The one big reason that ‘common design’ is a bad argument for creationism

Common ancestry? Very possible. Common design? Eh, not so much. (Public domain photo.)

One of the strongest and most broadly observable planks of evidence for evolution by common descent rests in the homology — a fancy, five-dollar word for “similarity” — observed in the animal kingdom, both in comparative anatomy and genetics.

In basic terms, the theory of evolution depends on similarities. It predicts that species branch off from common ancestors, but because this occurs through a slow, gradual process, we should observe a vast number of similar traits — both genetically and anatomically — in closely related species (i.e., ones that branched off more recently), such as chimpanzees and humans.

Evolution works too slowly for large numbers of traits to be changed simultaneously at a branching event. A fish will never beget a chicken; these things take time. So scientists look for commonalities; they find the stem that leads back to the stalk that leads back to the twig that leads back to the stick that leads back to the branch that, eventually, takes them all the way back to the tree.

If we did not find such similarities between closely related species, it would falsify evolution immediately. But, of course, we do. For example, humans share almost 100 percent of our bone structure, and roughly 96 percent of our genome, with chimps. That’s a pretty high degree of homology. Going further back, we find that humans — like all mammals — have hair, mammary glands and a single temporal opening in our skulls. And going even further, way, way back, we — like all life — are carbon-based and carry DNA within our cells.

I hope this simple explanation demonstrates — despite the anti-evolutionists who rail about the supposed conspiracies that rule “Academia” and desperately try to “prop up” their pet theory — how fragile the theory of evolution really is. If scientists ever discovered a single species that was fundamentally unlike any other, or even a species that was so wildly different from its closest relatives that it could not be explained by a gradual, stepwise process, the theory would crumble to the ground.

This discussion also illustrates how the scientific process operates. You start with the question — “Why does life bear seemingly hierarchical similarities?” — develop an explanation, then test that explanation through predictions, observation and experimentation. Evolution has great explanatory power in this regard, and it has been confirmed through repeated, independent tests in many different fields of inquiry, so it remains the prevailing theory.

But it is not the only explanation. There is another that is favored by anti-evolutionists, like the Discovery Institute’s Casey Luskin. Writing in response to the most recent “Cosmos” episode’s presentation of some of the genetic evidence for evolution, Luskin writes:

If not by “mindless evolution” and common ancestry, how can we explain the fact that genes in different organisms are so similar? Though Neil deGrasse Tyson never mentions it, a fully viable explanation or these functional genetic similarities is common design.

Intelligent agents often re-use functional components in different designs, which means common design is an equally good explanation for the very data — similar functional genes across different species — that Tyson cites in favor of common ancestry.

Interestingly — though the Disco Tute tries to distance itself from more openly religious groups like Answers in Genesis as much as possible, and vice versa — the “common design” argument is also used constantly by young-earth createvangelists. For example, AiG says in its “12 Arguments Evolutionists Should Avoid”:

Common body plans (homology), for example, do not prove common descent — that’s an assumption. A common Designer fits the evidence just as well, if not better.

I can’t really attempt to address the Disco Tute’s version of “common design,” since ID proponents’ definition of who or what the “intelligent designer” is — and how he/she/it works — is so vague and fluid it can refer to just about anyone or anything. But for those who openly admit that they believe “the Designer” can only be God, I can not only respond to the argument, but also point out that it is an exceptionally bad one.

Here’s why. Moving to the art world for just a second, let’s imagine that I was a critic analyzing two paintings: the “Mona Lisa” and the “Madonna of the Rocks.” And let’s say that I determined, based on the high degree of similarity in style and composition between the two works, that they were painted by the same artist (which is, of course, exactly the case).

So far, so good. But what if the next thing I suggested was that the same person who composed these two paintings was also responsible for every work of art that had ever been made — from the Venus of Willendorf to Beethoven’s Ninth — regardless of style, subject matter, materials used, date of composition or any other relevant details?

You’d probably think I’d gone insane. You can’t point to the similarities of two very similar things as proof that they came from the same artist, and then go on to suggest that the artist also made everything else — even things that are dissimilar in virtually every way.

Now, critics may respond, “Well, this is exactly what evolution does, though!” Except that it doesn’t. It’s true that evolution suggests humans share common ancestry, not just with closely related species like chimps and orangutans, but all other life — however, it also provides a predictable, testable and falsifiable model that explains exactly why some species look more similar, and others look less similar.

The alternative, “common design” theory has no such explanatory power. Why did God make this species similar to this other species? “No idea. That’s just the way he did it.” Why do these two species look so wildly different? “See above. God works in mysterious ways.” And so on.

But the problems go even further than this, because, while the theory of evolution is limited to living things, the theory of “common design” is not. Because the Christian common designer is the God who created, literally, the vast universe and everything in it, and “without him, nothing was made that has been made.”

So, to sum up: “Common design” suggests that the high degrees of similarity between humans and chimps suggest that the same designer created both. Fine. It’s not scientific (since supernatural forces lie outside the bounds of science), but I have no philosophical problems with the proposition. It makes sense.

“Common design” also suggests that the same designer created all living things. OK. Well, unlike evolution, this notion is not predictive or falsifiable or explanatory. But, like I said before, there are a few bare similarites shared by all life — despite its vast diversity. Perhaps I’d let it slide.

But then, “common design” also suggests that the same designer created and structured absolutely all matter in the universe, and that’s where the theory goes off the rails completely. Don’t get me wrong here: I’m a Christian. I believe that God made everything. But I don’t submit my belief in this matter as a scientific explanation for anatomical homology.

If similarity really were the mark of a common designer, and everything in the universe was specially created by the same designer, then we would expect to find the same level of similarity in every aspect of creation. Of course, we do not. We see in the universe humans and sturgeons and hippos and archaea and cyanobacteria and fungi and stars and quasars and galaxies and black holes and cosmic dust and dark matter and energy and plasma and magnetism and electricity and meteors and so much more — the only commonality being that they all exist in some form or fashion, which is not much to hang a theory on.

