Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

5,145 thoughts on “Common Design vs. Common Descent

  1. Allan Miller: You surely don’t need ‘a book on common descent’? I’ve never read one, as such, and I don’t feel it all all necessary to do so in order to grasp the basics. It derives pretty readily from easily-grasped first principles, whether talking of morphological commonalities or genetic ones.

    You would think that popular books on evolution, or textbooks on evolution, would devote at least a chapter to it.

    Take for example the book Evolution by Donald Prothero where the terms common ancestry, common descent, universal common ancestry, universal common descent, and nested hierarchy don’t even appear in the index.

    You seem to be telling me that your reasons for belief are no stronger or weaker than mine.

    If one has a process of descent with modification and bifurcation, one would expect a tree structure – nested sets – to be found in extant data, and that we find.

    A process like evolution, you mean? Yes, evolution could explain the nested hierarchy. Common descent doesn’t, unless by common descent one means descent with modification, aka evolution.

  2. stcordova: I’m afraid however, your thinking is too steeped and colored by phylogenetic phantasies that you are now arguing with circular reasoning.

    Poofamorphies and Other Phylogenetic Phantasies. Sounds like a book title.

  3. colewd to John Harshman:

    How much does your claim of “common descent” really explain if it cannot account for the origin of novel features?

    Well said.

    Because the conceptual nested hierarchies based on structure are defined by novel features, if common descent doesn’t account for the origin of those features they don’t account for the taxnomic/typologic/structural nested hierarchy defined by those features!

    We compare the novel features in the pigeon skeleton vs. the absence of those features in the lungfish skeleton and nest the pigeon in the bird group and the lungfish in the Sarcopterygiian fish group if we were doing purely structural classifications.

    Common descent doesn’t account for those. Therefore a conceptual nested hierarchy (such as the sets of skeletal architectures within vertebrates) is not accounted for by common descent.

    Bill, there is a reason John Harshman is fighting tooth and nail to avoid doing classification (and the resulting nested hierarchies) by structure alone. He keeps trying to do nested hierarchy by phylogeny, and I pointed out that is circular reasoning, and further it doesn’t agree with the nested hierarchy defined by structure.

    I said so in the OP (with different words):

    I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

    I posted the skeletal structures of a lungfish and a pigeon. Geometrically it’s absurd to say a pigeon skeleton nests within a lungfish skeleton. Elementary set theoretic concepts of math are mangled beyond all recognition because of the LSD of phylogenetic phantasies.

    John probably sense instinctively if we try to do classification and nested hierarchy based on structure, his argument will crumble because he claims common descent doesn’t explain those structures. Game over!

  4. Mung,

    You seem to be telling me that your reasons for belief are no stronger or weaker than mine.

    What actually is your belief, vis a vis common descent? Whether whatever it is you believe has a stronger, weaker or an equal basis is not clear, since you won’t actually say what it is.

    All I’m telling you is the rational basis for my considering common descent to be a fact. It’s up to you if you find it unpersuasive. Nonetheless, given a process of descent with modification and bifurcation, what else do you expect, other than nested sets?

    Allan: If one has a process of descent with modification and bifurcation, one would expect a tree structure – nested sets – to be found in extant data, and that we find.

    Mung: A process like evolution, you mean? Yes, evolution could explain the nested hierarchy. Common descent doesn’t, unless by common descent one means descent with modification, aka evolution.

    The point of your pedantic wordplay is lost on me. Honestly, those God-goggles are a real hindrance to sensible discussion. Show me a Creationist that can do anything other than pick at definitions.

    By common descent, one means descent from a common ancestor in multiple lineages. The process that effects divergence in that is evolution, operating in each of those lineages. The hierarchic nature of the data is explained by common descent of modern lineages. Where’s the actual objection to this?

  5. colewd: What do you mean here?

    Remember how the 3 different trees I made earlier were similar? That means they corroborate each other.

    You don’t get a result like that when making phylogenetic trees from the characters of cars.

    Suppose you decide to group cars by their characters, like cars made by Ford. You make a group defined by “4 doors”, a group of “2 doors”, a group of “6 doors” and so on.

    Those are now your groups. Then you look inside your “4 doors” group, and you decide to subdivide the “4 doors” group into “4wheel drive” and “2 wheel drive”. Then you look at the “2 doors” group, that one ALSO contains both “4wheel drive” and “2wheel drive” groups, so the groups are not exclusive, they overlap.

