Things That IDers Don’t Understand, Part 1 — Intelligent Design is not compatible with the evidence for common descent

Since the time of the Dover trial in 2005, I’ve made a hobby of debating Intelligent Design proponents on the Web, chiefly at the pro-ID website Uncommon Descent. During that time I’ve seen ID proponents make certain mistakes again and again. This is the first of a series of posts in which (as time permits) I’ll point out these common mistakes and the misconceptions that lie behind them.

I encourage IDers to read these posts and, if they disagree, to comment here at TSZ. Unfortunately, dissenters at Uncommon Descent are typically banned or have their comments censored, all for the ‘crime’ of criticizing ID or defending evolution effectively. Most commenters at TSZ, including our blog host Elizabeth Liddle and I, have been banned from UD. Far better to have the discussion here at TSZ where free and open debate is encouraged and comments are not censored.

The first misconception I’ll tackle is a big one: it’s the idea that the evidence for common descent is not a serious threat to ID. As it turns out, ID is not just threatened by the evidence for common descent — it’s literally trillions of times worse than unguided evolution at explaining the evidence. No exaggeration. If you’re skeptical, read on and I’ll explain.

Common Descent and ID

The ‘Big Tent’ of the ID movement shelters two groups. The ‘creationists’ believe that the ‘kinds’ of life were created separately, as the Biblical account suggests, and these folks therefore deny common descent. The ‘common descent IDers’ accept common descent but argue that natural processes, unassisted by intelligence, cannot account for the complexity and diversity of life we see on earth today. They therefore believe that evolution was guided by an Intelligence that either actively intervened at critical moments, or else influenced evolution via information that was ‘front-loaded’ into the genome at an earlier time.

Creationists see common descent as a direct threat. If modern lifeforms descended from a single common ancestor, as evolutionary biologists believe, then creationism is false. Creationists fight back in two ways. Some creationists argue that the evidence for common descent is poor, or that the methods used by evolutionary biologists to reconstruct the tree of life are unreliable. Other creationists concede that the evidence for common descent is solid, but they argue that it can be explained equally well by a hypothesis of common design — the idea that the Creator reused certain design motifs when creating different organisms. Any similarities between created ‘kinds’ are thus explained not by common descent, but by design reuse, or ‘common design’.

The ‘common descent IDers’ do not see common descent as a threat. They accept it, because they see it as being compatible with guided evolution. And while they agree with biologists that unguided evolution can account for small-scale changes in organisms, they deny that it is powerful enough to explain macroevolutionary change, as revealed by the large-scale structure of the tree of life. Thus guided evolution is necessary, in their view. Since common descent IDers accept the reality of common descent, you might be surprised that the evidence for common descent is a problem for them, but it is — and it’s a serious one. Read on for details.

The Problem(s) for ID

I’ve mentioned three groups of IDers so far: 1) creationists who dispute the evidence for common descent; 2) creationists who accept the evidence for common descent, but believe that it can be equally well explained by the hypothesis of common design; and 3) IDers who accept common descent but believe that unguided evolution can’t account for macroevolutionary change. Let’s look at these groups in turn, and at why the the evidence for common descent is a serious problem for each of them.

The creationists who dispute the evidence for common descent face a daunting task, simply because the evidence is so massive and so persuasive. I can do no better than to point readers to Douglas Theobald’s magnificent 29+ Evidences for Macroevolution for a summary of all the distinct lines of evidence that converge in support of the hypothesis of common descent. Because Theobald does such a thorough and convincing job, there’s no need for me to rehash the evidence here. If any IDers wish to challenge the evidence, or the methodologies used to interpret it, I encourage them to leave comments. The good news is that we have Joe Felsenstein as a commenter here at TSZ. Joe literally wrote the book on inferring phylogenies from the data, so if he is willing to respond to objections and questions from IDers, we’re in good shape.

I have yet to encounter a creationist who both understood the evidence and was able to cast serious doubt on common descent. Usually the objections are raised by those who do not fully understand the evidence and the arguments for common descent. For this reason, I emphasize the importance of reading Theobald’s essay. Think of it this way: if you’re a creationist who participates in Internet discussions, the points raised by Theobald are bound to come up in debate. You might as well know your enemy, the better to argue against him or her. And if you’re open-minded, who knows? You might actually find yourself persuaded by the evidence.

The evidence also presents a problem for our second group of creationists, but for a different reason. These are the folks who accept the evidence for common descent, but argue that it supports the hypothesis of common design equally well. In other words, they claim that separate creation by a Creator who reuses designs would produce the same pattern of evidence that we actually see in nature, and that common design is therefore on an equal footing with common descent. This is completely wrong. The options open to a Creator are enormous. Only a minuscule fraction of them give rise to an objective nested hierarchy of the kind that we see in nature. In the face of this fact, the only way for a creationist to argue for common design is to stipulate that the Creator must have chosen one of these scant few possibilities out of the (literally) trillions available. In other words, to make their case, they have to assume that the Creator either chose (or was somehow forced) to make it appear that common descent is true, even though there were trillions of ways to avoid this. Besides being theologically problematic for most creationists (since it implies either deception or impotence on the part of the Creator), this is a completely arbitrary assumption, introduced only to force common design to match the evidence. There’s no independent reason for the assumption. Common descent requires no such arbitrary assumptions. It matches the evidence without them, and is therefore a superior explanation. And because gradual common descent predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a ‘common designer’, it is literally not just millions, or billions, but trillions of times better at explaining the evidence.

What about our third subset of IDers — those who accept the truth of common descent but believe that intelligent guidance is necessary to explain macroevolution? The evidence is a problem for them, too, despite the fact that they accept common descent. The following asymmetry explains why: the discovery of an objective nested hierarchy implies common descent, but the converse is not true; common descent does not imply that we will be able to discover an objective nested hierarchy. There are many choices available to a Designer who guides evolution. Only a tiny fraction of them lead to a inferable, objective nested hierarchy. The Designer would have to restrict himself to gradual changes and predominantly vertical inheritance of features in order to leave behind evidence of the kind we see.

In other words, our ‘common descent IDers’ face a dilemma like the one faced by the creationists. They can force guided evolution to match the evidence, but only by making a completely arbitrary assumption about the behavior of the Designer. They must stipulate, for no particular reason, that the Designer restricts himself to a tiny subset of the available options, and that this subset just happens to be the subset that creates a recoverable, objective, nested hierarchy of the kind that is predicted by unguided evolution. Unguided evolution doesn’t require any such arbitrary assumptions. It matches the evidence without them, and is therefore a superior explanation. And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.

One final point. Most IDers concede that if the evidence supports unguided evolution, then there is no scientific reason to invoke a Creator or Designer. (It’s Occam’s Razor — why posit a superfluous Creator/Designer if the evidence can be explained without one?) It is therefore not enough for ID to succeed at explaining the evidence (which it fails to do, for the reasons given above); it’s also essential for unguided evolution to fail at explaining the evidence.

This is a big problem for IDers. They concede that unguided evolution can bring about microevolutionary changes, but they claim that it cannot be responsible for macroevolutionary changes. Yet they give no plausible reasons why microevolutionary changes, accumulating over a long period of time, should fail to produce macroevolutionary changes. All they can assert is that somehow there is a barrier that prevents microevolution from accumulating and turning into macroevolution.

Having invented a barrier, they must invent a Designer to surmount it. And having invented a Designer, they must arbitrarily constrain his behavior (as explained above) to match the data. Three wild, unsupported assumptions: 1) that a barrier exists; 2) that a Designer exists; and 3) that the Designer always acts in ways that mimic evolution. (We often hear that evolution is a designer mimic, so it’s amusing to ponder a Designer who is an evolution mimic.) Unguided evolution requires no such wild assumptions in order to explain the data. Since it doesn’t require these arbitrary assumptions, it is superior to ID as an explanation.

Here’s an analogy that may help. Imagine you live during the time of Newton. You hear that he’s got this crazy idea that gravity, the force that makes things fall on earth, is also responsible for the orbits of the moon around the earth and of the earth and the other planets around the sun. You scoff, because you’re convinced that there is an invisible, undetected barrier around the earth, outside of which gravity cannot operate. Because of this barrier, you are convinced of the need for angels to explain why the moon and the planets follow the paths they do. If they weren’t pushed by angels, they would go in straight lines. And because the moon and planets follow the paths they do, which are the same paths predicted by Newton on the basis of gravity, you assume that the angels always choose those paths, even though there are trillions of other paths available to them.