Now, it may still be true that God made everything (that’s what I believe), but if it is, similarity is obviously not his hallmark: Diversity is.

Which, to me, makes him look a whole lot more like the God of evolution than the God of “common design.”

Tyler Francke

  • Will

    “And going even further, way, way back, we — like all life — are carbon-based and carry DNA within our cell nuclei.”

    Not all life has nuclei. Eukaryotes do. An accurate sentence would be “And going even further, way, way back, we — like all life — are carbon-based and carry DNA within our cells.”

    There is also a grammatical error at “and then go on to the suggest that the artist also made everything else.” Either change “suggest” to “suggestion,” or remove the “the,” but splitting an infinitive with a hanging article is very weird.

    Otherwise, the article is quite good!

    • Right you are, in both instances. Thanks for the help, Will! Glad you liked the piece!

  • George

    Very good article! I am a philosopher and I absolutely enjoy the finesse you employ in bringing those two subjects to work together. 🙂

    • Wow, thanks, George! I really appreciate that! Glad you like it 🙂

  • John Wilkins

    I wish to cavil slightly: “homology” is not a fancy way of saying “similarity”. That is “homoplasy”. Homology is the identity of parts of organisms “under all forms and functions”, to paraphrase Richard Owen, who came up with the notion. Parts that do not resemble each other very much at all, like the malleus in reptiles that becomes the inner ear bone in mammals, can be homologous.

    • Grr, I knew somebody would knock me for that eventually! You’re right, I fudged the definition a bit. Thanks for the correction and the additional information 🙂

  • Larry Bunce

    Human desigers have limited resources, and often re-use solutions they have used before in solving problems. This often gives artists and composers a very recognizable style. Assigning human limitations to an Infinite Being may help personify God to us, but it diminishes God’s majesty. We can easily see defects in animal design: hard to reconcile with a Perfect Designer. Presumably God wouldn’t have bad days. How much more fantastic is God’s design for life to have set up the laws of chemistry so that self-replicating chemical reactions could become alive and pass on traits so that the defects we observe can be rectified in time, and so that life can adapt to its constantly changing environment.

    • Great points, Larry. Thanks! Always good to hear from you.

  • Paul Braterman

    The DI say “If not by “mindless evolution” and common ancestry, how can we explain the fact that genes in different organisms are so similar? Though Neil deGrasse Tyson never mentions it, a fully viable explanation or these functional genetic similarities is common design.”

    If DNA similarities reflected purposeful design similarities, we would expect parallel evolution (e.g. of marsupial and placental rodent-like mammals) to cause similarities of appearance and function. That does not happen, and for this reason alone, even without the others you mention, this purported explanation is not viable but stillborn.

  • Chiefley

    There is another asymmetry between the theory of evolution and the premise of design when it comes to the similarities in organisms. The basic premises of evolution predict a particular kind of pattern in the similarities and differences between organisms that evolved from a common ancestor. And it makes those predictions out of logical necessity, meaning that the pattern it predicts is inescapable from the way the premises work. In other words there can be no other outcome. This is what Tyler was alluding to when he said it ToE is fragile.

    Another term for fragility is that it takes predictive risk. In demanding such a precise and unique outcome (called a ‘prediction’ in science) in the relationship between evolved organisms it places itself at risk of being easily falsified if it is wrong. We rely on this property of falsifiability to judge between competing hypotheses based on failures in their predictions about nature. And so when science is evaluating whether a hypothesis is scientific or not, it looks to see how easy it would be to falsify the hypothesis if it is wrong. So we would ask the question for the theory of evolution,

    “What does the theory of evolution demand that we see in the relationship between evolving organisms (if it is true) and what does it forbid us to see in the relationship between evolving organism (if it is true)?”

    Consider the simple unconstrained premise of “common designer”. Try asking the same question:

    “What does the premise of “common designer” demand that we seen in the relationship between designed organisms (if it is true), and what does it forbid us to see in the relationship between designed organisms (if it is true)?”

    Notice that the same question about common designer is unanswerable. If you suggested something that we must see or must not see in designed organisms, you would then be asked to provide the logic for how that demand or that forbiddance comes about? You see, designers are free to do anything they want to do. They can design things that are very similar to each other or things that have no similarity to each other in any way.

    And this makes the notion of a common designer unfalsifiable. There is nothing we would see in nature that would refute the premise of design, as with design all things are possible. And where all things are possible, nothing is impossible. And where nothing is impossible, there are no tests you can run to rule it out.

    And this is why the premise of design is not accepted by the scientific community as a scientific hypothesis, as it cannot be tested.

    • Great points, @Chiefley:disqus! Thanks for taking the time to explain this!

  • sombodysdad

    Common design refers to Linnaean taxonomy and his archetypes. His nested hierarchy lays out the structure and the degree of similarity that should be expected.

    • Matthew Funke

      It seems to me that this is begging the question (or “circular reasoning”, if you prefer). Why does Linnaean taxonomy lay out the degree of similarity that should be expected? This is an interesting question, especially in light of the fact that the only known processes that specifically generated unique nested hierarchies are branching evolutionary processes — descent with modification.

      Separately-created things do not generally fit into nested hierarchies. For example, the cars, motorcycles, and trucks that Honda makes are designed by a single group of Honda engineers, but any attempt to sort them into a nested hierarchy eventually breaks down, because all defining characteristics in a group are not shared universally by members of that group. (A single radio model might appear in some trucks and some cars, for example. And even if you managed to impose some kind of scheme onto it, the scheme would be arbitrary — depending on whether you chose to sort by size or by color first, say. But the same nested hierarchy pops up for organisms whether you choose to sort by morphology or by genetics or by molecular biology. This argues strongly that the nested hierarchy is not illusory.)

