, on earth, dozens of times over. And, in many cases, the systems are examples of irreducible complexity as well, e.g. the avian lung vs the bellows lung. (Onlookers, notice how this case is consistently being ducked. Oops, pun unintentional.)

    Such cases again point to the reality of islands of deeply isolated function.

    Perhaps, I should cite here Meyer’s PBSW article, which of course — despite the politics that was played tot try to discredit it and to break the confidentiality of peer review [with retaliatory behaviour obviously on the agenda if that had been successful] — passed proper peer review by “renowned scientists”:

    The Cambrian explosion represents a remarkable jump in the specified complexity or “complex specified information” (CSI) of the biological world. For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993) . . . One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . .

    In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes–the very stuff of macroevolution–apparently do not vary. In other words, mutations of the kind that macroevolution doesn’t need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don’t occur . . .

    So, the issue is not that the two are the same, but that they face the same FSCO/I origin challenge. And, this then leads to the further challenge that if the branching tree of life model is true, it had to have a root. But, we have no good empirical warrant for a theory of a root.

    Then, we have to account for gradualistic development of major structures, with at most rather modest increments in complexity that have to be fixed in the population while we move on to the next stage. This would need solid empirical warrant per observations, not just for the avian lung but for ever so many other major features of life.

    Gould in his lat book, 2002, and in the decades before that too, consistently testified that that is exactly what is not there on the ground, across the different levels in the taxonomy of living things. (Do I need to point out that if the “evolutionary” sequence of Corvettes and the categorisation of paper clips etc on taxonomic principles are quite feasible, then this means that such do not by themselves constitute decisive evidence of common descent with modification by spontaneous and blind chance and necessity acting trough chance variation and differential reproductive success? As in, the listed items are of course DESIGNED.)

    Let’s hear Gould, again as the OP cites him:

    . . . long term stasis following geologically abrupt origin of most fossil morphospecies, has always been recognized by professional paleontologists. [The Structure of Evolutionary Theory (2002), p. 752.]

    . . . . The great majority of species do not show any appreciable evolutionary change at all. These species appear in the section [[first occurrence] without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants.” [p. 753.]

    . . . . proclamations for the supposed ‘truth’ of gradualism – asserted against every working paleontologist’s knowledge of its rarity – emerged largely from such a restriction of attention to exceedingly rare cases under the false belief that they alone provided a record of evolution at all! The falsification of most ‘textbook classics’ upon restudy only accentuates the fallacy of the ‘case study’ method and its root in prior expectation rather than objective reading of the fossil record. [[p. 773.]

    Of course, a self replicating system subject to variation will change, but the evidence is that such changes will be within a body plan, and often constitute a gradual loss of functional capacity by breaking something at molecular level that happens to be advantageous in an adverse situation, but which is not necessarily advantageous as a whole; nor do we see cases of the observed emergence of significant body plan elements like the avian lung, or the like. Think of the case with the Tomcod in polluted rivers.

    GEM of TKI

  391. ChasD:

    No it isn’t. The process of evolution continues today; the process of “OOL” does not. If you take any current population, it will, according to some very concrete mathematical, empirical, computational and theoretical work, evolve. Blindly, by natural means. We do not need to insert a designer to keep this process ticking over; it happens all by itself. You have to interfere to stop it.

    Yes, it is. The “process of evolution” you are speaking of is only the microevolutionary change, with the intervention of NS if and when it applies, that cannot in any way explain the origin of complex functional biological information.

    My statement was that “The same evidence that applies to OOL applies to further evolution.”

    The evidence I am speaking of, as should be clear from the rest of my post, is the evidence of the constant emergence of new complex functional information, such as the emergence of new basic protein domains. That evidence is abundant both at the origin of life and after. And your answer is in no way an answer to that.

    So you are segregating out the unavoidable, natural process of evolution through mutation and selection/drift (as I find myself repeating, the thing ID is not anti), and asserting that there was historic interference with it, even though a ‘blind’ process of evolution can and does occur all by itself.

    I am “segregating” nothing at all. I am speaking of the emergence of new complex functions, and your “unavoidable, natural process of evolution through mutation and selection/drift” cannot explain that.