Instead of extrapolating from earthly gravity to cosmic gravity, you assume there is a mysterious barrier. Because of the barrier, you invent angels. And once you invent angels, you have to restrict their behavior so that planetary paths match what would have been produced by gravity. Your angels end up being gravity mimics. Laughable, isn’t it?

Yet the ‘logic’ of ID is exactly the same. Instead of extrapolating from microevolution to macroevolution, IDers assume that there is a mysterious barrier that prevents unguided macroevolution from happening. Then they invent a Designer to leap across the barrier. Then they restrict the Designer’s behavior to match the evidence, which just happens to be what we would expect to see if unguided macroevolution were operating. The Designer ends up being an unguided evolution mimic.

The problem is stark. ID is trillions of times worse than unguided evolution at explaining the evidence, and the only way to achieve parity is to tack wild and unsupported assumptions onto it.

If you are still an IDer after reading, understanding, and digesting all of this, then it is safe to say that you are an IDer despite the evidence, not because of it. Your position is a matter of faith and is therefore a religious stance, not a scientific one.

450 thoughts on “Things That IDers Don’t Understand, Part 1 — Intelligent Design is not compatible with the evidence for common descent

  1. PaV:

    IOW, P2 flows from the premise that ‘intelligent designs’ strive for efficiency. Do you want to claim that this in not true?

    It is an assumption. It may or may not be true. Why should an unconstrained designer strive for efficiency? Why should an unconstrained designer produce the many inefficient kludges found in nature?

    Would you have a counter-example demonstrating this?

    No, and its not our job to do so. It’s your job to demonstrate that your P2 must apply to your unconstrained designer, otherwise it’s just an assumption.

  2. keiths:

    The fact that parts of the “tree” diverge from the tree pattern does not negate the fact that the tree pattern predominates and can be objectively identified. This is not a subjective judgment; it is backed up by statistical analyses.

     The problem for Darwin back then, and for Darwinists now, is the finding that all 30 major taxa existed in the Cambrian (IIRC, there might have been 1 major taxa that emerged later).

    Here’s how to imagine this:

    Imagine that you’re looking at a wonderfully formed elm tree.  Now imagine taking a saw and cutting along a horizontal plane located twenty feet up from the ground, corresponding to a height closer to the top of the tree than, say, its middle.  You count how many cut-off branches are exposed.  It turns out to be 30.  Now you take all the cuttings and examine them.  You find that at the bottom there is one, single ‘stalk’, let’s say, and that this ‘stalk’ bifurcates as you move from the ‘cut’ end to its distal end.

    The 30 ‘stalks’ represent the various phyla, the ‘major taxa.’  And they’re completely separated from one another.  The only thing that connected them was the tree on the ground that has now been cut flat at a height of 20 feet.

    But when we look at the Cambrian and the Pre-Cambrian, that “tree on the ground” is MISSING!!!  Darwin thought that if we looked hard enough and long enough, we’d find that ‘missing tree’.  But we haven’t.  

    So what we’re left with is the tops of the tree, which is a “collection” of 30 “mini-trees” (Think of a Bonzai tree which mimics a much larger tree).  And each of these “mini-trees” is, in fact, what we call a “nested hierarchy.”  

    So, we don’t have a “tree”; instead we have “tops of trees.”

    I don’t see the problems for Darwinism going away here at all, no matter how much you protest. 

    ketihs:

    This claim is justified in Prediction 1.3: Consilience of independent phylogenies in Theobald’s “29 Evidences for Macroevolution” essay. Take a look. If you still disagree after reading that section, please explain why you think Theobald is mistaken.

    What “Theobald” provides is a demonstration of “intelligent design” actually.

    His premise is that given all the possible permutations of known phylogenetic traits and characteristics, the total possible number of such permutations amounts to 1038.  

    But this does not say anything about “accuracy”; instead, it gives us the probability of such a phylogenetic tree being put together by “chance.”

    Now, if his calculation is on the money, then this means that the chance of obtaining the currently accepted ‘phylogenetic tree’ by ‘chance’ is ONE in 1038.  What this then demonstrates is that ‘intelligent’ agents, using reason, have effectively searched through a very large ensemble of possibilities to find a reliable classification scheme.  This is what ID in fact premises.  So this exercise demonstrates in a vivid way how intelligence is able to fashion a ‘pattern’ in the face of a huge mountain of possibilities. 
     

  3. PaV:

    P2 is not properly formulated.

    You’ve used a definite article before “intelligent designer(s)”.  Why?

    P2 should read:  ”Intelligent designers strive for efficient designs.  Hence, in the case of the genome, an intelligent Designer would not include large amounts of non-functional DNA in the genome.

    IOW, P2 flows from the premise that ‘intelligent designs’ strive for efficiency.  Do you want to claim that this in not true?

    Would you have a counter-example demonstrating this?

    The intelligent designers of this biosphere with their 99.9 extinction rate might qualify as a counter example, don’t you think? I agree that living designers have that trait, but non-living designers are a closed book to us, don’t you agree?

    But even with the assumption that our extinction loving designers strive for efficiency (when will they get around to re-routing the Laryngeal Nerves of animals with necks, I wonder?), you don’t get your prediction. Non-functional DNA can sometimes be incorporated in the system and gain a function. If our efficient designers are designing with future adaption and evolution in mind, they might want to have large quantities of non-functional DNA (it doesn’t get in the way) in order to increase the chances of mutation creating something productive from it.
     
    Another problem is that we don’t know how directly the designers design. If they let things roll without intervention for long periods of time, they could also inadvertantly end up with large quantities of non-functional DNA produced by mutations in their absence.

    So, for those and other reasons, any percentage of DNA being non-functional is compatible with a general I.D hypothesis. For prediction, you need to come up with a specific I.D. hypothesis, like the young earth creationists, which would make clear statements about what we should and should not observe in reality. It can then be tested against observations of reality, like evolutionary theory and YEC.

    BTW, congrats for giving keiths his answers. I’ll maybe get round to the Cambrian and some other things in your reply in the next few days if I’m not too busy. 

    Cheers.

  4. kairosfocus,

    Toronto: “Why don’t IDists like kairosfocus submit their theory to the same level of testing they do for the competition? . . .”

    kairosfocus: “Here Toronto is being willfully misleading, hoping to profit by his misrepresentation being perceived as truth.”

    ********* A simple test for KF that shows ID is improbable:

    Take any two resistor values of your choosing, and make a voltage divider that will give you 4 volts at the junction.

    After you choose the resistors, I’ll choose a power supply voltage and we’ll see how close you get to 4 volts.

     

  5. JoeG: (as if you couldn’t guess).

    dr boo-who-

    Answer the following- this will tell if your position makes any testable hypotheses-

    How does it follow that my answering the following will tell if my position has any testable hypotheses?

    How can we test the claim that any bacterial flagellum evolved via accumulations of random mutations?

    My prediction is that you are going to blather incoherently, as usual.

    How did you test it? You’ve declared that you’ve established that, “for all intents and purposes”, bacterial flagella are intelligently designed. Therefore, you must have tested and falsified all alternative naturalistic hypotheses. Remember Newton’s rules? So, how did you test and falsify the hypothesis you’ve mentioned above? And why are you pretending that it’s untestable if you’ve tested it?

    Why do you need to keep on contradicting yourself?

  6. Mung: No tree pattern to diverge from. Koonin calls it the FoL – Forest of Life.

    Did you even read what you quoted? 

    Koonin: the tree-like evolution is by far the strongest single trend in the FOL

    Here’s an even more direct citation.

    Puigbò, Wolf & KooninSearch for a ‘Tree of Life’ in the thicket of the phylogenetic forest, Journal of Biology 2009: A comprehensive comparative analysis of a ‘forest’ of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer.  

    A consistent phylogenetic signal. 

  7. critical rationalist:

    Furthermore, ID does not explain why a designer would necessarily choose one particular concrete adaptation over another. This is because ID’s designer is abstract and has no defined limitations. 

    You find a watch.  You notice that it is made with a green watch face.  Your reaction is: tell me why the intelligent agent who made the watch chose ‘green’ for the watch face.

