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. I am willing to answer questions about methods for inferring phylogenies (evolutionary trees) here, within reason. Questions posed over at UD I will answer if I happen to see them (someone can re-raise them over here if they feel ignored).

    Let me toss out (in both senses of the phrase) one issue here. Creationists often reject the tree of life by pointing out that issues like horizontal gene transfer show that the “tree” isn’t a perfect tree. Therefore there is no tree of life. That there are parts of the TOL that aren’t exactly treelike is not new: for example we have known about lineages in the tree that came from hybridization in plants since at least the early years of the 20th century. So the genealogy of life is not perfectly a tree, and this is not news. Unfortunately, in the enthusiasm for work on phylogenies, some of my colleagues have made a habit of going around making statements that sounded as if there were no departures ever from a perfect tree.

    There is a genealogy of life, showing common descent. Most of it is a tree, especially in eukaryotes. Pointing out that parts of it are not treelike does not make the evidence for common descent go away. 

  2. Another issue that we can dispose of quickly is the issue of common design, which was mentioned in the post by keiths. Common design does explain all the data. It proposes that the patterns that appear to be common descent are just there because that’s the way the Designer wanted the species to be. It certainly cannot be rejected by any evidence. It explains everything we see. Alas, it also explains everything we don’t see as well. It explains why elephants are large and gray and lumber across the plains, but it also explains why elephants are small, pink, and flit around singing as they pollinate flowers.

    Which is an immediate clue to something. In old murder mysteries the detective was always looking for Motive, Means, and Opportunity. But if the designer is everywhere at all times, has infinite powers, and if her motives are imponderable, then we can’t predict whether she will make elephants big, gray lumbering herbivores or small, pink flying pollinators. 

    In short Common Design by an designer who is omnipresent, omnipotent, and inscrutable is not a scientific theory, period. 

  3. Against Common Design I would also add the congruence of apparent ‘fluff’ with phylogenies inferred on functional regions. Transposons, inversions, viral insertions, repeats, deletions, silent substitutions and so on … unless one insists that the designer insists that every base is necessary for the species, one must allow for a certain amount of latitude between individuals while still being considered a legitimate member of a species. If that is not so, how can we have variation?

    Such variation is, indeed, the reason we can have paternity tests and forensic DNA analysis, genealogical tracking, location of the source of novel viruses and bacteria – we can use evidently nonessential, variant markers. 

    But the ID-er has to do some particularly unseemly contortion to allow that the above methods are valid, and yet cannot be used to support the inference of common descent in more distant relationships – the phylogeny of cetaceans, for example, well-supported by SINE insert variation at a higher taxonomic level.

  4. keiths: “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. “

    This shows ID for what it is, a “patchwork” theory.

    ID believes life needs a designer more complex than the complexity he’s supposed to be the explanation of!


  5. I have not read Behe’s Edge, but I saw his list of evidences for common descent. He does not argue against common descent, but he also doesn’t list ERVs as evidence. I thought that was odd, since it would seem to be one of the strongest lines of evidence.

  6. Well, of course creationists refuse to acknowledge that there is junk DNA of any kind, for theological reasons (I say “creationists” rather than IDers because in this case their argument is not strictly speaking an ID argument).

    They also don’t like it for the reason you give — that it provides multiple independent assessments of the pattern of common descent. 

  7. The really strongest class of evidence, which persuaded Darwin’s generation, some even before Darwin published, is the concordance between the patterns of similarity of organisms from multiple mostly-independent parts of the anatomy. The phylogeny you get from the skull can be compared to the one you get from the pelvis, etc. That leads to the “natural” classification being hierarchical. Even Linnaeus started to waver towards a bit of common descent in the mid-1700s. By Darwin’s time the pattern was fairly overwhelming.

    ERVs are nice, though.

    By the way, notice another supporter of common descent. UD poster “vjtorley” posted there on whale anatomy recently, arguing that the changes were too big to be done by natural selection and random mutation. But vjtorley did fully accept common descent.

    Strangely, no one there disputed that with vjtorley. I wonder why?  😉 

  8. Yes, I studiously avoided the j-word! But even if we concede an unrealistically low percentage for junk, noncoding sequence which varies to no apparent effect between members of a species must be in it.