    Okay, you move on, you decide to sort cars by “4 cylinders”, “6 cylinders”, “8 cylinders” and so on.
    Then you look inside the “4 cylinders” group, and you want to divide it up into other groups. You divide it into “2 seats”, “4 seats”, “6 seats” and so on. But again the problem appears, because the “6 cylinders” group also contain “2 seats”, “4 seats”, “6 seats” and so on.

    Okay, you move on again. Maybe you can subdivide them by “has aircondition”. Nope, “has aircondition” is not exclusive to any of the other groups. You find that no matter what kind of subdivision you come up with they do not corroborate each other. The trees are not similar.

  6. Mung: I’m sorry, but you know better than to utter the name of the designer.

    I know it always sends ID proponents into a dither.

  7. Allan Miller: What actually is your belief, vis a vis common descent? Whether whatever it is you believe has a stronger, weaker or an equal basis is not clear, since you won’t actually say what it is.

    What? I gave you one link.

    http://theskepticalzone.com/wp/common-descent-munged/

    Here’s another when it came up in a discussion with Tom.

    http://theskepticalzone.com/wp/a-worksheet-targeted-for-high-school-students-proving-once-and-for-all-that-photosynthesis-is-not-irreducibly-complex/comment-page-7/#comment-199789

    ETA: See also …

    http://theskepticalzone.com/wp/a-worksheet-targeted-for-high-school-students-proving-once-and-for-all-that-photosynthesis-is-not-irreducibly-complex/comment-page-6/#comment-199683

  8. Rumraket,

    Okay, you move on again. Maybe you can subdivide them by “has aircondition”. Nope, “has aircondition” is not exclusive to any of the other groups.

    Not a feature found in motorcycles.

  9. I mentioned earlier I think it is simplistic and naive to model the difference in genes/proteins between species with a random walk rather than functionally coordinated changes.

    Many individual amino acids on a protein can function as a reverisble read/write Random Access Memory that has can also influence the protein fold. One of these read/write operations is the phosphorylation or de-phosphorylation of individual amino acids like Serine (“S”) or Threonine (“T”). In the diagram below, I show the individual locations where a read/write head must be precisely positioned to effect a read or a write. This is the magic of the phosphoproteome!

    I earlier mentioned the differences in the phosphoproteome of species. Below I highlight reasons why the phosphoproteome of humans must in principle be different than that of yeast in the Topoisomerase II protein because the sequences differ in “S” (serine) and “T” (threonine) in corresponding positions.

    I aligned the yeast (1st row) with the human (2nd row) Topoisomerase II enzymes in MEGA 6.0. I then used red triangles to highlight confirmed location of phosphorylation changes.

    The coordinates of the phosphorylation sites can be gotten from UNIPROT, and I posted a comment earlier

    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-88/#comment-204343

    with the exact coordinates which I used in conjunction with MEGA 6.0 and MS Paint to provide the diagram below.

    NOTE: “SD” is a motif that is frequently associated with a read/write site. So it’s not just about putting an S where there was none, but putting “SD” in numerous places on the protein to make the read/write position active. How the read/write head is positioned almost surely involves using the protein sequence as a road sign. Ergo, the protein sequences are not random, but functionally coordinated.

    The diagram only caputures a fraction of the read/write changes listed here:
    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-88/#comment-204343

    Click to Enlarge image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/12/phosphorylation_comparisons_v2.png

  10. Rumraket,

    Those are now your groups. Then you look inside your “4 doors” group, and you decide to subdivide the “4 doors” group into “4wheel drive” and “2 wheel drive”. Then you look at the “2 doors” group, that one ALSO contains both “4wheel drive” and “2wheel drive” groups, so the groups are not exclusive, they overlap.

    You look at two animals and you decide to group them into egg laying and placental animals. You then decide to subdivide to 2 legs and 4 legs. You look at the egg laying group and see both 2 leg and 4 leg animals. You look at the placental group and you see both 2 legged and 4 legged animals. The sub features overlap.

  11. colewd:
    Rumraket,

    You look at two animals and you decide to group them into egg laying and placental animals.You then decide to subdivide to 2 legs and 4 legs.You look at the egg laying group and see both 2 leg and 4 leg animals.You look at the placental group and you see both 2 legged and 4 legged animals.The sub features overlap.

    They’re all tetrapods.

    Glen Davidson

  12. colewd:
    GlenDavidson,

    Yes, and motorcycles, cars and trucks are motorized vehicles.

    Yes. But the tetrapods you alluded to all have four limbs (snakes and the like are a different matter, but then they do develop four limb buds). Cars, motorcyles, and trucks don’t all have four cylinders, and some don’t even have internal combustion engines.