    How is this preoccupation relevant to whether or not an intelligent agent was involved? 

    critical rationalist:

    Yes, there are cases where the tree isn’t always tree-like. But, for the vast majority of cases, we have good explanations for those exceptions, such as hybridization or HGT.

    It’s actually worse than that.

    As I pointed out above concerning Theobald’s thesis, it rises and falls on evolution being a Markov Chain process.  This is assumed to be the case.  There’s no reason for this assumption—except that this is what you think happens.  So any results you get becomes tautalogical.

    Over at PhysOrg.com today, they have an article regarding the ‘phylogenetic tree’ and the authors point out that there are very high degrees of divergent results when you use a concatenation method (catenation is Latin for ‘chain’, as in: Markov Chain Monte Carlo process, which, when linked together into a “supermatrix” gives you con-catenations[from what I can quickly gleen]).  They say that a multispecies coalescent model gives better results.  This model presumes a lot of HGT, and, at most taxnonomic levels.  This doesn’t look good for the thesis being forwarded on this thread.

    Here’s a quote:

    Beyond controversies in eutherian mammal phylogeny, similar phylogenetic controversies also exist in other clades – for example, the relationships among nemerteans, annelids, and molluscs with regards to arthropods. “Because the phylogenic reconstruction in the Tree of Life has so far been mostly based on concatenation methods,” Wu adds, “it’s likely that concatenation methods are the major cause of phylogenetic incongruence across the Tree of Life.”

    Read more at: http://phys.org/news/2012-10-forensic-speciation-splicing-genetic-phylogenic.html

     

  8. Pav: “You find a watch.  You notice that it is made with a green watch face.  Your reaction is: tell me why the intelligent agent who made the watch chose ‘green’ for the watch face.

    How is this preoccupation relevant to whether or not an intelligent agent was involved?”

    It’s relevant when you establish a context for your question.

    e.g. Why did the designer choose a green watch face when the numerals and hands are also green?

    People don’t tend to ask questions “randomly”.

     

  9. PaV,

    The problem for Darwin back then, and for Darwinists now, is the finding that all 30 major taxa existed in the Cambrian (IIRC, there might have been 1 major taxa that emerged later).

    Not true. Take a look at Figure 1 in Theobald’s essay. The 30 taxa emerge over a huge span of time, from well before the Cambrian to well afterward.

    Even if you weren’t wrong about that, it still wouldn’t help your case, because the taxa in question form a single objective nested hierarchy. As I’ve explained, ID gives us no reason to expect an objective nested hierarchy, whereas unguided evolution predicts it.

    Unguided evolution predicts one type of pattern — an objective nested hierarchy — versus the trillions of other possible patterns. Independent lines of evidence give the same objective nested hierarchy, to an accuracy of 1 in 10 38. The prediction is spectacularly confirmed.

    ID makes no such predictions and enjoys no such spectacular confirmations. Unguided evolution is the better theory, by far.

    Now, if his [Theobald’s] calculation is on the money, then this means that the chance of obtaining the currently accepted ‘phylogenetic tree’ by ‘chance’ is ONE in 1038. What this then demonstrates is that ‘intelligent’ agents, using reason, have effectively searched through a very large ensemble of possibilities to find a reliable classification scheme.

    No, there are many reliable classification schemes that don’t involve objective nested hierarchies. The Designer could have picked any of them. Instead, according to you, he picked exactly the one scheme that happens to make unguided evolution appear to be true.

    It’s the antithesis of ReMine’s “Message Theory“. Instead of making design obvious to observers, the Designer disguises his work to make it look like the product of unguided evolution.

    Or more likely, it looks like there’s no Designer because there really is no Designer.

  10. Zachriel asks Mung:

    Did you even read what you quoted?

    If he did, he didn’t understand it.

    Mung:

    Your problem is that you assume there’s a tree and then when something doesn’t fit with that assumption you call it a divergence.

    Mung,

    You’re still confused about subjective versus objective nested hierarchies. Read this section in Theobald for an explanation of the difference.

    That’s subjective and ad hoc and essentially protects your claims from falsification. You see what you want to see. Grats.

    Not true. From the same section in Theobald’s essay:

    Potential Falsification: 

    It would be very problematic if many species were found that combined characteristics of different nested groupings. Proceeding with the previous example, some nonvascular plants could have seeds or flowers, like vascular plants, but they do not. Gymnosperms (e.g. conifers or pines) occasionally could be found with flowers, but they never are. Non-seed plants, like ferns, could be found with woody stems; however, only some angiosperms have woody stems. Conceivably, some birds could have mammary glands or hair; some mammals could have feathers (they are an excellent means of insulation). Certain fish or amphibians could have differentiated or cusped teeth, but these are only characteristics of mammals. A mix and match of characters like this would make it extremely difficult to objectively organize species into nested hierarchies. Unlike organisms, cars do have a mix and match of characters, and this is precisely why a nested hierarchy does not flow naturally from classification of cars.

    If it were impossible, or very problematic, to place species in an objective nested classification scheme (as it is for the car, chair, book, atomic element, and elementary particle examples mentioned above), macroevolution would be effectively disproven. More precisely, if the phylogenetic tree of all life gave statistically significant low values of phylogenetic signal (hierarchical structure), common descent would be resolutely falsified.

    In fact, it is possible to have a “reciprocal” pattern from nested hierarchies. Mathematically, a nested hierarchy is the result of specific correlations between certain characters of organisms. When evolutionary rates are fast, characters become randomly distributed with respect to one another, and the correlations are weakened. However, the characters can also be anti-correlated—it is possible for them to be correlated in the opposite direction from what produces nested hierarchies (Archie 1989; Faith and Cranston 1991; Hillis 1991; Hillis and Huelsenbeck 1992; Klassen et al. 1991). The observation of such an anti-correlated pattern would be a strong falsification of common descent, regardless of evolutionary rates.

  11. Mung:

    dr who:
    What is the difference between 4^10^7 choices and an infinite number.

    One is finite and the other isn’t?

    One is a number and the other isn’t?

    Mung,

    You’re misattributing that quote to dr who. PaV actually wrote it. Fight it out with him.

  12. Mung responds:

    So, PaV. I guess dr. who was just quoting you?

    That’s right, Mung, it was PaV, not dr who. That means the little lecture you prepared for dr who on the difference between finite numbers and infinity can now be delivered to PaV, complete with insults.

    Have at it.

  13. JoeG:


    How can we test the claim that any bacterial flagellum evolved via accumulations of random mutations?

    My prediction is that you are going to blather incoherently, as usual.

    dr boo-who:

    How did you test it? You’ve declared that you’ve established that, “for all intents and purposes”, bacterial flagella are intelligently designed. Therefore, you must have tested and falsified all alternative naturalistic hypotheses. Remember Newton’s rules? So, how did you test and falsify the hypothesis you’ve mentioned above? And why are you pretending that it’s untestable if you’ve tested it?

    Yes, ANOTHER prediction fulfilled. Man, I am good.

    Hey Mung, wasn’t onlooker and other TSZ poseurs whining about answering questions with questions and trying to shift the onus?

    I like this one:

    Therefore, you must have tested and falsified all alternative naturalistic hypotheses.

    Can’t do that if there isn’t one to falsify. If there isn’t anything to test/ falsify we can just move on to the design criteria and see if that is met.

    We lean on you to be able to come up with testable hypotheses for your position. It isn’t up to us. If you can’t do it then we just move on and see if our criteria is met. And wrt bacterial flagella, it is.

    So wrt to Newton it is a cooperative- your failure coupled with our success. And we thank you.

    So, we’ve established that I.D., according to Joe, relies on the incorrect claim that naturalistic, non-telic evolutionary theory is untestable, unfalsifiable, and doesn’t generate any testable hypothesis. Therefore, it seems, supernatural intelligent design is the default.

    I’m sure many I.D. advocates, Michael Behe and Douglas Axe included, must disagree with this, as they keep trying to test evolutionary hypotheses.

    Joe, here’s a lesson in what testable and falsifiable mean in science.

    Let’s take your suggested hypothesis as stated.

    Hypothesis: Bacterial flagella evolved via accumulations of random mutations.

    So, to find out what predictions it makes, we ask ourselves “if the hypothesis is correct, what would logically follow”? For this, we use deductive logic.