    We can argue about what it can create

    Yes, I do argue about that! That’s why I am here, discussing in favour of ID.

    but essentially, left to its own devices, a population experiencing birth and death will evolve, inexorably. Mutations will become fixed, and there is no going back.

    And so? If that “evolution” cannot explain complex functional information, it is totally irrelevant to what we are discussing.

    So when you talk of ‘further evolution’, you have to offer some means to distinguish that which can occur naturally from the interference.

    What do you think we are doing here? Have you ever read one of my detailed discussions about dFSCI?

    IC is one such attempt.

    It is a very successful “attempt”! But IC, as defined by Behe, is about complex molecular machines made by many complex individual parts. My argument is about basic protein domains, and has nothing to do with that, but rather with dFSCI, and with the arguments made by Axe and Abel and Durston.

    But it remains entirely in accord with the ID inference, as stated, to allow for an ID OOL, and then NO further interference. The two are not subject to identical considerations.

    I don’t agree. The problem of the emergence of new dFSCI is extremely obvious both at OOL and after. Therefore, a design inference is equally mandatory both for OOL and for further evolution that implies new complex functional information. Therefore, the two problems are subject to identical considerations, at least from this fundamental point of view.

  392. GP: Very well said, as usual. (Dunno if I have said it, but you are one of my very favourite commenters and contributors at UD, I would love to hear more from you, why not consider a regular “column” here, say once a week?) KF

  393. Gene: very well said, and obviously well informed. KF

  394. Gene:

    It would be wonderful to get a guest-post from you on the front loading hyp. Why not go to my handle, LH column, and click then use the onward contact me? KF

  395. Thanks a bunch for your comment kairo. I sent you an email – hope I sent it to the right email address.

  396. Champignon,

    Jigsaw puzzles were presented as an example. Consider the number of pieces and the number of ways you can put them together (provided pieces are identical in shape). This problem is NP-complete which suggests that with the number of pieces growing, it quickly becomes intractable (unless, of course, P=NP). However, only one of those cofigurations presents the solution.

    More generally, functionality implies choice with intent towards improving utility (on massive evidence to this effect vs no evidence to the contrary). Borrowing the terminology from David Abel, physicality (=physical reality) does not have intent or goal. Control as a process that steers events to potential function testifies to agency, upon massive observations. So as soon as we see genuine control anywhere, we can infer to intelligent cause. Note that our inference to intelligence is legitimate until such times as evidence to the contrary is produced and demonstrated to be statistically significant (see here).

    The word “process” itself etimologically comes from “procedure” which is a formalism and, consequently, an artefact. In the strict sense or this word, stochastic processes are self-contradictory.

    The example of jigsaw puzzles is particularly nice because it clearly demonstrates the decoupling of the rules of the game from the underlying physical reality, which does not care which particular configuration is winning. So the jigsaw puzzle cannot be reduced to simply configurations of atoms. On the contrary, the semantic load (function) is attached to it via intelligent choice, which examplifies a formalism. So in the end, the attachment of function to a configuration of matter is what counts, not that particular solving configuration (which might have been chosen by us absolutely differently irrespective of the physical layer).

    Another example is the TCP/IP protocol stack. You get meaningful information only after it is processed and “lifted up” all the way from the physical layer to the application layer. To assert that meaning can be spontaneously organised at the physical layer is absolute nonsense.

  397. Oh boy, I got the closing href tag muddled.

  398. Got it, looks good to me!

  399. 399

    KF

    You will notice a telling silence for days in response to the Avian Lung or comparable case raised in the previous page and in the original post, it is not just at molecular level.

    Perhaps if you went out into the world beyond UD you could find the answers you so desperately seek.

    The fact that nobody has given you an answer that satisfies you does not mean that no such answer exists.

    And if you to claim victory on that basis then it’s a hollow victory indeed.

    Tell me, have you ever tried typing “evolution bird lung” into google scholar?

    You appear to be confusing your inability to imagine a pathway as evidence that such a pathway cannot exist!

    In this case it takes but a simple valve to convert bidirectional flow, as in a mammal’s lung, to unidirectional flow, as in a bird’s lung.