    Of course, the same kind of element fixed becomes the sine qua non of sheep, goat etc! It is not even possible that these descend from fixation of neutral sequence, because there is no such thing … ? Even the position of the sequence on the chromosome must be essential. Which is a heck of a burden to maintain.

  9. At UD “Mung” has noticed this thread and asked me questions.  They are about what a fitness landscape is (in simple models of evolution, a function assigning a fitness to each genotype), and whether I (“or anyone else over there at TSZ”) have read two books by Elliott Sober and one by Eugene Koonin.

    Yes, I have read Elliott’s earlier book (in fact, before publication — see the acknowledgements in the front of the book), parts of the second book, but not yet Koonin’s book. Elliott is an old friend. Does Mung know him? I’ve also met Eugene a couple of times.

    If Mung has some relevant statement, such as whether he agrees with vjtorley, a UD poster, that there was common descent, Mung should say. Particularly if Mung can give some reasons why. OT stuff like precisely defining fitness I will not bother with here.

  10. kairosfocus: “The debate can run in parallel and the onlookers can see for themselves just what is going on. “

    There would be no reason to have any debates in parallel if KF and the others would simply debate here.

    The only difference is that KF and BarryA would lose the ability to control the debate by banning, modifying and deleting our side’s comments.

    Charges of “bigotry” just show the lack of any sort of substance on the ID side of the “debate”.


  11. A parallel debate? Bringing a whole new angle to the concept of ‘talking past each other’!

  12. Mung:

    Note how since keiths cannot put forth a positive case for as requested by the OP in this case, he has to go on the attack against ID.

    The entire OP was an explanation of why unguided evolution is literally trillions of times better than ID at explaining the evidence. Did you somehow miss that?

    Can you identify any fatal flaws in my argument, or do you concede that it is correct?

  13. Mung:

    Well, I read all the way through. keiths seems to be arguing not for common descent, but for universal common descent. There’s a difference, and the evidence is different, depending on which you are arguing for.

    As the OP explains, the evidence is a problem for ID whether or not you accept common descent. Unguided evolution is literally trillions of times better at explaining the data, regardless.

  14. Kairosfocus,

    …slanderous lie…bigotry…red herrings…strawmen soaked in ad hominems and set alight through incendiary words…poison…polarise the atmosphere.

    Next time, just say “ditto”. We’ve heard it all before. Dozens of times.

    I won’t derail this thread into a discussion of the censorship and bannings at UD. The evidence speaks for itself.

    …bigotry…Yes, bigotry…bigotry…bigotry…Conspiracy theory-level bigotry…bigotry, ingrained bigotry…

    Yes, we know you’re offended. Hardly a day goes by that you aren’t offended for some tiny or imaginary slight. It’s gotten very boring.

    Please put your exaggerated personal sensitivities aside and respond to the argument in the OP.

    If you can, that is. If not, then admit it.

  15. ID/creationists certainly seem dead set on trying to erase their history. Not only do they attempt to deny their “Big Tent” strategy, they even deny that ID grew out of “scientific” creationism to get around Edwards v. Aguillard of 1987.

    That history has now been fully documented; and we have the Wedge Document as part of the public record. Kitzmiller v. Dover put that documentation into the court record. Yet they continue to try to demonize Judge Jones as a lackey for the ACLU because the ACLU is “bad.” ACLU = BAD is part of a fairly well-defined socio/political movement.

    It wouldn’t make much difference if the socio/political history and activities of the ID/creationists were not all that well documented. What links the ID crowd to the “scientific” creationists is their common set of misconceptions and misrepresentations of science.

    Those misconceptions and misrepresentations were concocted to prop up sectarian beliefs, and they are unique to the ID/creationist community. They contain everything from peculiar definitions of “information,” to their unique brand of thermodynamics, to “entropy” barriers between “microevolution” and “macroevolution,” to their own definitions of science, to their seething hatreds of practicing scientists, to their socio/political tactics for getting their pseudoscience into the public schools.

    The YECs over at AiG and the ICR hate the ID crowd over at the DI. They express jealousy over who came up with their “arguments” against evolution first. AiG doesn’t like Reasons to Believe and vice-versa. In fact, AiG’s Ken Ham doesn’t seem to like anybody very much. Yet all of them see themselves in a common war against the secular world and “materialistic” science.