    So, for example:

    Prediction 1: If bacterial flagella evolved via accumulations of random mutations, then bacteria must mutate.

    Prediction 2: If [hypothesis], then at least some of those mutations must be random.

    Prediction 3: Deductive syllogism:

    P1. Bacterial flagella evolved via accumulations of random mutations. (the hypothesis).

    P2. Bacterial flagella are advantageous characteristics to the organisms, improving the way they function in their environments.(Observable fact).

    C1. Accumulations of random mutations must be able to produce advantageous characteristics in bacteria. (Prediction, following logically from the two premises).

    So, let’s test. Prediction 1 is easily testable and verifiable, but if bacteria were never observed to mutate, the hypothesis would be falsified.

    Prediction 2. Test: We take bacterial clones and, after analyzing the genome, make two seperate cultures in the same medium, and leave them for a few months. We then look at the genomes and compare them to each other and the original. If we find that, for example, about twenty mutations are present in each, and the two cultures have different sets of mutations, we’ve reasonably established randomness. (For further confirmation see next test). If we could never identify any randomness in such experiments, and mutations always happened in predictable patterns, then the hypothesis could be reasonably falsified.

    Prediction 3. As with test two, we take bacterial clones, this time making about 12 cultures all in the same medium. This time, we make the environment one in which they can survive, but is far from ideal for them (to encourage adaption). We wait. If one of the cultures makes an advantageous adaption, we analyze the genome to see if an accumulation of two or more mutations has caused the adaption. If this is the case, we’ve verified prediction 3. If the mutations are not present in the other eleven cultures, and the same adaption does not take place, we have reasonably confirmed the randomness in the mutations involved.

    Assuming all the above goes well (and in real life, it actually has), then where does it leave our hypothesis? Certainly not proven, as conclusive proof of any hypothesis about ancient history would be impossible without a time machine. But the questions we must ask is “is the hypothesis well supported compared to others we can make and can it qualify as a current best explanation?”

    So, let’s make a hypothesis comparison. A group known as intelligent design advocates have proposed the general hypothesis that (necessarily) non-living intelligent designers are responsible for life. Within that general hypothesis, they propose the hypothesis: Non-living intelligent designers designed and created bacterial flagella.

    The equivalent to my first prediction (mutations in bacteria exist) would seem to be that non-living intelligent designers exist. It is largely because this hasn’t been established that I suggested to Joe that he needs to falsify all alternative naturalistic hypotheses in order to establish his as the best explanation. 

    Let’s observe and test, Joe, compare the hypotheses, and see which comes out with the most confirmed predictions. 🙂

    And Joe, try to stop contradicting yourself.

  14. keiths: The fact that parts of the “tree” diverge from the tree pattern does not negate the fact that the tree pattern predominates and can be objectively identified.

    Mung: This isn’t about parts of the tree diverging from the tree pattern. It’s about no tree at all. No tree pattern to diverge from. Koonin calls it the FoL – Forest of Life.

    But, according to Koonin, there is an objectively discernible tree. “A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria”. Any ambiguity occurs primarily near the root of the tree when horizontal mechanisms were prevalent. Not even sure why this is particularly helpful to ID. 

    CONCLUSIONS: Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete.

    Mung: Did you even read what you quoted?

    In fact, we did. Koonin believes simplistic views of the tree of life have been supplanted by a deeper understanding of early evolution. Nevertheless, your original statement, “no tree at all”, was much too broadly drawn. 

     

  15. Joe:

    Nope, I never said that. OTOH YOU are proving that it doesn’t generate any testable hypothses.

    Joe clearly can’t understand with the post above, has no idea what “testable hypotheses” means, and doesn’t realise how he’s contradicting his heroes, like Michael Behe.

    Would any other I.Dists at U.D. like to support Joe’s claim that naturalistic non-telic evolutionary theory is untestable, and does not generate testable hypotheses?

    Please, someone, copy that question into the “essay” thread over at U.D.

  16. Joe:

    dr boo-who:

    Joe clearly can’t understand the post above, has no idea what “testable hypotheses” means, and doesn’t realise how he’s contradicting his heroes, like Michael Behe.

    I clearly understand that you are a delusional liar and a scientifically illiterate chump.

    And your inability to provide a testable hypothesis for unguided evolution tells everyone that I am correct. So again I thank you.

    It is obvious that dr boo-who doesn’t know what a testable hypothesis is…

    I note that you quoted part of my post, but you left out the question. Are you worried that your colleagues at U.D. won’t agree with you?

    Here’s the question again, followed by the request I made.

    Would any other I.Dists at U.D. like to support Joe’s claim that naturalistic non-telic evolutionary theory is untestable, and does not generate testable hypotheses?

    Please, someone, copy that question into the “essay” thread over at U.D.

    There’s surely no need to be afraid of subjecting your ideas to review by your I.D. peers, is there?

    Or is there?

    Post the question, and let’s see.

  17. It looks as though Joe doesn’t have the confidence in his claims to repeat my question on Uncommondescent.

    I’ll repeat it here on the Sandbox, and keep on asking, as it would be interesting to find out if any of the I.D. regulars understand what “testable hypothesis” means. They certainly haven’t corrected Joe.

  18. Mung,

    I’m not sure why you think it’s a winning strategy to pretend that I haven’t made an argument. My argument is right there in the OP for everyone to see. If they read the comment threads here and at UD, they’ll also see that no one has been able to refute it. Certainly not you.

    You can pretend there’s no elephant in the room, but you’re not fooling anyone.

  19. CR: Furthermore, ID does not explain why a designer would necessarily choose one particular concrete adaptation over another. This is because ID’s designer is abstract and has no defined limitations. 

    PaV: You find a watch.  You notice that it is made with a green watch face.  Your reaction is: tell me why the intelligent agent who made the watch chose ‘green’ for the watch face.

    Wrong. 

    My reaction is to point out the entire watch is a concrete adaption of raw materials into an object that serves the purpose of telling time. It’s not a raw material itself. Nor could it have been laying there forever. Is the watch mechanical? Does it have hands or a digital display? Does it need to be manually wound, run on a battery or use the wear’s own movements to wind itself?

    While people today can choose between mechanical and quartz based digital watches, this wasn’t an option 300 years ago. We had yet to create the knowledge of how to adapt raw materials into a digital watch. We can explain the particular concrete adaptations, in part, based on our limitations at the time. Specifically, our limitations of knowledge pertaining to how to adapt matter into an object that can tell time. 

    In the future, we will have even more options. And they will be possible then, but not now, because we will have created new knowledge we did not possess before.  

    PaV: How is this preoccupation relevant to whether or not an intelligent agent was involved? 

    Human beings are good explanations for watches because of our specific limitations. 

    CR: Yes, there are cases where the tree isn’t always tree-like. But, for the vast majority of cases, we have good explanations for those exceptions, such as hybridization or HGT.

    PaV: It’s actually worse than that.

    I’m not following you. How did we get from what I wrote to “worse” than what I wrote? Do we *not* have good explanation for the majority of exceptions? Why is discovering exceptions that do not conflict with Darwinism “bad” which you’re suggesting is actually worse?

    PaV: As I pointed out above concerning Theobald’s thesis, it rises and falls on evolution being a Markov Chain process.  This is assumed to be the case.  There’s no reason for this assumption—except that this is what you think happens.  So any results you get becomes tautalogical.

    Wikipedia: A Markov chain… is a random process usually characterized as memoryless: the next state depends only on the current state and not on the sequence of events that preceded it. 

    That’s not my assumption. Rather, my explanation is that Darwinism genuinely creates non-explanatory knowledge of how to build biological organisms through a form of conjecture and refutation. Specifically, conjecture, in the form of genetic variations that are random in respect to any problem to solve, and refutation, in the form of natural selection. This knowledge may not have existed before or it could have existed in some other form, such as convergence of eyes in mammals and cephalopods, etc. 

    In other words, Darwinsm is part of our current, best universal explanation of the grown of knowledge. This includes the growth of knowledge of how to make improvements in biological organisms. 

    Does ID fit into any explanation about the growth of knowledge? Do you think we make progress because “that’s just what some designer must have wanted” as well? 

    PaV: Over at PhysOrg.com today, they have an article regarding the ‘phylogenetic tree’ and the authors point out that there are very high degrees of divergent results when you use a concatenation method. 