    Glen Davidson

  13. GlenDavidson,

    Yes. But the tetrapods you mentioned all have four limbs (snakes and the like are a different matter, but then they do develop four limb buds). Cars, motorcyles, and trucks don’t all have four cylinders, and some don’t even have internal combustion engines.

    As you say some have 0 2 and 4 limbs. Some eat meat others don’t. Some are cold blooded others are not. Some have hair others don’t. Some have feathers others don’t. Some fly others don’t, They are categorized by similarity and differences.

  14. colewd:
    GlenDavidson,

    As you say some have 0 2 and 4 limbs.Some eat meat others don’t. Some are cold blooded others are not.Some have hair others don’t. Some have feathers others don’t.Some fly others don’t, They are categorized by similarity and differences.

    I didn’t say that, and the rest is pretty much vague, meaningless generalization.

    Glen Davidson

  15. Allan Miller,

    All I’m telling you is the rational basis for my considering common descent to be a fact.

    You don’t see calling this hypothesis a fact a marketing tactic?

  16. Bill, yes, you CAN find examples of subcategorizations of vehicles where an attribute of one group is not shared by another. The problem is you can’t find examples where multiple such attributes that define a categorization, corroborate each other. That was the point I was making.

    Again, the 3 phylogenetic trees I made earlier corroborate each other. They are pretty much identical. In real biology, there are thousands, some times tens of thousands of independent phylogenetic trees that corroborate each other.

    Yet you can’t find even a single example of grouping of designed objects with a particular character, that you can corroborate with another character (that divides into the same groups).

  17. colewd:
    Rumraket,

    I have to admit you are resourceful

    I have to concede I found your suggestion plausible when I read it, but tried googling it any way. You never know.

    I also tried googling 4 wheeled motorcycle and lots of other silly things. I think what we can learn from this is that some one has thought about such a thing before either of us, and then tried to make it. 🙂

  18. Mung,

    Sorry, didn’t follow the link. I only tend to skim, even text, not follow every labyrinth down which I am sent.

    It would, I suspect, have been easier to say than to ferret out those links.

  19. I’ll state my reasoning again, in slightly different form.

    There is a process that can cause genetic identity: template based DNA polymerisation. In fact, it is the only known cause of genetic identity. Therefore, if I find extensive genetic identity, this process is my go-to explanation for that. The identity need not be complete, since fidelity is not 100%.

    Why am I wrong?

    Alternatively, what makes this a ‘belief’ on equal footing to whatever-it-is-Mung-believes?

  20. colewd,

    You don’t see calling this hypothesis a fact a marketing tactic?

    How can a statement regarding what I consider to be a fact be a ‘marketing tactic’? You are skating rather close to breaching the ‘good faith’ rule. I wouldn’t normally complain, but given that I am posting honestly, I rather resent that smarmy sneer as to my reasons for stating my case.

  21. stcordova: Here is the best lungfish skeleton example I could find.

    But a lungfish isn’t really a fish. Or something.

    Ecologically speaking, many people lump all swimming vertebrates with fins together as “fish.” But not all fish are the same. Lungfish are actually more closely related to amphibians, reptiles, and us than they are to a tuna fish. In taxonomic terms, lungfish do not belong with fish but with the four-legged to land animals in a group known as the Sarcopterygii (the lobe-finned fish and their descendants).

    – Donald R. Prothero

    So a lungfish is a fish, but it’s also not a fish. It’s a proto-human. 🙂

  22. Allan Miller: It would, I suspect, have been easier to say than to ferret out those links.

    Well, it wasn’t all that clear what it was you wanted to know.

    Allan Miller: You seem to say your reason for accepting common descent is due to groupthink. Is that fair?

    Not really. I don’t believe in common descent because you and Rumraket and John do. And the number of people who reject common descent could well outnumber those who accept it. But what “science” has to say about it does enter into my acceptance of it. But that is by no means the only factor.

    For example, let’s assume that I say that I think all dogs share a common ancestor but that dogs and cats do not. Now I have no way of defending that claim. So I am more inclined to accept that they share a common ancestor than to reject it. If that makes sense. And that has nothing to do with group-think, imo.

    I don’t know where or how to draw the boundaries, common descent here, not common descent there, so I don’t have a reason to reject common ancestry.

  23. Mung,

    Where does my argument break down? Given that sequence identity is only known to be caused by template based nucleic acid polymerisation, at what taxonomic level should we stop inferring common descent when we encounter it?

    Or, put another way, is my argument valid at any level?

  24. stcordova:

    John Harshman:

    You don’t seem to have any comprehension of how nested hierarchy works.