    They may all hate each other (sectarian blood wars forever!), but they all have the same “intellectual” roots as well as their sectarian loathing of secular science.

    Another thing that characterizes their leaders is their obsessive desire to be “rock stars” in the intellectual world. They all seem to have intense investments in their own “theories;” and they bypass peer review by marketing them to the public as though they believe these ideas deserve to become the memes of society simply by the sheer force of their “obviousness.” That is a characteristic that is found in most pseudoscientists. They hate real science, and they all think they are predestined to replace science with their own ideas if it were not for that damned cabal of scientists that keeps getting in their way.

  16. If I were the Designer and I wished to guide the process of evolution, most likely I would do so by controlling the environment. You know, an impact here, a glaciation there, an ocean or air current here, some mountain building over there, and so on. Shouldn’t be too much trouble to engineer Designed extinctions for mistakes, and grease the skids for the cute things.

    Now, why is this approach to intelligent design NOT compatible with common descent? 

  17. Why bother with the environment when you can just smite the organisms you don’t like and resurrect the ones you do?

    According to the Bible, God is good at smiting and resurrecting. 

  18. Joe G: No, it was more of an uneducated rant. Theobald’s “evidences” do NOT support unguided evolution. And unguided evolution can’t even construct new protein machinery that require more than two new protein-to-protein binding sites.

    Heck, keiths, you can’t even provide a testable hypothesis pertaining to unguided evolution.

    Dear Joe, if you think there are no testable hypotheses pertaining to to unguided evolution, what are you doing in the I.D. movement? And why don’t you write to people like Michael Behe and give them your opinion that they are wasting their time in trying to falsify the general hypothesis that non-intelligently guided evolution is responsible for the diversity of life that we see around us, as that hypothesis is, in your opinion, untestable?

  19. Mung:

    There is no scientific methodology which can measure the extent to which some process is guided or not guided.

    True, and we also can’t prove that angels aren’t pushing the planets around. We reject that theory not because angels are logically impossible, but rather because the theory of gravity is more elegant, requires fewer assumptions, and is better at explaining the evidence.

    Likewise, scientists reject ID not because it is logically impossible, but rather because the theory of unguided evolution is more elegant, requires fewer assumptions, and is better — trillions of times better — at explaining the evidence.

    Yet we repeatedly have to deal with the argument as if it’s a scientifically settled issue.

    Yeah, those arrogant astronomers are so sure that there aren’t angels pushing the planets around, but what do they know? It’s not a scientifically settled issue.

  20. I can’t find Mung’s comment.  I had read “Evidence and Evolution”.  I think it is one of the best books on the subject around.  What is the other Sober book?

  21. If this is true, as Mung says:
    There is no scientific methodology which can measure the extent to which some process is guided or not guided.

    Then what does that say about ID? About what ID can ultimately aspire to? It kind of rules out design detection full stop, no Mung? 

    Mung is a poe out to sow confusion.  And he’s doing a grand job. 

  22. Perhaps we will find out why Mung asked me whether I had read those books. Surely it can’t just have been an attempt to make Mung look well-read. Mung chose books in my own field. In the 1980s I was involved in a lot of controversy over parsimony and likelihood methods in phylogeny. Elliott Sober and I disagreed then on the logical basis of the parsimony method, but unlike some other people of that era Elliott was trying to engage in open discussion of the issues.

    In fact Elliott and I had a back-and-forth discussion on these issues in 1983 in two adjacent review articles in Annual Review of Ecology and Systematics, and in 1986 Elliott and I jointly authored a discussion paper in the journal Systematic Zoology. In it we made back-and-forth arguments — we had to do that by regular (non-e) mail so it was very slow to write. When Elliott came to write his 1988 book he asked me for comments on the manuscript, and thanked me for them in the acknowledgments section.

    So yes, Mung, I am aware of Elliott and his arguments. Now we await Mung, who will perhaps reveal what the point of the question was …   Mung’s fitness landscape question was simply OT but perhaps these book club questions are not.