      Interestingly, Linnaeus tried to classify minerals into a nested hierarchy after his success with organisms. He failed miserably, precisely because minerals are created separately and resist sorting into a nested hierarchy.

      So why would a Common Designer sort organisms into a hierarchy that is extremely atypical for separately-created things and also perfectly suited to common descent? Is the Common Designer just screwing around with us?

      • sombodysdad

        No, descent with modification does not produce nested hierarchies. Linnaean taxonomy is a nested hierarchy and doesn’t have anything to do with evolution. Transitional forms, by their very nature, would blur all lines of distinction between groups- nested hierarchies require distinct sets without any overlap..

        A common design is a great way to control your design. It prevents you from re-inventing things along the way.

        • Matthew Funke

          No, descent with modification does not produce nested hierarchies.

          Really? Students, teachers, and practitioners of linguistics, ancient manuscripts, epidemiology, phylogenetic analysis, parasitic virulence, bioinformatics, genetic programming, pharmaceuticals, pattern recognition, data mining, military strategy, enzyme creation, neural nets, and countless other disciplines would like to have a word with you.

          Simply saying “no” doesn’t prove anything when those who study how organizational patterns are formed know otherwise. Entire branches of analysis (e.g., linear regression analysis and analysis of variance) at use in literally hundreds of industries and fields of study are predicated on the notion that descent with modification produces nested hierarchies.

          In the face of human understanding and experience, it would seem to take a certain amount of hubris to stand there and just shake your head. I’m going to need a bit more than that.

          Transitional forms, by their very nature, would blur all lines of distinction between groups

          No, they wouldn’t. Think of family trees. Sure, some lines would be blurry — and in taxonomy, some lines are blurry. (Some grasses are really hard to tell apart, for example; at least ten percent of bird species are similar enough to produce fertile hybrids (citation below); and there are phenomena like ring species where determining boundaries can be tough.) But others are rather distinct, simply because the branches separated some time ago and have gone their separate ways, because ecological niches are not continuous, and because death and extinction go in only one direction. Hyperbole about “all lines of distinction” isn’t helping you here.

          Weiner, Jonathan. The Beak of the Finch: a story of evolution in our time. New York: Knopf, 1994. pp. 198-199

          Now, your turn: Why are some things that perform the same function very similar in some cases, but very different in others? For example, the wings of a bat, a bird, a pterosaur, and an insect are all very different from one another, but they accomplish much the same goal: Flight. Likewise, the fin of a fish, a dolphin, and a plesiosaur look very different from one another. Evolution not only predicts that you will find similarity in some places, but when you should expect which kind of similarity, and when you should expect which kind of difference. So far, life on Earth hasn’t run afoul of its predictions. Does the idea of a Common Designer, by itself, offer that kind of predictive power? Or does it have any explanation as to why these things look exactly as if they had evolved? Or does it offer any kind of reason for why a Common Designer would want to re-invent things some times, but not others?

          • sombodysdad

            Family trees do not produce a nested hierarchy. Just because nested hierarchies can be laid out as a branching tree doesn’t mean every branching diagram is a nested hierarchy.

            Again Linnaean Taxonomy is the observed nested hierarchy and it doesn’t have anything to do with evolution. The USArmy can be placed in a nested hierarchy and it also has nothing to do with evolution.

            http://evolution.berkeley.edu/evolibrary/article/evo_10

            Because the Linnaean system is not based on evolution, most biologists are switching to a classification system that reflects the organisms’ evolutionary history.

            Can you please reference this theory of evolution so we can see what it really predicts?

          • Matthew Funke

            Just because nested hierarchies can be laid out as a branching tree doesn’t mean every branching diagram is a nested hierarchy.

            When did I say that branching diagrams are only nested hierarchies? What exactly are you arguing, and whom are you arguing with?

            (One must also consider the consilience of the evidence. The nested hierarchy of life strongly argues for the correctness of evolution (as opposed to separate and instantaneous creation), but it is far from the only and far from the strongest evidence.)

            Can you please reference this theory of evolution so we can see what it really predicts?

            I’m not sure what you’re asking here. The taxonomy based on the theory of evolution is commonly referred to as the phylogenetic tree, if that helps. Are you trying to assert that Linnaean taxonomy is correct, and that the phylogenetic tree is not?

          • sombodysdad

            No, family trees do not produce a nested hierarchy. The parents do NOT consist of nor contain their children. With a nested hierarchy there is a superset that consists of and contains all subsets. The animal kingdom consists of and contains Phyla which consist of and contain Classes, which consist of and contain Orders and so on. Family trees are an example of a pecking order.

            Read this- http://www.botany.wisc.edu/allenlab/AllenLab/Hierarchy.html

            and this:

            http://www.mobot.org/plantscience/resbot/Repr/Add/Knox1998BJLS.pdf

            Regardless of what is eventually learned about the evolution of Clarkia/Heterogaura, the complex nature of evolutionary processes yields patterns that are more complex than can be represented by the simple hierarchical models of either monophyletic systematization or Linnaean classification. page 34, Eric B. Knox, “The use of hierarchies as organizational models in systematics”, Biological Journal of the Linnean Society, 63: 1–49, 1993

          • Matthew Funke

            The parents do NOT consist of nor contain their children. With a nested hierarchy there is a superset that consists of and contains all subsets.

            I think I was unclear about which sets one should regard in this case.

            In a family tree, the “sets” are not individuals represented by the tree nodes. (Individuals cannot be sets.) The sets are parental inheritances which are possessed by those individuals. As such, the parental inheritances of the children are subsets of the parental inheritances of their parents. The children cannot obtain parental inheritances from anything but the set of parental inheritances of their parents. The “superset” at the base of the tree (assuming one could go back far enough to find one) is the parental inheritances of the original parents. Which means that family trees are nested hierarchies.