    From the article:  Wu adds, “it’s likely that concatenation methods are the major cause of phylogenetic incongruence across the Tree of Life.”

    I have already addressed this, which you ignored. 

    CR: However, in cases were we have yet to identify a good explanation [for these incongruencies], these observations are neutral to Darwinism. They tell us nothing either way. We cannot extrapolate observations without first putting them into an explanatory framework. 

    Again, ID does not explain why a designer would necessarily choose one particular concrete adaptation over another.  “That’s just what a designer must have wanted” is a bad explanation because it is shallow and easily varied. Adding it to the mix serves no explanatory purpose in this respect. 

  20. Mung responds to my comment above:

    keiths:

    I’m not sure why you think it’s a winning strategy to pretend that I haven’t made an argument. My argument is right there in the OP for everyone to see.

    Then this should be easy for you, keiths.

    1.) Select just one evidence for common descent that you set forth in your OP.

    2.) Explain why Intelligent Design is not compatible with that particular evidence for common descent.

    3.) Show where you set out that piece of evidence in your OP and where you made an argument in your OP which shows why Intelligent Design is not compatible with that particular evidence for common descent.

    If they read the comment threads here and at UD, they’ll also see that no one has been able to refute it. Certainly not you.

    There’s nothing there to refute. How does one refute an untestable claim?

    Mung, My argument is laid out in the OP, with key points highlighted in bold print. If you can refute my argument, then stop wasting our time and do it. If you can’t refute my argument, then admit it and move on.

    As for this:

    There’s nothing there to refute. How does one refute an untestable claim?

    The testable claim is right there in the OP, also in bold print, to which you seem to be congenitally blind:

    And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.

    The prediction has been tested and confirmed. Unguided evolution is trillions of times better, as a theory, than ID. Deal with it.

  21. critical rationalist:

    My reaction is to point out the entire watch is a concrete adaption of raw materials into an object that serves the purpose of telling time. It’s not a raw material itself. Nor could it have been laying there forever. Is the watch mechanical? Does it have hands or a digital display? Does it need to be manually wound, run on a battery or use the wear’s own movements to wind itself?

    You’ve misunderstood what I was trying to convey by saying the watch face was green.

    Inspecting the watch, we have every evidence that it was intelligently designed.  And, if we study it sufficiently, then we might begin to understand why each part of the watch functions the way it does.

    But there’s no ‘explanation’ for the green watch face.  Now you and I know that that is but some simple choice.  Nevertheless, the “designer” chose that color (remember, the watch face had to have some color).  But we have no reason to know why.

    So the ‘green’ watch face is simply ‘symbolic’ of that which is ‘part’ of the ‘design package’, but something for which we cannot attribute a cause.

    Similarly, then, as we study biological systems, we can recognize how and even why they function the way they do; but there will be other parts of the biological systems that simply are the way they are, and no intelligent reason can make that known to us.

    But just because I can’t explain ‘everything’, doesn’t mean that I can’t explain ‘some things.’  And the ‘some things’ we can explain demonstrate that life is designed.  That’s the ID position, and for very specific reasons.  Now this doesn’t mean that if ID can’t explain ‘everything’, that it should not be taken seriously for ‘anything.’  This is a stretch.

     As to:

    PaV: As I pointed out above concerning Theobald’s thesis, it rises and falls on evolution being a Markov Chain process.  This is assumed to be the case.  There’s no reason for this assumption—except that this is what you think happens.  So any results you get becomes tautalogical.

    The point I’m making with this is that a Markov Chain process will result in a “nested hierarchy” simply because of the mathematics involved.

    From Wikipedia:

    Markov chains also have many applications in biological modelling, particularly population processes, which are useful in modelling processes that are (at least) analogous to biological populations. The Leslie matrix is one such example, though some of its entries are not probabilities (they may be greater than 1). Another example is the modeling of cell shape in dividing sheets of epithelial cells.[19] Yet another example is the state of Ion channels in cell membranes. 

  22. PaV,

    Inspecting the watch, we have every evidence that it was intelligently designed. And, if we study it sufficiently, then we might begin to understand why each part of the watch functions the way it does.

    But there’s no ‘explanation’ for the green watch face. Now you and I know that that is but some simple choice. Nevertheless, the “designer” chose that color (remember, the watch face had to have some color). But we have no reason to know why.

    The fact that your ‘arbitrary choice’ theory can’t explain the green watch face isn’t a strike against it per se. But it does become a problem if there is a competing theory that not only predicts the green watch face, but specifies the exact hue out of trillions of possibilities.

    Likewise, the fact that ID doesn’t predict the objective nested hierarchy wouldn’t be a problem if unguided evolution didn’t predict it either. But unguided evolution does predict it, out of trillions of alternate possibilities, and the prediction has been spectacularly confirmed. On the basis of this extremely specific and successful prediction alone, unguided evolution is vastly superior to ID. And that’s without mentioning the other ways in which unguided evolution fits the evidence extremely well, and far better than ID.

  23. PaV,

    As I pointed out above concerning Theobald’s thesis, it rises and falls on evolution being a Markov Chain process. This is assumed to be the case. There’s no reason for this assumption—except that this is what you think happens. So any results you get becomes tautalogical.

    Joe Felsenstein has already addressed your concern in detail. The whole comment is worth reading, but here is the concluding paragraph:

    Doug’s [Theobald’s] analysis of the shared signal in phylogenies from different genes would have allowed him to see if different genes had wildly-conflicting signals about what the phylogeny was. But they instead had a common underlying signal that reinforces itself as you look at more genes. The methods Doug used do not force the answer. They are state-of-the-art, and a beautiful confirmation of an underlying shared tree of ancestry.

  24. keiths:

    Not true. Take a look at Figure 1 in Theobald’s essay. The 30 taxa emerge over a huge span of time, from well before the Cambrian to well afterward.

    First problem: there’s no indication whatever of ‘time’ in Figure 1.

    Second problem: it’s not a taxonomic figure, but it, rather, a compilation of critical phenotypic traits. IOW, what we see along the top of the ‘figure’ are NOT major taxa; i.e., phyla, or ‘body-types.’

    Now, let’s focus on a logical flaw in Darwin’s argument, a flaw that plays into the discussion at hand.

    In the Origins, Darwin says:

    I see no reason to limit the process of modification, as now explained, to the formation of genera alone. If, in our diagram, we suppose the amount of change represented by each successive group of diverging dotted lines to be very great, the forms marked a214 to p14, those marked b14 and f14, and those marked o14 to m14, will form three very distinct genera. We shall also have two very distinct genera descended from (I) and as these latter two genera, both from continued divergence of character and from inheritance from a different parent, will differ widely from the three genera descended from (A), the two little groups of genera will form two distinct families, or even orders, according to the amount of divergent modification supposed to be represented in the diagram. And the two new families, or orders, will have descended from two species of the original genus; and these two species are supposed to have descended from one species of a still more ancient and unknown genus.

    Darwin’s basic view is that from some few ancient ‘species’, through a long process of ‘divergence’, groupings of new species arise which can be classified as genera, families, and orders.  He also sees these few ancient species forming, through divergence, entire ‘classes’ of species.

    But what about phyla–definitive body-plans?  

    Where did they come from?  How do they form?  What does Darwin have to say about them?  Nothing.

    If we are to presume that phyla developed over time from “one or many forms”, then how did they form?  And why haven’t any new ones formed in the almost 550 billion years since the Cambrian?

    Is Darwin ‘presuming’ that there were 30 ‘forms’ from the beginning?  But that would require a Creator of sorts.  But, of course, when Darwin speaks of “one or many forms” at the end of the Origins, he invokes the “Creator.”

    So, is Darwin simply conceding that he has no explanation for the appearance of the Cambrian phyla?  Well, certainly, he doesn’t provide any explanation otherwise.

    I, personally, find this very problematic.

     keiths:

    Even if you weren’t wrong about that, it still wouldn’t help your case, because the taxa in question form a single objective nested hierarchy. As I’ve explained, ID gives us no reason to expect an objective nested hierarchy, whereas unguided evolution predicts it. 