  23. kairosfocus brings up the “islands of function” canard:

    Similarly, despite many bland assurances from the evo mat establishment that there is simply a matter of cumulative effect between micro- and macro- evolutionary change, the fact of multi-part complexity dependent on tight integration of the components, and correct organisation to achieve function, shows that in the world of life we have reason to expect to see islands of function.

    There are three huge problems with the “islands of function” argument (plus others I will address in a later OP): 

    1. Neither KF nor any other ID proponent has mapped out the actual biological fitness landscapes. He simply doesn’t know that there are “islands of function”. That’s why he’s careful to say only that “we have reason to expect” islands of function.

    2. Even the watered-down claim is bogus. Petrushka sums it up nicely on another thread:

    ID therefore is assuming its conclusion. It is trying to prove that current configurations could not have been reached via stepping stones by invoking probability calculations that depend on there being no stepping stones.

    3. The pattern we see in nature — the objective nested hierarchy — is exactly what we would expect if there were no “islands of function” problem.

    KF is doing exactly what I described in the OP:

    a) he assumes the existence of an obstacle to unguided evolution (in this case, the “seas” between “islands of function”;

    b) he invents a Designer to surmount the obstacle;

    c) he assumes that the Designer just happens to choose, out of the trillions of options available, one of the tiny fraction of design patterns that make it look unguided evolution is operating. KF’s designer mimics unguided evolution.

    KF has to make three wild, unsupported assumptions to prop up ID. The hypothesis of unguided evolution requires no such props. It fits the evidence as is, and it fits the evidence literally trillions of times better than ID.

  24. I normally don’t bother responding to Joe, for obvious reasons, but in this case he is voicing a misconception that is shared by other more intelligent ID proponents:

    Just about anything can be placed in a nested hierarchy. Meaning nested hierarchies are not anything special. It just all depends on the criteria.

    Anything can be placed into a subjective nested hierarchy, but life forms an objective nested hierarchy. Douglas Theobald explains:

    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.

  25. 1. Neither KF nor any other ID proponent has mapped out the actual biological fitness landscapes. He simply doesn’t know that there are “islands of function”. That’s why he’s careful to say only that “we have reason to expect” islands of function.

    There is one and only one reason to expect islands, and that would be the rather limited research done by Douglas Axe for his PhD thesis. It suggests that improvements to mid level catalytic function is sparse.

    Axe did not test any evolutionary scenario, nor did he use any live sequences. Nor did he consider the possibility of multiple functions for a sequence. Nor did he test scenarios involving regulatory networks, which are the major source of phenotypic variation  in vertebrates.

    All in all, ID concentrates its theoretical efforts on protein coding, for which novelty is rare, and disregards variation in regulation and development, which is common. There would be no differences among individuals if function were isolated in pinpoint peaks having vertical cliffs. The existence of varieties is absolute refutation of the isolated island hypothesis.

    We see variation in extant organisms, and we see numerous evolutionary sequences of change, as  in the evolution of the inner ear. A rational person cannot overturn mountains of consilient evidence for “smooth” change simply by invoking one data point from a student thesis.

    Now if Thornton had looked for a transitional scenario and found nothing, that would be two data points. But instead, we have an ID advocate who carefully picks scenarios that no one thinks have anything to do with biology. Who is surprised when he finds that his scenarios do not support hypotheses that mainstream biology has never made.

    Perhaps we could characterize Behe and Axe as isolated islands of function in a morass of malfunction, having no connection to the mainland.

  26. 145 kairosfocus October 9, 2012 at 11:27 am

    F/N: Does KS understand that e.g. paper clips — a classic classroom study — come in nested hierarchies, so also do automobiles by a given manufacturer at a given time and across time, and that this is consistent with design and with the fact that there is no empirically warranted incremental blind functional- all- the- way incremental random walk based path from any one config to any other?

    (* Can this guy ever stop using run-on sentences? It pains me to read even one. *)

    Hey, KF, draw us a nested hierarchy for the Prius. Which car was its daddy?

  27. Any computer programmer recognizes this distinction, which I would call the difference between conventional and natural hierarchies. One common method of sorting in the computer world is to construct a binary tree. This is a great data structure because log2 searches are all that are necessary for a find/no find in a balanced tree, and simple recursive algorithms easily add to and search the tree. A binary tree is without question a nested hierarchy.