    Example the image here: http://tinyurl.com/birdlungschematic

    Under the “Respiratory System of Birds” heading.

    Notice the valve that controls unidirectional flow. Simply remove the valve, and you have a bidirectional system.* In birds, though, valving is thought to be aerodynamic, not mechanical.

    As for the pumping system itself, the most primitive system is buccal, where the mouth pushes air into the lungs, while elastic pressure pushes it back out. However, among amniotes, costal breathing, muscles associated with the ribs, is the primitive condition. Birds aspirate costosternally, by rotating the ribs and depressing the end of the sternum. Nor is bird respiration completely unidirectional as flow through the neopulmonic bronchi is bidirectional (though not fully developed or absent in some birds).

    As for exactly how and when the bird lung evolved, that is still not known with any certainty—lungs don’t normally fossilize—; however, it appears that air sacs and costosternal pumping predate birds.

    Sereno, et al., Evidence for Avian Intrathoracic Air Sacs in a New Predatory Dinosaur from Argentina. PLoS ONE, 2008.

    * Addendum: Even if the valving is not perfect, it will increase the efficiency of respiration. In other words, the valve can easily evolve incrementally.

    Cribbed from here: http://tinyurl.com/7msgwya

    Thanks Z!

    Now, KF, how does ID explain the origin of the bird lung?

  400. More to the point, how does ID explain the total absence of the efficient bird lung design in mammals, who have to make do with non-flow-through lungs?

    It makes total sense from a common-descent/Darwinian perspective, but none at all from an ID perspective.

    Any human designer, having hit on the flow-through design, would transfer it to other design lineages, surely. That’s why cars have air-con.

  401. 401

    BTW, the person who wrote that was asked by KF to stop mailing him. Funny how KF claims that nobody can provide an answer to his questions when he asks those very same people to stop communicating with him.

    Seems to me that one of the main weapons in the ID arsenal are fingers in ears.

  402. 402

    @Elizabeth Liddle:

    “More to the point, how does ID explain the total absence of the efficient bird lung design in mammals, who have to make do with non-flow-through lungs?

    It makes total sense from a common-descent/Darwinian perspective, but none at all from an ID perspective.”

    It makes perfect sense when one considers the fact that the Final Cause of the flow-through lungs in birds is for increased efficiency IN FLIGHT. We do not fly.

    And in anticipation of what will doubtless be your next challenge, namely “And why didn’t the designer make us with the capacity to fly?” I point out the fact that, despite the fact that the Wright Brothers “hit on” the design of the airplane wing more than a hundred years ago, it has not been transferred to cars. Why not? Because a car serves its Final Cause (efficient transport from place to place for the common man) perfectly fine without the capacity for flight. Similarly, we humans serve our Final Cause (the accumulation of knowledge) perfectly fine without the capacity for flight.

    And as to your objection to my identification of humanity’s Final Cause as the accumulation of knowledge, I point you to information which makes a case for our planet as an observatory of sorts, a platform from which we view the universe, and a place well suited to allowing us to do so. (our location between the galactic arms and away from the center allows us to see into deep space, the transparency of our atmosphere to visible light allows us to see through the atmosphere into space, etc. etc.)

    More information on the subject of our planet as an observatory:
    http://www.uncommondescent.com.....-our-home/

  403. F/N, for record: I have not been by this page for months, and when I visited just now, I saw:

    401 Peter Griffin January 18, 2012 at 5:29 am

    BTW, the person who wrote that was asked by KF to stop mailing him. Funny how KF claims that nobody can provide an answer to his questions when he asks those very same people to stop communicating with him.

    Seems to me that one of the main weapons in the ID arsenal are fingers in ears.

    This is totally twisted and irresponsible (and onlookers should recall that the threading of comments made it highly likely that when the thread was going, I would miss something like the above).

    I wish to remark:

    1 –> Let the record reflect the truth: I asked Zachriel to cease and desist from further communication with me because — in the teeth of my requests — he violated confidentiality; which I discovered. I take that sort of misbehaviour very seriously indeed, for good reason. And any claim that the motivation was otherwise is false.