    So explain it to me with the above skeletons. I studied all sorts of geometry even varieties of non-Euclidean geometry such as found in General Relativity. Why don’t you try explaining a nesting structure based on geometry for a change. Or how about set theory. You want to say I don’t comprehend, you can use some formal language to add some rigor to this discussion.

    I’ve done that before, but you don’t read. A nested hierarchy can be expressed as a relationship among all pairs of sets: either one is a subset of the other or they are disjunct. This structure can be perfectly represented as a rooted tree. Data have a nested hierarchical structure if they fit a particular rooted tree much better than expected by chance. Which is what phylogenetic algorithms do. Not sure what geometry you’re talking about.

    Much of the rest of your post is pointless digression, perhaps intended to show how clever you are, like the reference to non-Euclidean geometry above. Please stop this, since your posts are longwinded enough, and self-aggrandisement is not virtuous.

    Skipping ahead to something resembling meat:

    So we have the bird skeleton and the lungfish skeleton:

    they have a head (“anterior”) and a tail (“posterior”) as well as a back (“dorsal”) and a belly (“ventral”); therefore they also have a left side and a right side.

    And within the bilatarians we have vertebrates:
    https://en.wikipedia.org/wiki/Vertebrate

    All vertebrates are built along the basic chordate body plan: a stiff rod running through the length of the animal (vertebral column and/or notochord),[11] with a hollow tube of nervous tissue (the spinal cord) above it and the gastrointestinal tract below.

    There’s a problem already with your version of a nested hierarchy. Most vertebrates don’t have notochords as adults, so how can you say they’re chordates?

    Lungfish are veterbrates, Pigeons are veterbrates, kangaroos are vertebrates, frogs are vertebrates. So all these creatures nest within vertebrates.

    What’s the problem there? I’ll tell you what the problem is. They may all nest within vertebrates, and superficially this looks like an evolutionary pattern of all of them descending from a vertebrate ancestor. But the problem is, and has always been, as Matzke pointed out:

    https://uncommondescent.com/evolution/two-faced-nick-matzke/

    phylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry,

    So you can’t rigorously demonstrate we descended from a fish, at best you can only prove a Parrot and Lungfish are members of sister groups, and even then this assumes common descent to begin with!!!

    You clearly have no clue what Nick was saying. (I will charitably assume that the quote mine was from ignorance, not malice.) Common descent is a conclusion from the existence of nested hierarchy, not an assumption. If the nested hierarchy puts lungfish (and/or coelacanths) as sister group of tetrapods (which it does), and actinopterygians as sister group of the lungfish/tetrapod/coelacanth clade (which it does), then parrots are descended from fish or, speaking cladistically, are fish. Not an assumption, a conclusion.

    For the present discussion we are only describing nested hierarchy in terms of structure, not genealogy or phylogeny nor even common design.

    Apparently you’re having some serious problems classifying things based on geometry and structure. That’s probably a symptom of having your thought process being so mangled by phylogenetic thinking you can’t do straightforward structural comparisons anymore. It’s a PhD in mangled thinking.

    Thanks, your condescension is so very Christian.

    But let’s be a little meticulous. I see the bird skeleton having:

    toes
    claws
    humerus
    radius
    ulna
    etc.

    Why should this skeletal architecture be nested within a fish architecture that doesn’t have these things, but has some other things?

    You are mistaken. The fossil fish most closely related to tetrapods have humerus, radius, ulna, and metapodials. Now what?

    I think you’re having some issues with set theory and abstract concepts. You accuse me of lacking comprehension, but actually I think you’re the one suffering so badly from the effects of phylogenetic illogic that you aren’t able to see there are problems with your conception of these architectures in a framework of sets and geometry.

    I think, on the other hand, that you’re using “a framework of sets and geometry” as a meaningless buzzphrase.

    But lets review a little set theoretic approach. Bilatarians are the set of all animal that have bilateral symmetry, within Bilatarians are the set of creatures like vertebrates and a variety of in-vertebrates (like insects).

    Under that definition, echinoderms aren’t bilaterians. Does that bother you? The problem with you approach is that characters are gained, but also lost and transformed. That’s why you have trouble with snakes, and want to avoid thinking about them.

    Within the set of vertebrates are sets of other creatures like: mammals, birds, and various sets of fish. Birds have a skeletal structure distinct from fish.

    Again, you pick certain characters and ignore others. Within the set of vertebrates are sets of other creatures like Gnathostomata, which all have jaws. There’s a set for you, and gnathostomes have a skeletal structure distinct from agnathans. Or Osteichthyes, which all have endochondral bone. Another set. And Sarcopterygii, which all have paired fleshy fins with bony skeletons. And Tetrapoda, which all have sacral ribs. So why accept vertebrates and birds, but not those other groups?