    Problem is, as data points continued to be added, the tree can become unbalanced.  Since it’s a conventional rather than natural hierarchy, it’s a trivial matter to select some “central” data point and reconstruct the tree so that it’s balanced.

    In  the case of cars, the hierarchy depends on the ORDER in which characteristics are examined. Sorting model within color produces a different tree than sorting color within model. But so long as the characteristics are clearly defined, it doesn’t matter. I imagine some naturalists might like to “balance” the tree of life, because there are a lot of stumpy branches with few species, and then there is the beetle branch!

    And the tree of life COULD be rebalanced arbitrarily to eliminate these huge branches, but what would be gained? What’s important here is how the tree is initially created. If the algorithm of creation naturally produces a nested hierarchy, there’s no need to impose one by convention. 

  28. There is an important relationship between nested hierarchies, smooth fitness landscapes, and the formations of dendritic structures.

    As such tree structures grow, they must evolve as successive branches from points along the way.  This is the essence of exploring nearby wells or fitness peaks or whatever is easily accessible from the current state.  Matter is its soft state creeps into nearby states either due to thermal fluctuations or perturbations in its environment.  It doesn’t jump all over the place.

    Living organisms, by the mere fact that they are a very delicate phenomenon that exists within a very narrow energy window, simply cannot make large, energetic leaps all over the fitness landscape without destroying the organisms in the process.  It therefore creeps by way of its surrogate offspring.  Creeping is exploring nearby niches.

  29. Creeping is a plant metaphor. I have used Braille as a metaphor.

    Evolution explores niches in a plant like manner, by sending out variations, only some of which survive. Plants send out runners, seeds, spores and so forth. I believe there’s a Biblical parable about this. Most fall on barren ground.

    Plants have evolved methods of reaching beyond their immediate vicinity. And evolution has produced forms of mutation that reach farther than base point mutations.

    There are risks to this strategy. It requires enormous fecundity. Single celled organisms are naturally fecund. Sexually reproducing organisms reach similar levels because most of the mutations take place in sperm cells, only a few of which participate in fertilization. This makes possible a higher and riskier mutation rate than would be possible if there were a need for high success rate.

    I believe I read recently that something on the order of 97 percent of the human mutation load is from sperm mutations. Fatal mutations at this level are weeded out at a minimum energy cost.

  30. Mung has now quoted my comment (the one above), stopping at a point convenient for Mung:

    [Mung quoting me, the entirety of Mung’s quote]: Another issue that we can dispose of quickly is the issue of common design, which was mentioned in the post by keiths. Common design does explain all the data. 

    Mung uses this against keiths to argue that ID is compatible with the evidence for common descent. Unfortunately, if we read my comment a bit farther we find me saying that “common design” explains everything we see as well as everything we don’t see, so it isn’t a scientific hypothesis.

    I take it that Mung now acknowledges that the positive predictions of ID are not science. Right? 

  31. Besides quote mining Joe Felsenstein, Mung bizarrely seizes on a point that makes no difference whatsoever to my argument:

    I did not miss the shift from an assertion that ID was incompatible with the evidence for universal common ancestry to one in which you argue instead that unguided evolution is just a better explanation. A “trillion times” better. [emphasis Mung’s]

    Suppose you’re right, Mung, and ID isn’t incompatible with the evidence. It’s just trillions of times less compatible than unguided evolution. How does that help your case? Which theory should we prefer, the crappy one (ID) or the one that explains things trillions of times better (unguided evolution)?

  32. In a move that will surprise no one, Mung has quote mined my comment above.


    Instead of quote-mining, how about answering my questions? I asked:

    Suppose you’re right, Mung, and ID isn’t incompatible with the evidence. It’s just trillions of times less compatible than unguided evolution. How does that help your case? Which theory should we prefer, the crappy one (ID) or the one that explains things trillions of times better (unguided evolution)?

  33. Given its other connotations, I suppose the creeping metaphor may not convey what I was getting at; I should have stayed closer to the physics and chemistry.