     Well, in fact, it gives a perfectly good explanation for what we find in nature.  The Designer brings life into existence in stages, and diversifying that life at His pleasure.  Once this basic ‘body-types’ are established, they then adapt to various environments through built-in mechanisms suited to such adaptation.  This includes mechanisms that can involve horizontal gene transfer.  Over time, many diverse forms arise.  Once environmental niches are satisfactorily filled, relative stasis continues.

    It’s possible that the Designer implants information in a particular ‘body-type’ that includes that information that will only be needed in future forms.  It is also possible that, at intervals, the Designer infuses new information into a particular ‘body-type’.

    What would we see?  Pretty much what we now see: similarly related species involving a basic ‘body-type’. IOW, “nested hierarchies.”

    keiths:

    Unguided evolution predicts one type of pattern — an objective nested hierarchy — versus the trillions of other possible patterns. Independent lines of evidence give the same objective nested hierarchy, to an accuracy of 1 in 10 38. The prediction is spectacularly confirmed.

    What ‘prediction’?

    The Linnean Classification system is based on “nested hierarchies ”  And it predates Darwinism by a century.  How can you ‘predict’ what has been known and seen for centuries (going back to the Greek philosophers).

    You know Michael Behe accepts common descent.  Your whole preoccupation with “nested hierarchies” flows from this notion.  So how does this in any way present a problem to ID if one of its principal champions accepts it as fact?

    I don’t accept it.  Nor does Wm Dembski.  But we believe in a commonality of descent, which is very much akin to common descent.  So, again, where is the problem here?

    As to the 1038 possibilities, my explanation still stands.  If you have a winning lottery ticket, it doesn’t have an “accuracy of 1 in 107“.

     keiths:

    PaV: Now, if his [Theobald’s] calculation is on the money, then this means that the chance of obtaining the currently accepted ‘phylogenetic tree’ by ‘chance’ is ONE in 1038. What this then demonstrates is that ‘intelligent’ agents, using reason, have effectively searched through a very large ensemble of possibilities to find a reliable classification scheme.

    keiths:  No, there are many reliable classification schemes that don’t involve objective nested hierarchies. 

    The Linnean classification system is BASED on “nested hierarchies.”   Here’s “http://evolution.berkeley.edu/evolibrary/article/history_05” a Berkeley website on evolutionary thought.  The title of the website:

    “Nested Hierarchies, the Order of Nature: Carolus Linneaus”

    And they write:

    He classified genera together in groups he called families, which he then placed in larger groups called orders, and then kingdoms, like boxes within boxes. 

     Well, if there are per Theobald 1038 different ways of classifying all these critical phenotypic traits, then Linneaus found his way through all of the ‘classifcation-space’ and came up with his system.  This demonstrates the power of intelligence to overcome and effectively sift through enormous large probability spaces.

    keiths:

    The Designer could have picked any of them. Instead, according to you, he picked exactly the one scheme that happens to make unguided evolution appear to be true.

    You have it backwards here.  Darwin believed he had a theory that could explain what was evidently already true: the Linnean classification of life.  And you’re correct: Darwin’s theory only ‘appears’ to be true, but only to segment of society.

  25. Pav: As I pointed out above concerning Theobald’s thesis, it rises and falls on evolution being a Markov Chain process.  This is assumed to be the case.  There’s no reason for this assumption—except that this is what you think happens.  So any results you get becomes tautalogical.

    It ‘rises and falls’ more simply, on the fact that organisms have offspring. The current population got all of its DNA from the previous generation – specifically, each individual from its parents – plus a contribution from mutation. The next population will get all of its DNA from the current one, plus a contribution from mutation.

    If, instead of being copied, the next generation’s DNA simply appeared out of thin air, there would be no possibility of reconstructing any kind of genealogy, since there would not actually be a genealogy. The fact that one can reconstruct a genealogy at all from DNA and other ‘family traits’ – routine in paternity testing, forensic DNA analysis, disease tracking, population movements – is thumping support for the thesis that the local, obvious fact of common descent within a species builds into a higher-level pattern of common descent of species.

    Otherwise, we have to introduce a curious, and arbitrary, demarcation point. Common sequence in a species is uncontroversial common descent, maybe, if pressed, in a grouping of species – bears, or big cats, etc – but suddenly, the exact same signals stop giving the same information, commonality due to descent, round about the bear/cat divide. Commonality = Common Design among these much more different organisms, while it’s accepted as Common Descent among closer cousins – ie, the less alike creatures are, the more strongly Common Design is argued for!

    It’s nonsensical to do that without a reason.

  26. And that really should be the end of it but I doubt PaV et al will see it that way. 

    The “it’s a tautology!” is the last desperate cry of someone seeing their argument crumble.

  27. Alan  Miller:

    . . . but suddenly, the exact same signals stop giving the same information, commonality due to descent, round about the bear/cat divide. Commonality = Common Design among these much more different organisms, while it’s accepted as Common Descent among closer cousins – ie, the less alike creatures are, the more strongly Common Design is argued for!

    It’s nonsensical to do that without a reason.

    How does Darwinism (neo-Darwinism) explain this additional ‘information’ that distinguishes bears from cats?  There isn’t one that comes close to making any sense at all.

    As to “nonsensical”, it is nonsensical to believe Darwin was right without convincing evidence and without some kind of explanation for how the process works, without ‘good reason’ for doing so.  And, unfortunately, there isn’t ‘good reason’ for doing so.  Even some atheists don’t believe in Darwinism.  Why?  

     

     

  28. PaV,

    As to “nonsensical”, it is nonsensical to believe Darwin was right without convincing evidence and without some kind of explanation for how the process works, without ‘good reason’ for doing so.

    Yet you accept “Intelligent Design Theory” without *any* explanation of any process or any other actual data other then “it was designed”. 

    How does Darwinism (neo-Darwinism) explain this additional ‘information’ that distinguishes bears from cats?

    How does “Intelligent Design Theory” explain this additional “information”? At least there is a proposed mechanism from “darwinists”, even if you don’t accept it (and it’s incomplete anyway).
    Why would you accept the ID version when there is far far far less actual evidence (i.e. none at all) instead of the version that is actually supported by evidence, however thin you think it might be there is verifiably more of it then there is for ID. 

  29. How does Darwinism (neo-Darwinism) explain this additional ‘information’ that distinguishes bears from cats?  There isn’t one that comes close to making any sense at all.

    The ‘additional information’ comes from you looking and saying “ooh look, a bear” or “ooh look, a cat”! You are looking at two bunches of twigs and convincing yourself that, because they are locally categorisable as “things that are quite similar”, but separately as “things that are very different”, they cannot possibly have any underlying relation in the same supporting tree. Yet molecular and morphological evidence says that there is a tree for uncontroversial “things-that-are-not-so-different” – individual cats, or different cat species – and the same techniques reveal a tree for relationships between “things-that-are-more-different”. So a (neo)-Darwinist would explain it simply as an individual’s tendency to regard the current end-points of a longer process of serial anagenesis in separate lines as categorically discrete, while accepting the twigs of shorter processes as categorically related. The more different things become, the less likely we are to lump them together. Which might not ‘come close to making sense’ to you, but that’s where the evidence points. Oh, and fossils. 

    As to “nonsensical”, it is nonsensical to believe Darwin was right without convincing evidence and without some kind of explanation for how the process works, without ‘good reason’ for doing so.  And, unfortunately, there isn’t ‘good reason’ for doing so.  Even some atheists don’t believe in Darwinism.  Why?  

    In my experience, people are usually misinformed or misled by their conceptions! For example, they exhibit the discrete, ‘essentialist’ vision of types above a certain taxonomic class which you do. There is no support whatsoever for this vision, but we humans love to classify! And get very heated about it. “It’s Folk!” “It’s Country!”. As to ‘how the process works’ – as far as Common Descent is concerned, the process works by organisms having offspring, and carrying on doing so for a very long time. Whether NS can build eyes etc is a different issue, but on Common Descent, how much evidence do you need before acceptance of it stops being ‘nonsensical’?

  30. Alan Miller said:

    Yet molecular and morphological evidence says that there is a tree for uncontroversial “things-that-are-not-so-different” – individual cats, or different cat species – and the same techniques reveal a tree for relationships between “things-that-are-more-different”.  

    A quibble: within species, the molecular and morphological evidence does not show that the differentiation of individuals is treelike. My genealogy is not treelike because (shock! horror!) I actually had not one ancestor, but two: my mother and my father. Samples of individual gene loci have trees of ancestry — coalescent trees — but they differ from locus to locus.