    Structural classification is about structure and geometry, John, not phylogeny. We can also extend this to physiology. But it’s not about phylogeny.

    Correct. But only phylogeny explains the nested hierarchy in which those structures are arranged.

    The discussion was common design vs. common descent. So you can’t use phylogeny which assumes common descent to argue that common descent is real! You can’t only use the assumption of common descent in a “proof by contradiction” where common descent is assumed for the sake of argument.

    No problem, since I don’t assume common descent. Common descent is a conclusion from nested hierarchy, the only explanation for that hierarchy.

    You can’t use phylogeny to do structural classification

    I don’t know what you mean by that.

  25. Don as quoted by Mung:

    Lungfish are actually more closely related to amphibians, reptiles, and us than they are to a tuna fish. In taxonomic terms, lungfish do not belong with fish but with the four-legged to land animals

    Donald Prothero

    OK Don, look at the bird skeleton and the lungfish skeleton. Now compare the lungfish skeleton with that of a tuna (below).

    Is the lungfish skeleton more similar to that bird or a tuna! I’d say the lungfish are more tuna like that bird like.

    This shows how much uncritical acceptance there is of certain paleontological claims.

    But this is The Skeptical Zone, where acid of skepticism removes the fluff from fluffy.

  26. Mung,

    Well, it wasn’t all that clear what it was you wanted to know.

    What the ‘it’ was whose grounds for belief were equivalent to mine.

  27. Allan Miller: Or, put another way, is my argument valid at any level?

    I’m not even sure how we are at odds, lol. I’m not arguing against common descent.Your argument has what statement as it’s conclusion?

    There is a process that can cause genetic identity: template based DNA polymerisation. In fact, it is the only known cause of genetic identity. Therefore, if I find extensive genetic identity, this process is my go-to explanation for that. The identity need not be complete, since fidelity is not 100%.

    I would prefer to not call it genetic identity if what we really mean by that is genetic similarity. And I agree. That certainly sounds plausible.

    How genetically similar are you to your siblings?

  28. stcordova: Well said.

    Because the conceptual nested hierarchies based on structure are defined by novel features, if common descent doesn’t account for the origin of those features they don’t account for the taxnomic/typologic/structural nested hierarchy defined by those features!

    That doesn’t follow. The origin of a feature and the origin of the nested hierarchy in which those features are arranged are quite different. Common descent explains nested hierarchy, period. In evolutionary theory, the origins of features are explained by mutation, drift, selection, etc. You may not like that explanation of the features, but it doesn’t matter for common descent whether features arise by natural processes or poofing. Let’s put it another way. Can you explain the shape of the great pyramid without explaining where limestone comes from or how it forms?

    We compare the novel features in the pigeon skeleton vs. the absence of those features in the lungfish skeleton and nest the pigeon in the bird group and the lungfish in the Sarcopterygiian fish group if we were doing purely structural classifications.

    Nope. Sarcopterygii isn’t diagnosed by the absence of features but by the presence of novel features, and those features are shared with birds.

    Bill, there is a reason John Harshman is fighting tooth and nail to avoid doing classification (and the resulting nested hierarchies) by structure alone. He keeps trying to do nested hierarchy by phylogeny, and I pointed out that is circular reasoning, and further it doesn’t agree with the nested hierarchy defined by structure.

    Neither of us has any idea what “do nested hierarchy by phylogeny” means. I don’t even think you know what “nested hierarchy defined by structure” means. You seem to be referring to morphology, as if there were some essential difference between morphological and molecular characters, but beyond that it isn’t clear.

    I posted the skeletal structures of a lungfish and a pigeon.Geometrically it’s absurd to say a pigeon skeleton nests within a lungfish skeleton.

    I don’t think you know what you mean by “geometrically” either. Of course skeletons don’t nest within each other, but skeletal characters do show that birds are within Sarcopterygii, and this was known long before there were any DNA sequences. Hey, it’s structural!

    John probably sense instinctively if we try to do classification and nested hierarchy based on structure, his argument will crumble because he claims common descent doesn’t explain those structures.Game over!

    Once again, common descent doesn’t explain structures. It explains nested hierarchy. What’s your explanation? Why will you never attempt an explanation?

  29. Mung,

    I’m not even sure how we are at odds, lol. I’m not arguing against common descent.

    It’s never clear whether you are or aren’t. You seem to think that evidence which I consider strong is weak, though that is of course your prerogative.