    There is a pretty general feature of complex systems of atoms and molecules that continues right up the chain of complexity; the average binding energies for these systems decrease and as a result, they become more sensitive to the fluctuations in the environment in which they are immersed. This becomes especially true for systems that are soft within the temperature ranges in which they exist because these kinds of systems are already close to coming apart if their temperature is increased.

    This means that any such system that persists within its environment is going to be affected more by environmental forces acting on the weakest parts of the system; not those parts of the system that are far more tightly bound. Any changes that take place in the system – changes that leave the system still identifiable as having evolved from some original system – could only have occurred through modifications requiring less energetic changes. More energetic jumps will be more likely to tear the system apart.

    In slightly more quantitative terms, complex molecular systems are collections of atoms and molecules that contain myriads of energy states of different sizes. The probability that something in a complex molecular configuration will change is proportional to

    exp(- εi / kT),

    where εi is the ith energy barrier involved in jumping or tunneling to another state.

    Smaller energies or higher temperatures will lead to higher probabilities; so transitions to nearby states are more probable. Thus, fitness landscapes are “smoother” the more complex the system because there are so many finely-spaced energy states; and provided that the system is kept within an energy range that doesn’t destroy it. For example, we already know that in some species, incubation temperatures can affect the sex of the emerging offspring. Hyperthermia and hypothermia are also evidence of the effects of energy and temperature on the behaviors of complex molecular systems.

  34. I wrote:

    The entire OP was an explanation of why unguided evolution is literally trillions of times better than ID at explaining the evidence. Did you somehow miss that?

    Mung asks:

    A trillion times huh?

    Not a trillion times. Trillions of times.

    How did you measure that?

    Why don’t you do the reading, Mung? It’s all there.

    The money quote:

    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.

    ID gives us no reason to expect an objective nested hierarchy at all, much less one that is known to 38 decimal places!

    Do the math, and you’ll see that “trillions of times better” is an understatement. Unguided evolution absolutely crushes ID as a theory.

  35. I’m a bit lost in this discussion. You seem to be describing energy states that could cook or freeze, or otherwise produce developmental abnormalities. I thought I was discussing copy errors that are rare but normal. I don’t think there is any way to correlate the magnitude of copy error with magnitude of somatic effect.

  36. That Mung character:

    Do probability calculations enter into the determination of “Shannon information”?

    IOW, to calculate the “amount of information” in Shannon terms, what must be either known or assumed?

    Does anyone here think it would do any good to show him the formula?

  37. The probability of copy errors in complex, replicating systems behave according to physical laws; just like any complex system at the molecular level.

    Freezing and cooking refer to taking the system outside the temperature range in which it remains soft and functional. This means the system has to be in contact with a much larger environment that holds it within a narrow temperature range.

    Copying errors are simply transitions in the system that send its replicas on a different evolutionary trajectory. But copying is subject to thermal perturbations as well as larger energetic effects such as hits by UV or gamma photons. If such errors are critical to downstream effects, they could very well kill the organism.

    Errors that have such large effects yet do not kill the evolution of the system are relatively rare simply because they have to involve the larger binding energies in the system. And the arrangements that depend on the higher binding energies are usually the underlying templates for the lower energy structures that build on top.

    These ideas apply to nearly all complex system. Those of us who have constructed atomic and molecular assemblies for research have to deal with these issues in order to gain careful control over what we produce. Thermal effects have to be carefully controlled as well as do contaminants and other environmental perturbations by substrates or the containers in which these systems are constructed.

    Complex biological molecules are extremely sensitive to the environments in which they are immersed. The temperature window encompassed by liquid water is only a few hundredths of an electron volt wide. Most biological systems have to have soft parts within that window.

    The main point that relates to nested hierarchies is that nested hierarchies are a consequence of the fact that biological systems cannot jump all over the place to evolve; they have to explore relatively smooth landscapes because nearby states have to be energetically accessible without destroying the organism.

    Oleg’s example of the Prius is a nice analogy because its subsystems are so different from any other car that they didn’t evolve as successive small modifications of earlier subsystems.

  38. Kairosfocus:

    Onlookers, observe the pattern of attempted turnabout of the burden of proof.