            “The use of hierarchies as organizational models in systematics”

            Yes. All this quote is saying is that monophyletic systemization — e.g., Linnaean categorization — is not possible for the organisms under discussion because the categories are difficult to distinguish, which is because the continuum between organisms is hard to splice into distinct subsets — which, you’ll note, as indicated by the quote, Linnaean taxonomy is particularly ill-equipped to grapple with. This in no way contradicts the idea that a phylogenetic tree is an appropriate way to understand the descent of these organisms; it just means that we don’t yet know enough to set up the proper paraphyly for these organisms. It also does not indicate that the phylogenetic tree is not a nested hierarchy. (You’ll note that the phylogenetic tree is not monophyletic. It has monophyletic groups, which it calls “clades”, but it is not itself monophyletic.)

            Is it your contention that Linnaean taxonomy is correct, and that the phylogenetic tree is not?

          • sombodysdad

            That so wrong. Family trees are not nested hierarchies. You can even send an email to the experts I referenced and ask them.

            Phylogenetic trees are not nested hierarchies either. You have no idea what you are talking about.

          • “Nuh uh! You’re wrong! All the experts agree with me! You’re stupid! Waaaaah!”

          • Matthew Funke

            Family trees are not nested hierarchies.

            I admit my usage was unorthodox, and that I did not explain myself well. But if you consider it in terms of descent with modification, the structure is certainly there.

            Phylogenetic trees are not nested hierarchies either.

            If they were not, then Markov chains (and Markov mathematics generally) would not be applicable to them. Do you have evidence that this is the case?

            Is it your contention that Linnaean taxonomy is correct, and that the phylogenetic tree is not?

          • sombodysdad

            Phylogenetic trees are not nested hierarchies. Just because a nested hierarchy can be depicted as a branching tree does not mean all branching trees are nested hierarchies.

            It is my contention that Linnaean taxonomy is a nested hierarchy as it matches the accepted definition of one.

            Please post your definition of a nested hierarchy along with valid support of that definition.

          • Matthew Funke

            Just because a nested hierarchy can be depicted as a branching tree does not mean all branching trees are nested hierarchies.

            Again, when did I say that branching diagrams are only nested hierarchies? What exactly are you arguing, and whom are you arguing with?

            It is my contention that Linnaean taxonomy is a nested hierarchy as it matches the accepted definition of one.

            That doesn’t answer my question. Is it your contention that Linnaean taxonomy is correct, but the phylogenetic tree is not?

            Please post your definition of a nested hierarchy

            In loose terms, a hierarchy is an arrangement of items which depicts a ranking system. A nested hierarchy is one which depicts nested sets, i.e., sets in which “subsets” are completely contained within “supersets”. There can be multiple “subsets” within each “superset”, but each “subset” has only one immediate “parent” (i.e., “superset” one level above it).

            Even though the different “levels” of the phylogenetic tree do not themselves correspond to sets, it still depicts those sets. If you know cladistic terms and how they work, explaining why this is so will go much more quickly. Do you?

          • sombodysdad

            Is it your contention that Linnaean taxonomy is correct, but the phylogenetic tree is not?

            I don’t think either are correct. But that isn’t the point.

            Phylogenetic trees may depict sets but they do not depict nested sets.

            My point is that Common Descent does not predict a nested hierarchy. That is because it predicts numerous transitional forms which would blur any and all lines of distinction between any sets you try to form. Dr Denton goes over this in “Evolution: a theory in crisis”. Darwin used well-timed extinction events to try to explain how the distinct sets arose. Meaning he tried to explain why we see a nested hierarchy not that CD expected one.

            Cladistics are a nested hierarchy because clades consist of and contain other clades. But that is just how it is designed by us. With evolution defining traits can be gained and lost. Not so with a nested hierarchy.

            http://www.botany.wisc.edu/allenlab/AllenLab/Hierarchy.html

            Only a common design would expect a nested hierarchy because that is how a designer would set it up.

          • Matthew Funke

            I don’t think either are correct.

            Ah, okay. I was just trying to see what you were driving at.

            That is because it predicts numerous transitional forms which would blur any and all lines of distinction between any sets you try to form.

            Okay. In that case, you’re going after a red herring. While a complete phylogenetic tree would have fuzzy boundaries, we expect to find distinct boundaries now for several reasons.

            First of all — and you hinted at this — extinction is one-way, and the fossil record is horribly incomplete. (Complete enough to derive and defend evolution, but not nearly complete enough to blur the boundaries of all sets.) Thus, we don’t see some intermediates, and we may never find them. Therefore, the boundaries can only become more distinct among extant organisms at any instant over time. As it is, of course, when we go beyond extant organisms, fossil records have only served to make things more blurry, not less so (or allowed sets to remain static), which is exactly what we’d expect from common descent. (For example, the boundary between dinosaurs and birds, or between land mammals and whales, or between reptiles and mammals, or between lots of other transitions, is really hard to nail down thanks to fossil discoveries.)

            Moreover, environments do not transition smoothly, and natural selection predicts conformance to an environment. This leads us to expect that specialization for various tasks will cause apparent boundaries to show up. For example, canids generally take down their prey as packs in long chases. Felids are generally solitary hunters, capable of intense, short bursts of speed and impressive stealth, but not sustained chases. It is hard to employ both specialized hunting systems in a single organism, and compromises will lose competitively to specialists. Thus, as specialists evolve, compromises will tend to become extinct, leading to an apparently sharp boundary.