    Your argument has what statement as it’s conclusion?

    If we encounter ‘extensive’ genetic identity (yes, I know, thresholds), we can reasonably infer common descent from that.

    I would prefer to not call it genetic identity if what we really mean by that is genetic similarity. And I agree. That certainly sounds plausible.

    No, I actually think identity is an important issue, and is what gives the power to molecular approaches. It’s the difference between the analogue and the digital. If we have two sequences AAAAAAGGG and AAAAAAGGA, one could reasonably say that they had a certain percentage similarity, but it is important to note that this consists of a long run of identity, and one difference.

    How genetically similar are you to your siblings?

    That question introduces an unnecessary confusion. We are diploid, and inherit just half of our genes from each parent – a different ‘half’ in each case.

  30. Once again it appears like Salvador has a valid point. When you look at a fossil what are you looking at if not the structure of the organism?

    Or are fossils just not relevant in creating cladograms?

  31. Allan Miller,

    How can a statement regarding what I consider to be a fact be a ‘marketing tactic’? You are skating rather close to breaching the ‘good faith’ rule. I wouldn’t normally complain, but given that I am posting honestly, I rather resent that smarmy sneer as to my reasons for stating my case.

    Sorry Allan. I did not consider you marketeer here. How would you back up the statement that common descent is a fact?

  32. Mung:
    Once again it appears like Salvador has a valid point. When you look at a fossil what are you looking at if not the structure of the organism?

    Or are fossils just not relevant in creating cladograms?

    Of course they’re relevant, and where Sal says “structure” I read “morphology”. The only way to create cladograms from fossils is morphology. That’s what we do. Not sure of Sal’s point.

  33. Rumraket,

    The problem is you can’t find examples where multiple such attributes that define a categorization, corroborate each other. That was the point I was making.

    If we take the case of computers there are clear delineations between laptops desktops and handhelds. There is also commonality between each. Computers appear closer to biological design then cars. There are lots of common chips, common software and common operating systems. They are also very distinct mechanically.

    Life is quite different as the software (DNA etc) can create that hardware or a physical plant or animal. The restrictions of how cells are made could very well drive the patterns we see. How many amino acid combinations can construct a vertebrae which can protect electrical signals that coordinate all the bodies movement. If it is indeed limited then design can explain the nested hierarchy as there are only so may ways you can build these key biological parts with amino acids and other cellular molecules.

    The claim of common descent ultimately is one of the nested hierarchy being the result of reproduction. I simply don’t agree at this point that common descent is the only explanation for both the morphologic and phylogenetic patterns we are observing. Common design is a very limited explanation but ultimately may be the right one.

  34. Here are 3 sets of skeltons. Let the reader make their best estimate of which two skeletons are the most similar.

    Lungfish:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/04_African-lungfish_Skeleton1.jpg

    Tuna:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/caljsiol_sio1ca175_060_118a1-1024×689.gif

    Pigeon:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/bird_skeleton1.jpg

    If you say Lungfish and Tuna are more similar than Lungfish and Pigeon (or Tuna and Pigeon), then well, you’re agreeing with my point that Tetrapods (like a Pigeon) are less closely related to Sarcopterygiian fish (like a lungfish) than Sacopterygiian fish are to Actinopterygii fish (like Tuna) if we are talking in terms purely of structure.

    It takes a PhD evolutionary biologist to argue, structurally speaking, the Lungfish and Pigeon are more similar to each other than the Lungfish and Tuna!

    And that my friends, is an example of why I don’t get along that well with evolutionary biologists. We aren’t even talking creation, ID, or common design, we’re arguing over what skeletal structures are more similar: Lunfigh vs. Tuna, Tuna vs. Pigeon, Pigeon vs. Lungfish. It shouldn’t be that hard, but it takes a PhD evolutionary biologist to mangle what a kindergarden kid or 1st grader can see!

  35. colewd:

    I simply don’t agree at this point that common descent is the only explanation for both the morphologic and phylogenetic patterns we are observing.

    But common descent doesn’t even explain the morphological pattern. The hard-core evolutionists are insisting that despite skeletal data such as that which I just provided:
    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-93/#comment-204986

    that the pigeon and lungfish are more similar than a lungfish and tuna. They can’t even agree on what pattern is being explained, much less actually explaining it!

  36. Allan Miller:

    If we encounter ‘extensive’ genetic identity (yes, I know, thresholds), we can reasonably infer common descent from that.