    The burden of proof is on you. You are

    1) inventing a barrier to evolution (“islands of function”) despite having no evidence that such a barrier actually exists in real biological fitness landscapes;

    2) inventing a Designer for no reason other than to get around your imaginary “islands of function” barrier:

    3) a Designer who just happens to choose, out of the trillions of options available, one that exactly matches the pattern we would expect unguided evolution to produce.

    The burden of proof falls on you to support your ridiculous and arbitrary assumptions, just as it would fall on someone who claimed that gravity doesn’t operate away from earth, that angels are pushing the planets around, and that the angels just happen to choose the same planetary paths that gravity would have produced had it been in operation.

    Evolutionary biologists do not have to make ridiculous assumptions like the ones you are making. Unlike ID, unguided evolution fits the evidence without being twisted and mangled beyond recognition.

  39. Mung has elsewhere attempted to draw a line between ‘common ancestry’ – the thing it is hard to doubt, up to some personal threshold – and ‘universal common ancestry’ – given the enormous diversity and signal-scrambling, a harder pill for many to swallow, particularly if one does not fully grasp the nature of the first.

    But of course the one builds into the other – or so theory would predict, up to a particular origin. If there are strong discontinuities, they should be recoverable. Yet even at the highest taxonomic level of all, statistical tests favour universal ancestry, as shown in this paper by Theobald (not free, sadly). There can be little doubt that, at the very least, the Designer wants scientific analysis to reveal common descent, and so must drag metaphorical brushwood across his tracks. And yet, despite the mountains of data and careful, objective analysis, still the b-b-burden of proof is on the evolutionist!

  40. The various challenges continue to be issued – 6,000-word essays, your best knock-down evidence etc etc. On referring to the ‘mountain of data’, one is invited to ‘step up’ and show it. So you offer a pebble from this mountain. “Sorry, couldn’t carry the rest”. It is wafted away. So you trot off and get another. It is similarly dismissed. That game could go on for some time. You offer grosser stats on larger chunks of the mountain or, as best you can, the mountain itself. Still nothing. “This mountain. It’s just a figment of your ideology, isn’t it? No, I have no intention of actually exploring it myself”.

  41. It’s a more interesting challenge to do it indirectly.

    Not if you’re omnipotent – then it’s just as interesting and challenging doing it directly (or not doing it at all) 🙂

  42. Mung:

    Chalk one up for ID predictions.

    ID predictions? I wonder. Mung, what does I.D. predict in relation to there being an objective nested hierarchy in a biosphere?

  43. JoeG:

    dr boo-who:

    what does I.D. predict in relation to there being an objective nested hierarchy in a biosphere?

    Evolutionism definitely doesn’t predict one. And the one Linneaus put forth was based on common designs.

    Well, one member of the broad church clearly can’t answer the question. Anyone else? Mung? What does I.D. predict in relation to there being an objective nested hierarchy in a biosphere?

    If nothing, more generally, can you give me a list of some of the predictions of I.D.?

    What possible observations can you think of that would be incompatible with it?

  44. Actually, I would suggest that any evidence is compatible with an abstract designer with no limitations. So, the issue is not evidence but explanations for that evidence. 

    While it is not incompatible with ID, per se, Darwinism’s explanation for that evidence is incompatible with creationism. They cannot be held concurrently because they contradict themselves.  

    Apparently, I’ve been banned for pointing this out, despite the following going unanswered and the actual substance having been carefully removed.

    If CR wishes to participate in these threads, he knows what he needs to do, which is reasonable. KF

    Which I’ve already addressed. Apparently, I need to spell it out in excruciating detail.


    Where is the quote for this supposed infraction, in context? Why is it absent?

    It seems I have to do KF’s work for him…

    CR: Mung,

    Resources are not scarce. What’s scarce is the knowledge of how to utilize them. Again, unless it’s prohibited by the laws of physics, the only think that would prevent us from using energy from the sun, the massive amounts of hydrogen in intergalactic space, or even an entire uninhabitable solar system is knowing how. For example, have you ever heard of a Dyson sphere?

    Not to mention, we cannot predict the impact new knowledge we will create will have in the future. For example, people in 1920 didn’t consider nuclear power or the internet unlikely. They didn’t conceive of them at all. As such, it’s unclear how they could factor them into how they will effect the future.