            Beyond that, if it were not for boundaries, we would not name groups at all. We tend to lump similar organisms into the same group; thus, places where boundaries are especially fuzzy tend not to have attention drawn to their distinctions. So in places where the boundary remains fuzzy tend to be overlooked by people looking for boundaries. (And there are plenty of these places even now. Some species of grasses, for example, are very difficult to distinguish. At least a tenth of bird species can be interbred to create fertile hybrids. Even Darwin noted some places where groups that were thought to be distinct became harder to distinguish as intermediary populations were brought to light.)

            Given that evolution concerns populations and the possibility of extinction and specialization, in other words, even if some of the boundaries are hard to define, common descent expects a nested hierarchy. (In other words, common descent knows that these things exist and anticipates them. The idea that Darwin was making an excuse is only valid if you don’t understand the roles of extinction and specialization. He was explaining to a lay audience, remember.)

            But that is just how it is designed by us.

            … Not entirely. Please refer back to examples where we cannot sort separately-created things into a nested hierarchy. Moreover, claiming that this nested hierarchy is just an artifact of our somewhat arbitrary conscious decision ignores the fact that phylogenies derived using different and independent phenomena and criteria converge.

            With evolution defining traits can be gained and lost.

            That’s only true if you refuse to stick to apomorphies and include plesiomorphies. (You’ll note that which are which depends on which group you’re considering.) In other words, in order to assert what you claim, you have to cherry-pick; you have to choose characters that do not universally apply to the group under consideration.

            I’m trying to figure out how your citation supports what you claim apart from this, but in the meantime, here are some that pretty straightforwardly support mine:

            Maddison, W. P., and Maddison, D. R. (1992) MacClade. Sunderland, MA: Sinauer Associates, p. 49.

            Kitching, I. J., Forey, P. L., Humphries, C. J., and Williams, D. M. (1998) Cladistics: The Theory and Practice of Parsimony Analysis, Second Edition. The Systematics Association Publication No. 11. Oxford: Oxford University Press, chapter 1.

            Brooks, D. R., and McLennan, D. A. (1991) Phylogeny, ecology, and behavior. Chicago: University of Chicago Press, pp. 35-36.

            Only a common design would expect a nested hierarchy because that is how a designer would set it up.

            Why? Why would a designer set it up to look exactly as if common descent is true?

          • sombodysdad

            It doesn’t look like common descent is true. We have no idea how to validly test the concept.

            While a complete phylogenetic tree would have fuzzy boundaries, we expect to find distinct boundaries now for several reasons.

            You have to include the complete tree. You don’t get to cherry pick. And you have no idea what organisms are going to be extant at any point in time. Common Descent definitely did NOT predict this current crop of extant species

            Beyond that, if it were not for boundaries, we would not name groups at all.

            Possibly. That is my point.

            Please refer back to examples where we cannot sort separately-created things into a nested hierarchy.

            We can’t put everything nature produces in nested hierarchies either.

            Look, Linnaean taxonomy is based on the archetype, ie a Common Design. It has nothing to do with evolution. And it is a nested hierarchy. The only nested hierarchy in biology. The US Army is also placed in a nested hierarchy. It too has nothing to do with evolution.

            A nested hierarchy is the best way to control and follow a complex design. Software developers use them.

            And if defining traits could not be lost then where are our gills? The point is the loss of traits is the NORM for Common Descent.

          • Matthew Funke

            You have to include the complete tree.

            I don’t know why you think I’m not trying to consider the entire tree. In fact, I’ve pointed out why inclusion of the entire tree answers your objections.

            And you have no idea what organisms are going to be extant at any point in time.

            I don’t? That’s… surprising. Do you know what “extant” means? Or do you think I lack the ability to look around?

            Common Descent definitely did NOT predict this current crop of extant species

            It was one small possibility among many, and it was impossible to determine which possibility would become realized, but that’s irrelevant. The “current crop of extant species” (redundant much?) indicates common descent. It’s important to recognize why the inability to perfectly predict the future from the past has no bearing on the ability to understand the past from the future.

            Possibly. That is my point.

            Sort of. You have claimed that common descent would lead to a continuum that would make it impossible to delineate categories. That is not so, since divergence occurs over time, and pruned “branches” do not re-grow. It’s also different from the point that there are groups where that difficulty of delineation still exists.

            We can’t put everything nature produces in nested hierarchies either.

            =sigh= Please go back to some of the things that I listed that are produced by nature, but which do not fit nested hierarchies (e.g., Linnaeus’ failed project with minerals). A nested hierarchy is only an indication that things were not separately designed, not that things were exclusively produced by nature.

            Look, Linnaean taxonomy is based on the archetype, ie a Common Design.

            So what? You’ve stated that Linnaean taxonomy is not correct. How, then, could you possibly use it for evidence of anything?

            It has nothing to do with evolution.

            I’m not using Linnaean taxonomy to support or deny evolution. I don’t know what you’re after here.

            And it is a nested hierarchy. The only nested hierarchy in biology.

            So Linnaean taxonomy is inaccurate, but it’s in biology? You’re sounding increasingly confused.

            The US Army is also placed in a nested hierarchy.

            Yeah, that very same analogy was used by your last reference. I can tell, though, that you haven’t read any of my references. Even your reference, though, points out that the army is a nested hierarchy, whereas the soldiers are not. If you can grasp this difference, you should be able to see why the phylogenetic tree depicts a nested hierarchy.

            It too has nothing to do with evolution.

            Not every nested hierarchy indicates evolution. Descent with modification produces a nested hierarchy, however.

            A nested hierarchy is the best way to control and follow a complex design. Software developers use them.

            Only for certain applications — i.e., when code reuse would be common, or the same class and methods are needed in different data types that all need to change when a base class changes, or when the hierarchy is pretty shallow and future development by other programmers with more levels is unlikely (otherwise, inheritance can become difficult to ensure and maintain).

            Sometimes, other design paradigms are more useful and allows for more efficient control mechanism — e.g., if you’re mixing unrelated types together, or if it is not necessary to inherit implementation, or when classes cannot be used, an interface is more useful than inheritance.