    That’s only true if one creature after N-generation can give rise to another kind of creature. If there are mechanistic barriers to this, then the pattern of similarity is due to common design, not common descent. In other words, “God did it because evolution can’t.”

  37. John Harshman: Of course they’re relevant, and where Sal says “structure” I read “morphology”. The only way to create cladograms from fossils is morphology. That’s what we do. Not sure of Sal’s point.

    Congrats ,Mung

  38. The fossil fish most closely related to tetrapods have humerus, radius, ulna, and metapodials.

    You mean this one below. Amazing the reconstruction of this creature put a tail on it when it is clearly missing from the fossil. Even other paleontologists complained of the quality of this fossil to make much of any inference. You’re going to argue that this thing has a radius and ulna that proves something like it can give rise to a Pigeon?

    But, in any case, it doesn’t look much like a pigeon does it? C’mon John, you studied birds, does that look like a pigeon?

  39. The two scientists who found the lion’s share of walking whale fossils essentially created the best fossil proof of evolution using plaster models and drawings and supplied these to museums and science magazines. In each case, they started with incomplete fossils of a land mammal. Whenever a fossil part was missing, they substituted a whale body part (blowholes, fins and flukes) on the skeletal model or skull that they distributed to museums. When these same scientists later found fossils negating their original interpretations, they did not recall the plaster models or drawings. Now museums are full of skulls and skeletons of ‘walking whales’ that are simply false.” Dr. Werner went on to say, “I suspect some curators are not aware of the significance of these substitutions nor are they aware of the updated fossils. Museums should now remove all of the altered skeletons, skulls and drawings since the most important parts of these ‘walking whales’ are admittedly made up. Museums will also have to delete these images from their websites as they are misleading the public.” –

    The Grand Experiment
    http://www.thegrandexperiment.com/whale-evolution.html#sthash.6yKOHtL5.dpuf

    Given the rather low standards of what counts as evidence, some claims that a fossil actually has a feature when it doesn’t should be treated with skepticism. Seriously, look at that mangled piece of mud they call Tiktaalik. How much can we actually know from that mangled piece of mud. Look at what evolutionists have extrapolated from that mangled piece of mud above to the fanciful “reconstruction” below. Half of the creature is missing in that fossil, so how did they reconstruct the missing half? Uh, well, they really needed something that can evolve into a tetrapod so they attached some leg-like appendages to it!

    Should anyone place much trust on such a bad sample of data? I wouldn’t:

  40. stcordova
    Should anyone place much trust on such a bad sample of data?I wouldn’t:

    Should anyone place much trust on such a bullshit claim from a science-free Creationist website? Honest, intelligent people wouldn’t.

  41. John Harshman:

    The fossil fish most closely related to tetrapods have humerus, radius, ulna, and metapodials.

    Fossil fish, like Lungfish and Coelecanths, you know, “living fossils”.

    Where are the toes in the lungfish again, John?

    Below is Tiktaalik before it got reworked. Where are the toes and legs in that fossil again, John?

  42. Rumraket: Creationists usually agree it is microevolutionary change.

    They do huh? Is that a blanket discovery of yours, so you also decided you accept it?

    Rumraket: phoodoo: Yea, about as dumb as showing photos of different dog skulls, and claiming its evidence of evolutionary change.

    It is a manifest instance of evolutionary change.

    Its not a instance of evolutionary change, unless every time someone has a baby that is short, or has curly hair, or has severe overbite, those are also all instances of evolutionary change. And if that is what you call micro-evolution, then why should we ever believe it becomes macro evolution, unless you think poodles are the start of a new line of creature.

    Its also happens to be problematic for all the paleontologists who dig up hominid bones and try to say these are some distinct form of species, because that would be like simply digging up a dog skeleton and claiming its also a distinct species just because it looks different that some other wolf. If dogs bones look more different from each other than Australopithecus looks like man, than why not just assume its just another version of a man?

    Furthermore, why do we bother calling Siamese kittens a different animal than a African lion? Cats can vary as much as dogs right? The whole creationist “kind” thing doesn’t seem so crazy after all.

  43. colewd:
    Rumraket,

    If we take the case of computers there are clear delineations between laptops desktops and handhelds. There is also commonality between each. Computers appear closer to biological design then cars. There are lots of common chips, common software and common operating systems. They are also very distinct mechanically.

    … and?

    That’s not a nested hiearchy, nor does it exhibit convergence of independent phylogenies towards a common branching genealogical relationship.

    You seem unable to fathom what a nested hiearchy is. It’s NOT “they’re sort of similar”. It is that multiple independendent characters are phylogenetically informative and can be used to define the same nesting groups.