    This is why I keep pointing out the genuine creation of knowledge is the key point of conflict between creationism (and it’s variants, such as ID) and Darwinism.

    What I have done here is group creationism and ID based on properties they share, or lack, in regards to the following…

    CR: Any theory of an organism’s improvement raises the following question: how is the knowledge of how to make that improvement created?

    Creationism and ID are variants in that they both lack an explanation for [how] this knowledge [was created]. That is my criticism of them both.

    If there is some falsehood that I need to apologize for, then KF should point out which of the following two are false – therefore invalidating my inclusion of Creationism and ID in the same group.

    A. Creationism doesn’t explain how this knowledge is created. To do so would make Creationism internally inconsistent as it thinks this knowledge was eternal and therefore could not be created. (See StephanB’s explicit claim regarding God’s knowledge above)

    B. ID [does not] explain how this knowledge was created.

    Which of the above claims are deliberately falsehoods I presented, which requires an apology on my part?

    Does KF disagree with StephanB on [A]? Is KF suggesting that ID provides an [explanation] for how this knowledge was created? If so, what is it?

    Or perhaps, KF is suggesting that ID is *not* completely agnostic about the designer because it proposes the knowledge said designer used to build our biosphere was eternal? If so, how is this assumption “empirically grounded”? Also, this would rule out other intelligent design scenarios, such as the biosphere being created by a highly advanced, ancient alien civilization. How would is ruling out this intelligent design scenario for our biosphere be “empirically grounded” as well?

    IOW, I have presented a detailed, specific criticism that applies to both creationism and ID. Neither of them provide an explanation for how this knowledge was created.

    In fact, if anyone should be making an apology, it should be KF for misrepresenting my criticism of ID as merely “Creationism in a cheap tuxedo”, which would be false unless he denies [A] or [B].

  45. What possible observations can you think of that would be incompatible with it?

    My answer would be none at all. Joe et al’s usual would say that if only we were to observe natural processes (“Darwinism”, “Evolutionism” etc) creating CSI/FSCI/FSCIO etc then ID would be disproved. Yet that does not rule out a designer at all. Perhaps the designer did not implement that particular CSI. And anyway, Joe specifically has a fall-back position that covered absolutely everything anyway. No matter how random it seems to us, it might not be. I’ve tried to pin Joe down on if he therefore believes that there is no such thing as a “fair dice” but of course he goes of into “who is throwing the dice and where did they get them from eh eh” irrelevancies. So there is literally no way to win any argument, debate or get a concession on a single point. There are literally no possible observations that would be incompatible with ID.

  46. Evolutionism definitely doesn’t predict one.

    Really? I presume this is Joe’s old “an ancestor does not contain all its descendants” view of the nested hierarchy.

  47. Joe

    Who do you think we should side with, the father of modern science or an anonymous loser?

    Joe links to Four Rules of Scientific Reasoning from Principia Mathematica by Isaac Newton.

    admit no more causes of natural things than are both true and sufficient to explain their appearances

    Yet ID adds a designer when we have a better explanation already.

    to the same natural effect, assign the same causes,

    Joe’s designer designed the cosmos. We’ve yet to observe such a designer in action. We’ve observed evolution in action both at small (directly, Lenski, Nylon) and large scales (by the physical evidence left). Yet Joe want’s to assign a designer anyway. 

    qualities of bodies, which are found to belong to all bodies within experiments, are to be esteemed universal, and

    We have never observed any designer intervention in experiments such as Lenski’s. Yet nonetheless a designer is added by ID.

    propositions collected from observation of phenomena should be viewed as accurate or very nearly true until contradicted by other phenomena.

    We have identified a process that explains the complexity found in nature. Despite not being able to identify any evidence of a designer at all other then some percieved holes in somebody else’s theory ID demands that it is viewed as accurate until contradicted by other phenomena. As Joe says

    All you have to do is demonstrate blind and undirected processes can produce it and I have nothing to say.

    See Origin of Species.

    Of course there isn’t any such thing as A “fair DICE”- dice is plural, duh.

    duh indeed. So what’s your answer Joe? Can a die (sigh) ever be fair? Are you willing to go on the record? What does “fair” even mean to you in this context?

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