            The simple fact that an industry uses a particular design paradigm (especially as one paradigm among many) for certain applications does not answer the question of why a different area of study would use that paradigm. Why is a nested hierarchy useful for life in particular? What does a nested hierarchy afford for biology in particular that other organizational schemes would not?

            And if defining traits could not be lost then where are our gills?

            If you’re asking, more specifically, “Why don’t we have developed gills as adults?”, then you’re confusing plesiomorphies for apomorphies. Any clade that includes humans does not include gills as apomorphic.

            The point is the loss of traits is the NORM for Common Descent.

            Plesiomorphies, yes, but not apomorphies, as I already mentioned. Which is only appropriate, since apomorphies define different groups. You seem to be losing the thread.

            Now, your turn: If a designer created different original forms de novo, what are those different original forms? Can you name them?

            Are ducks, for example, related to geese, and/or all members of the Anseriformes order? Are members of the Anseriformes order related to members of the Galliformes order, and/or all Neonates? Are Neonates related to Paleonates? Are any extant birds related to Ichthyornis, Hesperornis, Enaliornis, Baptornis, or other Hesperornithiformes? Are Hesperornithiformes related to Archaeopteryx or Confuciusornis? Are early Aves related to Velociraptor, Microraptor, or any non-avian dinosaur? Are dinosaurs related to phytosaurs, pterosaurs, or other archaeosaurs?

            Or we could go in a slightly different direction. If these different groups were separately created somewhere, do you accept that there are places in phylogenetic cladograms that evidence an evolutionary ancestry? Do you also accept that there are places in these cladograms where different groups are sufficiently different that they can no longer interbreed with other contemperaneous members of their separately-created group, nor with the ancestor of their separately-created group? How would this reproductively isolated group be different from a separately-created group?

            Are Burmese and Bengal tigers related, and are all tiger species related to each other? Are tigers related to panthers? Are panthers related to scimitar-toothed cats, felines, and/or all felids? Are felids related to viverrids or nimravids, and how do we know? Are all phyla under the order Carnivora related to each other?

            Can you show me, in other words, where the boundary for a separately-created group lies, and how we know, and how we can test it?

            And why would we expect this from a common designer, given that other things ostensibly put in place by that very same designer (like minerals) don’t fit that organizational structure? Worse, if that designer created everything, how do you know when you’re looking at an organizational paradigm typical of that designer and when you’re not?

          • sombodysdad

            Wow- no one predicted the extant organisms. Common Descent would be perfectly OK if humans never evolved.

            You have claimed that common descent would lead to a continuum that would make it impossible to delineate categories.

            Even Darwin recognized that fact. He wrote about it (1859).

            That is not so, since divergence occurs over time, and pruned “branches” do not re-grow.

            Divergence is a simplistic model. Every population could have an asterisk pattern stemming from it.

            A nested hierarchy is only an indication that things were not separately designed, not that things were exclusively produced by nature.

            Nature cannot produce a nested hierarchy. Only we can. A nested hierarchy is a sure indication that there was intentional design involved.

            You’ve stated that Linnaean taxonomy is not correct.

            It is the only nested hierarchy with respect to biology. It shows the groups within groups required of the concept.

            If you can grasp this difference, you should be able to see why the phylogenetic tree depicts a nested hierarchy.

            I grasp the difference. Clearly you do not. A phylogenetic tree shows ancestor-descendant relationships. The parent population at the diverging points does not consist of nor contain the daughter populations at the tips of the branches.

            Descent with modification produces a nested hierarchy, however.

            Nope, evolution is too complex a process and too messy to produce the pristine order required of nested hierarchies.

            Which is only appropriate, since apomorphies define different groups.

            Exactly as predicted by a Common Design- ie Linne’s archetypes

            If you’re asking, more specifically, “Why don’t we have developed gills as adults?”,
            We don’t have gills ever. Clearly you have been duped with respect to developmental biology. And if we are descended from fish then we should be in the same clade as fish because, guess what? A clade includes a population and all of its descendants.

            If a designer created different original forms de novo, what are those different original forms?

            Linnaean taxonomy is a good start. I never said that it is totally wrong. The rest is for science to determine.

          • Matthew Funke

            Common Descent would be perfectly OK if humans never evolved.

            Um, yeah. Why is that a problem?

            Even Darwin recognized that fact. He wrote about it (1859):

            How is that different from what I’ve been claiming?

            Divergence is a simplistic model. Every population could have an asterisk pattern stemming from it.

            At least.

            A nested hierarchy is a sure indication that there was intentional design involved.

            Why?

            The parent population at the diverging points does not consist of nor contain the daughter populations at the tips of the branches.

            Right. Soldiers also do not contain each other.

            Nope, evolution is too complex a process and too messy to produce the pristine order required of nested hierarchies.

            You must not be paying much attention if you think the nested hierarchies of biology are pristine.

            Exactly as predicted by a Common Design- ie Linne’s archetypes

            Linnaeus’ archetypes lead to incorrect sorting by Linnaeus himself, though — e.g., Asian elephants.

            So I have to ask again: Why does what we see cause us to expect common design?

            We don’t have gills ever. Clearly you have been duped with respect to developmental biology.

            I didn’t claim we did (though we do have pharyngeal slits during our embryonic development). I was trying to answer a more specific question, making a stab at what you meant, because the general question is too general to answer efficiently.

            And if we are descended from fish then we should be in the same clade as fish because, guess what? A clade includes a population and all of its descendants.

            Right. And if you draw a clade including the ancestral fish and man, gills are not apomorphic traits.

          • sombodysdad

            How is that different from what I’ve been claiming?

            It supports what I have been claiming.

            Why?

            Because nested hierarchies can only arise intentionally.

            You must not be paying much attention if you think the nested hierarchies of biology are pristine.