    Life is quite different as the software (DNA etc) can create that hardware or a physical plant or animal. The restrictions of how cells are made could very well drive the patterns we see.

    What “restrictions” are you talking about on “how cells are made”, and what pattern is it you think they are supposed to explain? Are these “restrictions on how cells are made” supposed to explain the nested hiearchy of life? Are they supposed to explain why there is convergence of independent phylogenies?

    I don’t think you even know what you’re saying. I think you just type words that enter your consciousness without even really understanding what it means, you just sort of feel like it might be relevant. You don’t speak as person attempting to communicate, you just flail and bluster incompetently seemingly out of some irrational compulsion to reply with barely coherent technobabble.

    You should actually be ashamed. You are completely out of your depth and to such an extend you can’t even say something on the subject that makes logical sense.

    How many amino acid combinations can construct a vertebrae which can protect electrical signals that coordinate all the bodies movement.

    Is that a question? There is no question mark at the end.

    If it is indeed limited then design can explain the nested hierarchy as there are only so may ways you can build these key biological parts with amino acids and other cellular molecules.

    No, that doesn’t explain the nested hiearchy.

    The proposition “there is a limited number of “amino acid combinations” which can construct a vertebrae which can protect electrical signals that coordinate all the bodies movement” does actually not explain the nested hiearchy. At all. In any way.

    If you disagree, then do it, explain the nested hiearchy from the premise:
    Premise 1: There is a limited number of “amino acid combinations” which can construct a vertebrae which can protect electrical signals that coordinate all the bodies movement.
    Premise 2: ?
    Premise 3: ?
    Conclusion: Therefore… what? Therefore there should come to be a nested hiearchy of groups within groups where multiple independent characters shared between different species of organisms, exhibit convergence of phylogenies.

    Good luck filling in those missing premises.

    The claim of common descent ultimately is one of the nested hierarchy being the result of reproduction.

    Well, the mechanism of reproduction, splitting of populations and so on, yes. That inexorably yields branching genealogical structures where independent characters converge on the same tree structure. As was proved to you in this very thread.

    I simply don’t agree at this point that common descent is the only explanation for both the morphologic and phylogenetic patterns we are observing.

    You can disagree all you want. Nobody can force you to agree when it is so clear you simply don’t want to.

    Common design is a very limited explanation but ultimately may be the right one.

    As was proved to you with concrete examples in this very thread, common design does not actually explain why there is a nested hiearchy with convergence of independent phylogenies.
    The re-using of parts does not result in a nested hiearchy. The re-using of slightly altered parts does not result in a nested hiearchy. The re-using of slightly altered parts that has to bind together and are therefore mutually constrained in their properties to be interdependent, does not result in a nested hiearchy.

    In every way you have been able to try to imagine that “common design” would result in a nested hiearchy, it didn’t do so.

  44. phoodoo: They do huh?

    Yes.

    Is that a blanket discovery of yours, so you also decided you accept it?

    No, that’s not why I accepted it.

    Its not a instance of evolutionary change, unless every time someone has a baby that is short, or has curly hair, or has severe overbite, those are also all instances of evolutionary change.

    Yes, those are also instances of evolutionary change.

    They’re changes brought about by evolutionary processes: Mutation and recombination of genes, subject to changes in frequencies of such alleles in populations over generations.

    And if that is what you call micro-evolution, then why should we ever believe it becomes macro evolution, unless you think poodles are the start of a new line of creature.

    That’s like asking why you should believe that a tree will grow taller. You’ve only observed it grow a tiny amount, why should it get any taller?

    Its also happens to be problematic for all the paleontologists who dig up hominid bones and try to say these are some distinct form of species, because that would be like simply digging up a dog skeleton and claiming its also a distinct species just because it looks different that some other wolf.

    Some times those things are actually debated yes.

    But it is no better for creationists who can’t even agree amongst themselves. Some creationists say that some particular hominid fossil is “fully ape”, others will say it is “fully human”. Some creationists even change their minds later and completely revert their positions.
    Creationist assessments of hominid fossils 01.
    Creationist assessments of hominid fossils 02.
    That’s pretty good evidence that some of the fossils are transitional forms.

    But that just makes it all the more hypocritical and perplexing why you creationists think evolution can’t change the morphology of one species into a different one, when you are fine accepting that within a single species it is possible to generate so much variation that if you didn’t know any better, you would claim they were different species and an unbridgeable macroevolutionary gap.

    You are fine accepting that the microevolutionary changes within a species are possible. A->B is fine. B->C is fine. C->D is fine. But A—->D? IMPOSSIBLE!

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