    2 –> Now, this makes what I now see in a public forum even worse, for, obviously Zachriel and I were the two parties tot he exchange, so if a twisted version of why I terminated it has been released to the public, it is because of a FURTHER violation of the confidentiality of a personal email exchange, in the teeth of specific requests, and knowing that having found out violations I protested them. It therefore evident from this thread that he has twisted my request that he respect confidentiality, into a ducking of issues and trumpeted that to the public elsewhere. Shameless.

    3 –> The issues unanswered by darwinists on matters that are strongly supported inductive signs of design are well known. So, the fingers in ears claim above is, again, highly misleading.

    4 –> Instead of dealing with science and the underlying issue of the logic of induction, what I consistently have found from too many objectors to design theory is just what the just cited post shows: habitual resort to red herrings, led away to strawmen soaked in ad hominems and set alight to cloud, poison, and polarise the atmosphere.

    5 –> In this case, multiplied by violations of trust, even in the teeth of protest that trust has been violated. It seems we are dealing with the utterly amoral, and untrustworthy. Which amorality, of course is a consequence of evolutionary materialism that is usually hotly denied or contested by advocates of evolutionary materialism. But here we see it in action, yet again.

    6 –> Plainly, not all such advocates — and by no means any more than a small minority of adherents — are amoral and untrustworthy, but the problem is that when a worldview is corrosive of morality, the corrosion tends to be effective. And ever since Plato in The Laws, Bk X, we have been warned that evolutionary materialist skepticism has this as a problem and tends to lead to ruthless factions who live by the principle that the highest right is might.

    7 –> It is plain to me that Zachriel, the pseudonymous advocate of darwinism, has violated trust because he thought it would be to his advantage and he could get away with it. Let the record reflect this, for all to see.

    8 –> I do not doubt that in the penumbra of hostile and hate sites around UD this slander above has been repeated as gospel truth, with the intent of harming reputation as a substitute for actually addressing matters on the merits.

    9 –> What a sadly revealing reflection on those who take that sort of position or tolerate it.

    Good day.

    GEM of TKI

  404. KF,

    I suggest the “ID Foundations” posts be collected and placed under the Resources in the main menu, for ease of navigation, somewhere next to ID Defined. Thanks.

  405. F/N; Kindly see my for the record follow-up post here. That includes a few remarks on the claimed substantial issue that put it in an utterly different light than is pretended to above in the comment I am responding to.

  406. Dr Selensky, thanks for kind words. I have no control of that, but have collected the posts in a category, ID Foundations. Click the link and you will see all such posts in reverse chronological order, the numbered posts being of course the main series. (There are also several supplementary posts.) Onlookers may also find the IOSE draft course here on, helpful. The online notes accessible through my handle may also be helpful. Google books also has snippets of several major ID books. Do a Google search, then look under books. KF

  407. KF, Great! Thanks.

  408. Welcome

  409. F/N: Cf what is now 14 above. See how it anticipates the pattern that developed and has now played out with a violation of confidence. KF

  410. F/N: Kindly observe 326 above, as it is now numbered, which anticipates PG’s objections. KF

  411. Evolutionary theory would produce nested hierarchies, no doubt, but so would the created kinds of Genesis. But in this context, so what? Both postulations beg the question posed by the original post in particular and by ID in general, “Whence the complexity?

    Arguing on the basis of a nested hierarchy is relevant only to extent that the hierarchy being used “ascends” and “descends” along an axis that is relevant to the question.

    The axis that ID is concerned with runs from simple to complex, along which “islands” are not the exception, they are the rule. Against which cladistic proofs for common descent are not only utterly irrelevant, seeing them rehashed time and time again has become tedious in the extreme.

  412. Actually my first paragraph @411 is wrong, Genesis doesn’t beg the question. It says “God did it.” Then ID comes along, showing with some rigor, “Well somebody had to.”

    What is significant, to me anyway, being confirmed both as a Christian and a non-scientist, isn’t that both answers upset the materialists. Of course they do. Considering the predominance of their paradigm in science, the academy, and culture at large, what is significant is the dullness of their ripostes.

    Interesting times.

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