            Nested hierarchies are pristine. If what you have is not then it isn’t a nested hierarchy.

            Linnaeus’ archetypes lead to incorrect sorting by Linnaeus himself, though — e.g., Asian elephants.

            And Darwin thought whales evolved from bears. Linne was not a geneticist. He did not have the tools we now have.

            So I have to ask again: Why does what we see cause us to expect common design?

            Just about everything along with the fact no one can demonstrate Common Descent.

            I didn’t claim we did (though we do have pharyngeal slits during our embryonic development).

            No slits just folds.

            And if you draw a clade including the ancestral fish and man, gills are not apomorphic traits.

            Cherry picking. Clades are based on shared characteristics. So what do humans share with fish such that you could place them in the same clade?

          • Matthew Funke

            It supports what I have been claiming.

            Okay. But how is it different from what I’ve been claiming?

            Because nested hierarchies can only arise intentionally.

            On what basis do you claim this?

            Nested hierarchies are pristine. If what you have is not then it isn’t a nested hierarchy.

            If that’s your private definition, it would have been nice to know that up front.

            And Darwin thought whales evolved from bears. Linne was not a geneticist. He did not have the tools we now have.

            Not my point. My point is that we have no reason to think that things like Linnaean archetypes are correct. Therefore, we have no reason to think that apomorphies defining different groups are something that is predicted by common design, as you asserted.

            So, once again, I have to ask: Why does what we see cause us to expect common design?

            Just about everything along with the fact no one can demonstrate Common Descent.

            Pedantically, in the sense that science can never demonstrate anything with 100% certainty, you’re right. The nature of the evidence before us, however, leads us to believe that we’re substantially correct, to a degree of confidence better than ideas like the heliocentric model of the Solar System.

            Cherry picking. Clades are based on shared characteristics. So what do humans share with fish such that you could place them in the same clade?

            We’re eukaryotic (which differentiates us broadly from groups like molds, fungus, and plants), spinal cords, skulls, vertebrae, a jaw, teeth, four limbs…

            If you’re looking for us to have all the same characteristics as fish, again, it seems like you’re mistaking plesiomorphies and apomorphies.

            Now, how about those two separately-created groups, along the lines of the histories of birds or cats as I mentioned earlier? How do we know when we have a separately-created group?

          • sombodysdad

            On what basis do you claim this?

            Knowledge of nested hierarchies.

            If that’s your private definition, it would have been nice to know that up front.

            What? Clearly you don’t know what a nested hierarchy entails. It has to be pristine or else you get objects in two different sets as transitional forms would be. Nested hierarchies do not allow overlapping.

            Why does what we see cause us to expect common design?

            Direct experience with the concept along with the fact that Common Descent can’t be tested. You have no idea if any amount of genetic change can account for the anatomical and physiological differences observed

          • Matthew Funke

            Knowledge of nested hierarchies.

            What aspect of that knowledge? What, specifically, do you know?

            It has to be pristine or else you get objects in two different sets as transitional forms would be. Nested hierarchies do not allow overlapping.

            Which can mean either that (a) you’re looking at something that isn’t a nested hierarchy (which I understand you’ve been maintaining), or (b) you have the wrong nested hierarchy and the nested hierarchy that accurately reflects the data is a different one. The fact that (b) seems to bring us closer and closer to a unified understanding of genetics, morphology, molecular cellular machinery, and other fields of study seems to indicate that it’s really the right answer.

            Direct experience with the concept

            Such as? Be sure to indicate what aspects of the nested hierarchy indicate that nested hierarchies must be the result of design.

            along with the fact that Common Descent can’t be tested.

            I’m sorry, but I can’t accept that simply on your say-so, especially since we test it all the time. We may not be able to test it comprehensively — but surely, you’re not falling into the “we don’t know everything, therefore, we know nothing” fallacy, are you?

            You have no idea if any amount of genetic change can account for the anatomical and physiological differences observed

            Yes, I do, because the only kinds of genetic change necessary to create the anatomical and physiological differences we see have been directly observed. Would you like citations?

          • sombodysdad

            Pristine means neat/ clean and with nested hierarchies the subsets have to fit neatly and completely within their supersets. All organisms must fit neatly and completely within their respective set. Transitional forms would not allow that to happen and Common Descent predicts numerous transitional forms.

          • Matthew Funke

            Transitional forms would not allow that to happen and Common Descent predicts numerous transitional forms.

            Transitional forms do allow that to happen, as your quote from Darwin indicates. We’ve also found transitional forms, which common descent predicts, in precisely the places and times where common descent predicts them — which serves as further corroboration that common descent is correct.

            How do we know when we’re looking at separately-created groups?

          • Matthew Funke

            It doesn’t look like common descent is true. We have no idea how to validly test the concept.

            Actually, we do. There are lots of fairly simple things that could, in principle, falsify common descent. Every discovery of a new species, every organ found, every gene sequenced, every molecular machine identified in a biotic cell, is a test that has the potential to falsify common descent once and for all. So far, all of these things remain consistent with common descent.

          • sombodysdad

            Actually, we do. There are lots of fairly simple things that could, in principle, falsify common descent

            You don’t even have a mechanism shown to be capable of producing the anatomical and physiological differences observed. Given starting populations of prokaryotes you don’t have a mechanism capable of producing something other than more populations of prokaryotes. Endosymbiosis only gets mitochondria and chloroplasts, and that is very debatable.

            The alleged evolution of vision systems remains untestable. We are just now understanding how they develop.

            You need a way to test the concept, not just a way to falsify it. IOW as Michael Shermer said in Scientific American you are to take the concept you think is true, assume it is false and then figure out how to test it to refute that assumption.

          • Matthew Funke

            Given starting populations of prokaryotes you don’t have a mechanism capable of producing something other than more populations of prokaryotes. Endosymbiosis only gets mitochondria and chloroplasts, and that is very debatable.