    Above the species level the pattern rapidly becomes treelike, and that is where the dispute between PaV and Alan is mostly occurring, but within species the pattern is not a single tree.

  31. A quibble: within species, the molecular and morphological evidence does not show that the differentiation of individuals is treelike.

    Agreed, and perhaps poorly worded – ‘genes in individual cats’, I should have said. As you say, you can take particular markers and construct trees for them, supporting the common descent of those sequences, rather than of those individuals, which are mosaics (though even those mosaic elements will display coalescence over the longer term). Since it is always sequences we are talking about in molecular studies, both above and below the species level, I (cautiously) stand by my continuum from the individual and its parents outwards, for the purposes of pinning down exactly where Creationists feel molecular data suddenly loses traction.

    Constructing a consensus phylogeny using multiple markers is of course a different issue above species (due to whole-genome coalescence as well as the lack of recombination) as compared to below. But individual haplotypes often have sufficient persistence to be ‘tree-like’ in descent, if a little fuzzy round the edges.

  32. PaV: How does Darwinism (neo-Darwinism) explain this additional ‘information’ that distinguishes bears from cats?

    What additional information? Just seems like different information. Microevolution. In any case, it’s thought they evolved from a common Carnivoran ancestor in the middle Eocene.

  33. Jerad: You cannot just look at the fossil record and point to gaps as an argument.

    Mung: LOL! How then do you suppose we can dispute the following assertion?

    Jerad: … the fossil evidence is consistent with universal common descent given that not all life forms formed fossils.

    It’s called the nested hierarchy, which is the consequence of bifurcating descent with modification. You don’t have to fill in every blank to confirm the nested hierarchy.

  34. Does ‘microevolution’ lead to “information”?

    Based on The Edge of Evolution, and a new report about chloroquine resistance developing in mosquitoes again in areas where chloroquine had stopped being used, it only makes Behe’s thesis clearer: adaptation (=microevolution) is a “loss” of information, not a gain.

    The real world facts contradict neo-Darwinian assertions.  Doesn’t that trouble you? 

  35. keiths:

    Thanks for pointing me in the direction of Joe Felsenstein’s response.  Never saw it.

    Joe writes:

    Markov process models are the basic ones used in inferring evolutionary trees (phylogenies). Of course they are models, and thus approximations of nature. The famous statistician George Box once wisely said that “All models are wrong; some models are useful.”

    This confirms the central point of my thesis.

    So of course we can’t prove that the models are accurate representations of nature.

    This confirms another central point of my thesis.

    But we extend them to become more and more accurate, adding Gamma distributed variation in rates of evolution among molecular sites, adding Hidden Markov Models to allow for correlations of evolutionary rate among nearby sites, and making 3-site codon models to approximate changes in DNA in coding sequences. And so on. 

    I neither denigrate, nor deny, the intelligence, diligence, enthusiasm and competence of those working in this field.  I simply point out that if you choose a Markov Chain method, it is because you’re assuming “common descent”.  If your basic (to be refined later) model assumes this, why would it not confirm it?

    Yet, actually, the “divergences” they speak of do contradict the principle thesis of common descent.  That’s why I pointed out the better results, recently reported, of using a “multispecies coalescent” method.  The underlying suggestion of this method is that “genes” are inherited from even distant species.  I don’t see this as “confirmation” of the Markov Chain ‘assumption’ of common descent.

    But having said all of this, remember, Michael Behe already accepts “common descent”.  So, if you prove “common descent”, how does this in any way disprove ID?  I’m at a loss, really.  And I don’t write that simply for effect.

     

  36. PaV: Does ‘microevolution’ lead to “information”?

    You’re the one who suggested there was “additional ‘information’ that distinguishes bears from cats.

     

  37. keiths:

    The fact that your ‘arbitrary choice’ theory can’t explain the green watch face isn’t a strike against it per se. But it does become a problem if there is a competing theory that not only predicts the green watch face, but specifies the exact hue out of trillions of possibilities.

    You’re beating this horse to death. 

    Cladistics refines Linnaen classification, a system develop in the early 1700’s, more than a century before Origins.   But it doesn’t completely redefine it.

    Linnaeus used “nested hierarchies.”  You’re claiming that ONLY Darwinism can predict “nested hierarchies” via his belief in “common descent.”  Well, if only “common descent” predicts “nested hierarchies,” then how did Linnaeus stumble upon it, since he had 1038 chances, per your view, to get it all wrong?

    If Darwin talked about species, genera, families, orders, classes, it’s only because Linnaeus had already invented his classification system.

    Let me try and put this another way:

    If, per Linnaeus, there is a certain principle type which then deviates through adaption with time, then wouldn’t you expect that all of the classes, orders, families and genera forming the phyla be related?  And, as we consider all of this in our molecular biology age, wouldn’t you expect that there would be molecular similarities?

    I think the answer is: Of course!  The way, and only way, to differentiate between the two is by figuring out the direction of the radiation.  In the case of Darwin, he has species at the bottom and orders and families at the top of his “cone”.  Linnaeus would have classes at the bottom of his “cone”, and genera and species at the top of his cone.

    So, which is it?

    Well, when you have 30 phyla in the Cambrian, and possibly one more since, then it sure looks like the “classes” are at the BOTTOM.  

    But, I’m simply repeating myself.  This is the problem of the Cambrian Explosion, which seems lost on Darwinists.

    Yes, you have “chordate” radiations that are innovations within that “class”, but when we look at these “innovations”, guess what, we see “explosions” again, as in the “mammalian explosion”.  That is, no intermediate forms.  Rather, the new “orders” just simply show up in the fossil record.

    You can try and convince me otherwise, but these are the facts you’re working against. 

    And, lastly, of course, ID is fully consistent with the Linnaen system of classification.  So, it, too, predicts “nested hierarchies.”  The ONLY way this would not be true is if ID said, as Darwin argued was being said (his straw man argument), that the Designer designed each and every species we find, and that the only way for change to occur is via an intervention by the Designer.  But it does no such thing.

    Epigenetics looks to be a wonderfully designed system for organisms to adapt both to their environment and to one another.   Epigenetics only serves to make ID more tenable, while, at the same time, deals a devastating blow to the whole area of population genetics and the neo-Darwinian point of view.

  38. Based on The Edge of Evolution, and a new report about chloroquine resistance developing in mosquitoes again in areas where chloroquine had stopped being used, it only makes Behe’s thesis clearer: adaptation (=microevolution) is a “loss” of information, not a gain.

    The real world facts contradict neo-Darwinian assertions.  Doesn’t that trouble you? 

    How? You have referred to a report in a single species for a single trait, without even providing a link, and nodded in the general direction of a calculation in Behe which fails to take into account recombination and drift. So the only place the contradiction exists at the moment is in your head. Could you make more explicit why the things that bother you should bother ‘Darwinism’?

    There is no obvious sense in which adaptation could be considered a loss of information (though you might choose to define it such that it could). By adapting, genomes become enriched in ‘information’: What Survived Best In The Recent Environment. If the current environment is not terribly different, this is useful info to have. What information do you think is being lost when a population adapts?

  39. OMTWO:

    Why would you accept the ID version when there is far far far less actual evidence (i.e. none at all) instead of the version that is actually supported by evidence, however thin you think it might be there is verifiably more of it then there is for ID. 

     What evidence?

    Do you have evidence that amino acid substitutions can accumulate sufficiently in the required amounts of time to affect known differences between divergent species?  

    Simple answer: No.

    There are no intermediate forms in the fossil record, and, using neo-Darwinian methods, 14 billion years of time wouldn’t be sufficient to bring about even smallish changes let alone the dramatic changes known to exist.  This is just the way it is.  Point out where I’m wrong.

    OTOH: the fact that DNA is a “code” immediately suggests an intelligent origin.  Why?  Because the only known ‘codes’ are known by, and developed by, intelligent beings.

    And the more we look, and the more we study, lo and behold, the cell becomes more and more complex, and, hence, more and more beyond the scope of the extremely limited (almost irrelevant) neo-Darwinian mechanisms. 

  40. Perhaps PAV would care to address the Lenski experiment, which shows an unmistakeable gain of function with no corresponding loss.

    Not only that, but it reaches or exceeds Behe’s Edge in a decade, in a tiny population.

    Not only that, but it confirms the existence of duplication and recombination as useful mutation types.

    Perhaps PAV is of the opinion that because no on has observed a complete orbit of Pluto, that it may yet fall into the sun or require the intervention of Designers to maintain its trajectory.

  41. This is the problem of the Cambrian Explosion, which seems lost on Darwinists.

    More that the answer is lost on Creationists, who see only twigs. The Darwinist would assume that, if you happened to find yourself in the Cambrian seas, unencumbered by a knowledge of the subsequent 500 million years, you would find a recently-diverged set of species, not 30 different incipient phyla! A Creationist accompanying said Darwinist might even agree. A bunch of unprepossessing tubes, with a segmental development plan. Evolution a little above the species level – the kind intelligent Creationists agree must happen, even if only to account for speciation since the Ark!

    In their day, they were twigs. Fast forward and those tubes have adopted some very distinct developmental modes, from which pro-Arthropodal, pro-Molluscan and pro-Vertebrate species emerge – branches upon thickening limbs. They diversify, speciate and diverge for a few hundred million more years. Now you look back and see a cone, with phyla at the ‘bottom’, but it was built by divergence among relatives that were much closer initially, as the cone was being described in ‘species space’.

  42. And, lastly, of course, ID is fully consistent with the Linnaen system of classification.  So, it, too, predicts “nested hierarchies.”  The ONLY way this would not be true is if ID said, as Darwin argued was being said (his straw man argument), that the Designer designed each and every species we find, and that the only way for change to occur is via an intervention by the Designer.  But it does no such thing.

    No, you go for a halfway house that is neither fish nor flesh. All you are saying is that ID is consistent with the Linnaean hierarchy up to a point – you’re not daft enough to make that point every species separately created, so you go for family or class. But above that point, you are doing exactly what you claim is a strawman caricature – separate creation of [taxonomic class X and above]. Which makes no more sense, to someone who grasps that taxonomic classes start with species, and only become higher levels with passing time. You still have to explain the higher-level hierarchies.

    You can, of course, start with Designer-created ‘type’ species at your favoured taxonomic level, however long ago was necessary for that species to found the modern dynasty, but the discontinuity that this would predict is not observable, in the combination of fossils and molecular data. And you have a fair bit of work to do to stop your Chosen Lineage going extinct, and ensure that it fits in ecologically. It is an elaborate theory, entirely ad hoc, and explains nothing about the data.

  43. Allan Miller:

    In their day, they were twigs. Fast forward and those tubes have adopted some very distinct developmental modes, from which pro-Arthropodal, pro-Molluscan and pro-Vertebrate species emerge – branches upon thickening limbs.

    But if twigs turned into branches, why are there still twigs?

    You’ve pointed out yet another case where creationists, including the ID sub-species, mistake the map for the territory.  It’s as if they think that naming a group a phyla as opposed to a species somehow changes what actually occurred.  In another billion years their intellectual descendants will be talking about how the chihuahua order is far too different from the mastiff order for them to have a common ancestor.
     

  44. It’s interesting to see the same tired arguments recycled over and over.

    It has been some time since a mass extinction or massive environmental change, such as oxygenation. During periods of environmental stasis, evolution fills niches with highly specialized organisms.

    Highly specialized species are first against the wall during the mass extinctions. Some people think we are in the middle of one now, caused by humans.

    Humans are no threat to cockroaches or bacteria. But we are a threat to many “pretty” species that require lots of territory and specialized climates.

    Douglas Axe would like to score points by pointing out that highly adapted coding sequences are resistant to change. No shit. So are highly adapted physical and behavioral traits. When a new adaptation is required of a specialized species, say the passenger pigeon or dodo, they go extinct.

    It should not be a surprise to anyone that sudden radiations of new types is a characteristic of the aftermath of extinctions. Mammals after dinosaurs, for example. Evolution of bodily adaptations is mostly controlled by regulatory networks rather than by the invention of new proteins. Body plans can evolve quickly when the arena has been cleared of competitors.

    I think Darwin argued against mass extinctions, but he couldn’t have known about evidence that has been uncovered only in recent decades.

  45. Mung: Take just the fossils we have in the Cambrian strata. How many different phylum are represented?

    Depends on what you count as a distinct phylum, and what you mean by phylum. In its most generic sense, it’s just an artificial high-level categorization of organisms. Or you can consider it a grouping by general body plan. Some phyla originated before the Cambrian Explosion (such as cnidarians and sponges), while some phyla originated after the Cambrian Explosion (such as flowering plants).

    Mung: What makes those fossils consistent with universal common descent?

    They generally fit the nested hierarchy.

    Mung: Where are their ancestors?

    Organisms with soft body parts don’t fossilize well, but there is evidence of metazoans, including bilaterians before the Cambrian Explosion.

    Mung: Assume you’re an alien species come to earth at the end of the Cambrian. Would you believe in universal common descent?

    We would expect to see many unknown organisms, generally fitting the nested hierarchy. What we perceive today as separate phyla would be just incremental modifications of existing ancestral species.

    What would you expect to see?

    Mung: How many generations would you need to go back before a DNA test could not establish your relationship?

    All the way back to the most recent common ancestor of DNA life. 

     

  46. Mung’s misunderstandings would be tragic if they weren’t so funny:

    Unguided evolution (whatever that is) doesn’t predict anything. If it did it wouldn’t be unguided.

  47. PaV asks:

    But having said all of this, remember, Michael Behe already accepts “common descent”. So, if you prove “common descent”, how does this in any way disprove ID? I’m at a loss, really. And I don’t write that simply for effect.

    I explained that in the OP:

    What about our third subset of IDers — those who accept the truth of common descent but believe that intelligent guidance is necessary to explain macroevolution? The evidence is a problem for them, too, despite the fact that they accept common descent. The following asymmetry explains why: the discovery of an objective nested hierarchy implies common descent, but the converse is not true; common descent does not imply that we will be able to discover an objective nested hierarchy. There are many choices available to a Designer who guides evolution. Only a tiny fraction of them lead to a inferable, objective nested hierarchy. The Designer would have to restrict himself to gradual changes and predominantly vertical inheritance of features in order to leave behind evidence of the kind we see.

    In other words, our ‘common descent IDers’ face a dilemma like the one faced by the creationists. They can force guided evolution to match the evidence, but only by making a completely arbitrary assumption about the behavior of the Designer. They must stipulate, for no particular reason, that the Designer restricts himself to a tiny subset of the available options, and that this subset just happens to be the subset that creates a recoverable, objective, nested hierarchy of the kind that is predicted by unguided evolution. Unguided evolution doesn’t require any such arbitrary assumptions. It matches the evidence without them, and is therefore a superior explanation.And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.

  48. Allan Miller:

    You can, of course, start with Designer-created ‘type’ species at your favoured taxonomic level, however long ago was necessary for that species to found the modern dynasty, but the discontinuity that this would predict is not observable, in the combination of fossils and molecular data.

     This “discontinuity” is observable.  It’s called the Cambrian Explosion.

    Darwin, in the Origins, saw this as a real problem.  His expectation was that there would be a fossil record discovered stretching as far back from the Cambrian as the Cambrian is from present day, and that, e.g., in that fossil record there would be found descendants of the trilobite.

    Do you have any evidence for this?  Does any exist?

    Then, per Darwin, his theory should be abandoned.  So, when, exactly, will that happen? 

  49. petrushka:

     It should not be a surprise to anyone that sudden radiations of new types is a characteristic of the aftermath of extinctions. Mammals after dinosaurs, for example. Evolution of bodily adaptations is mostly controlled by regulatory networks rather than by the invention of new proteins. Body plans can evolve quickly when the arena has been cleared of competitors.

     Mammals and dinosaurs share the same body-plan: four limbs, eyes, jaws, etc, etc.  They’re both part of the SAME body-type: vertebrata, which is a sub-phyla of Chordata.

    From Wikipedia:

    Vertebrates /ˈvɜrtɨbrəts/ are animals that are members of the subphylum Vertebrata /ɑː/ (chordates withbackbones and spinal columns). Vertebrates include the overwhelming majority of the phylum chordata, with currently about 64,000 species described.[2] Vertebrates include the jawless fishesbony fishessharks and rays,amphibiansreptilesmammals, and birds.  

     

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