            You seem to have it backwards. There is strong evidence that endosymbiosis got mitochondria and chloroplasts; the evidence that these were obtained through endosymbiosis gives us confidence that we’re on the right track with respect to eukaryotic cells coming from endosymbiosis. It’s not the case that we can demonstrate that endosymbiosis only gets us mitochondria and chloroplasts.

            The alleged evolution of vision systems remains untestable. We are just now understanding how they develop.

            Keep waving your hands frantically; the breeze is refreshing.

            Even Darwin showed how vision could evolve, with examples of each step in extant organisms of his time to demonstrate their viability. Our picture has only become more refined since then. A complete pathway has been created, with calculations showing that the evolution of the eye can occur in fewer than 2000 steps (1829, according to the paper below; even so, note the term “pessimistic” in the title, because it’s important).

            Nilsson, D.-E. and S. Pelger, 1994. A pessimistic estimate of the time required for an eye to evolve. Proceedings of the Royal Society of London, Biological Sciences, 256: 53-58

            Besides which, arguments from incredulity (“I don’t know how it happened; therefore, it did not happen”) are invalid.

            You need a way to test the concept, not just a way to falsify it.

            Subjecting a concept to potential falsification is testing the concept.

            IOW as Michael Shermer said in Scientific American you are to take the concept you think is true, assume it is false and then figure out how to test it to refute that assumption.

            Exactly so. If you can’t see how that relates to evolved characters in a common descent model — just how many things there are to look for in order to assume the model false — we could devote yet another tangent to that.

            Let’s look at this with respect to the evolution of eukaryotic cells, which you mention above. If it did not happen through endosymbiosis, what would we expect to find? Do we find it? Be specific.

          • sombodysdad

            There is strong evidence that endosymbiosis got mitochondria and chloroplasts;

            No way to test the claim.

            Even Darwin showed how vision could evolve,

            No he didn’t. Showing various degrees of complexity for vision systems exists does not mean they evolved.

            Nilson/ Pelger didn’t even include the genetics of the system

            Subjecting a concept to potential falsification is testing the concept.

            No, it’s just a way to falsify it. You cannot test the concept as you have no idea what has to change to do it.

            You don’t even know what makes a human a human beyond a baby human is born to a female human after a successful mating with a male human.

            If it did not happen through endosymbiosis, what would we expect to find?

            Exactly what we see. How did the nucleus arise? No one sez “endosymbiosis” and is taken seriously. What about all of the other organelles? No answer for them either.

          • Matthew Funke

            No way to test the claim.

            Are you trying to assert that only direct observation of a claim qualifies as a test of that claim?

            Nilson/ Pelger didn’t even include the genetics of the system

            Why is that necessary? (Would it matter if some steps did have genetic steps, e.g., the Ciona beta-gamma-crystalin gene?)

            No, it’s just a way to falsify it. You cannot test the concept as you have no idea what has to change to do it.

            That’s a funny thing to claim when step-by-step lists are being thrown at you.

            You don’t even know what makes a human a human beyond a baby human is born to a female human after a successful mating with a male human.

            Yes, I do. I can describe what makes us distinct from every other member of Hominidae, and what makes us a member of Hominidae. Any organism with those specific characteristics is human.

            Exactly what we see.

            Nice dodge. I asked for specifics. What would we expect to see?

          • sombodysdad

            If they didn’t provide any genetics then they did not provide a test of the concept- duh

            That’s a funny thing to claim when step-by-step lists are being thrown at you.

            You don’t have any step by step lists to throw.

            Yes, I do. I can describe what makes us distinct from every other member of Hominidae, and what makes us a member of Hominidae.

            Boloney. Evo-devo doesn’t know what makes an organism what it is. Evos think we are the sum of our genome but there isn’t any evidence to support the claim

            I asked for specifics.

            No, you didn’t. And you have no idea what we would see if endosymbiosis was true.

          • Matthew Funke

            If they didn’t provide any genetics then they did not provide a test of the concept- duh

            No, that only means that they didn’t provide the test that you wanted. The predictions of the concept are more than merely genetic.

            You don’t have any step by step lists to throw.

            Why doesn’t Nilsson/Pilger count? (And don’t say “Because it’s not genetic”. Just because it’s not along a particular line doesn’t mean that it’s not step-by-step.)

            I asked for specifics.

            No, you didn’t.

            Here was my question, which you can see above, emphasis added:

            If it did not happen through endosymbiosis, what would we expect to find? Do we find it? Be specific.

            Misrepresenting the data is one thing. Misrepresenting what was said to you in a conversation in front of everyone’s faces is quite another.

            And you have no idea what we would see if endosymbiosis was true.

            Again, nice dodge. Care to answer the question?

          • sombodysdad

            What happened to the voles?

            http://www.purdue.edu/uns/html4ever/2006/060914DeWoodyVole.html

            All of that evolution “60-100 times faster than the average vertebrate in terms of creating different species” and they are still voles? They must not have got the right mutations, eh? Get some of those and CD is in the bag?

          • Matthew Funke

            All of that evolution “60-100 times faster than the average vertebrate in terms of creating different species” and they are still voles?

            Yup. Do you know what “stabilizing selection” is?

            Do you know that when an organism speciates, it does so at the lowest taxonomic levels?

            Why does this, in your mind, invalidate common descent?

          • sombodysdad

            They are all still voles even after all of that “evolution”. If voles remain voles even though they evolved faster than all other vertebrates it shows that evolution cannot produce new body plans.

          • Matthew Funke

            They are all still voles even after all of that “evolution”. If voles remain voles even though they evolved faster than all other vertebrates it shows that evolution cannot produce new body plans.

            “No, I have no idea what that is” would have been shorter and more accurate.