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. John Harshman as quoted by Mung:

    Not sure of Sal’s point.

    Here is the gameplan Mung. If you have Michael Denton’s book, Evolution a Theory in Crisis (1984), there are three sections, the Typological Perception of Nature.

    5.
    The Typological Perception of Nature
    6.
    The Systema Naturae from Aristotle to Cladistics

    12.
    A Biochemical Echo of Typology

    I’m arguing with John Harshman on the first part. All I’m first trying to establish are the notion of types. There are Mammals, Birds and Fish. I showed the lungfish, tuna, and pigeon skeletons.

    Notice Rumraket not willing to answer the question. Typology is not a comfortable thing for evolutionists when the question is examined in even modest detail like the skeletons of lungfish, tuna, and pigeons.

  2. colewd:
    Rumraket,

    Your example of three trees did not show what you wanted.

    Yes it did. The three trees were nearly identical, despite my exampe having several unrealistically large confounding factors, such as unrealistically short genes, unrealistically high mutation rates, and unrealistic longetivy of “species”.

    For all these factors, were I to make them more realistic, the nested hiearchy would become all the more apparent and undeniable.

    It demonstrated that random mutation will rapidly break down a sequence and you will not get any phylogenetic nested hierarchy over time.

    For a gene 20 nucleotides long and a mutation rate of 1 pr gene pr cell division, yes. For such a situation you will get breakdown of phylogentically informative sites rather quickly, you are correct to notice this. But that is as noted not the only thing my example shows. It still shows convergence of independent phylogenies and nesting hiearchical structure.

    You dismiss the computer example but you don’t have a counter argument yet.

    I don’t need to make a counter-argument to a blind assertion.

    You didn’t give a “computer example”, you just wrote the word “mac computers”. No example of a nested hiearchical arrangement of mac computers was given.

    You don’t seem to understand what is understood by an “example”. You’re supposed to show the thing, the actual example. Not just declare that you have one, or that something is an example.

    Me writing “Motorcycles are an example of a nested hiearchy” is not me giving an example of a nested hiearchy. It is me CLAIMING that something is an example of a nested hiearchy, but I’m merely making a claim there, I’m not backing it up.

    So get to work Bill. Give the actual example.

    You have stopped thinking through issues Rum and are grasping at assertions.

    Thanks Bill, coming from you that means… nothing.

    Common design may indeed be the right high level description of what we see.

    Why? Explain why. Why would common design yield nesting hiearchical structure in the data? Why would it yield convergence of independent phylogenies?

    Common descent isn’t even clearly defined yet and we are almost at 4700 comments.

    What part of common descent do you fail to understand? It just means two entities share a common ancestor. The thing about ancestors of course implies a genealogy, as in there is reproduction. Individual entities, be they DNA molecules, cells, or entire species, reproduce and leave descendants. Even if you thought common decsent was lacking a definition, I have now given one.

    Where have you defined common design? Where have you explained why it would yield convergence of independent phylogenies?

  3. GlenDavidson: I’d need a citation for that.

    December 17, 2017 at 1:44 pm

    quote:

    But the problem is that you have a hypocritical double standard for evolution that you require for no other area of scientific investigation, only for evolution. There are many processes taking place right now on Earth that are too slow for human beings to see complete in their life times. The formation and erosion of mountains is one,
    the generations and lives of stars in the universe is another. But you’re not all up in arms about geology and plate tectonics or astronomy.

    end quote:

    peace

  4. Rumraket: I it is not that they are supposed to be “more similar” in their shared characters, it is the presence of certain characters that yield particular groups. … Whether the shape of their skulls and spine are more similar between the lungfish and the tuna is irrelevant, as they are essentially a character shared by all three species…

    See, you’re not as ignorant as you think. But if the shape of the skull or spine is different can’t that qualify as a derived/advanced character rather than a primitive one and thus be used for cladistic classification?

  5. fifthmonarchyman: December 17, 2017 at 1:44 pm

    quote:

    But the problem is that you have a hypocritical double standard for evolution that you require for no other area of scientific investigation, only for evolution. There are many processes taking place right now on Earth that are too slow for human beings to see complete in their life times. The formation and erosion of mountains is one,
    the generations and lives of stars in the universe is another. But you’re not all up in arms about geology and plate tectonics or astronomy.

    end quote:

    peace

    I saw that. The difference is that I understood what Rum was saying there, which was that we can infer from the present into the deep past. He didn’t say that all of the processes are the same, merely that they involve deep time.

    How is this hard to understand?

    Glen Davidson

  6. stcordova: Here is the gameplan Mung. If you have Michael Denton’s book, Evolution a Theory in Crisis (1984)…

    I would say that I don’t read that Discovery Institute propaganda but it was not published by the DI Press. 😉

  7. Rumraket:

    I think you’re confused. I it is not that they are supposed to be “more similar” in their shared characters, it is the presence of certain characters that yield particular groups. So when chickens are grouped with lobe finned fish in sarcopterygii by the method of cladistics, it is because they share at least one particular character not present in actinopterygii.

    But the problem here is one could say Sarcopteriian fish (like lungfish) and Actinopterygii fish (like tuna) share gill respiration not found in Tetrapods (like pigeons). Rather than pick a few characters, total structure and physiology should be considered, and not just shared characters but ABSENT characters. That was my complaint about cherry picking. You are picking only shared characteristics and ignoring unshared characteristics between entire groups. That is illegitimate.

    I’m not the one confused, it is the phylogenetic approach that is confused. The phylogenetic approach as presented in this disscussion is analogous to looking at the shared character of a green colored car with a green colored lime and ignoring all the unshared characteristics.

    Clearly on in more comprehensive comparisons Sarcopteriian fish (like lungfish) and Actinopterygii fish (like tuna) are more similar to each other than they are to pigeons. One gets bizzare groupings when one cherry picks characters by excluding unique features of one group that aren’t present in another group.

    So when chickens are grouped with lobe finned fish in sarcopterygii by the method of cladistics, it is because they share at least one particular character not present in actinopterygii.

    In other words, cherry picking. It’s so systematically embedded into the methodology, and the methodology so extensively practiced, the underlying cherry picking isn’t even apparent anymore to the practitioners.

    An outsider who hasn’t had his though process mangled by phylogenetic “methods” will look at the lungfish and tuna and notice the two species don’t have legs, toes and wings like a pigeon. It takes a PhD phylogeneticist to find a way to systematically ignore characters (like legs, toes, wings, etc.) when creating hierarchical groupings.

    It’s the same thing with gene trees built only on shared genes rather than incorporating orphan genes (taxonomically restricted genes) as a way of building classifications. It’s cherry picking and data distortion all the way — all this in the name of building a case for common descent.

  8. Rumraket: Why would it yield convergence of independent phylogenies?

    Why would evolution?

    What part of common descent do you fail to understand?

    The part where people try to claim it’s not the same as evolution. The branching part.

    It just means two entities share a common ancestor.

    See.

    You’ve just divorced “common descent” from the nested hierarchy. So “common descent” does not explain the nested hierarchy.

  9. Rumraket:

    Hiearchies are defined by characters exclusive to a particular group.

    Oh, so why then would you say a Lungfish is more similar to a Pigeon than a Lungfish to a Tuna? The Pigeon has legs, toes, feathered wings… I don’t see them in the Lungfish and Tuna. The Lungfish and Tuna have gills to breathe with, the Pigeon does not.

    NOTE to colewd: the phylogeneticists here aren’t being very clear about what nested hierarchy the are actually defending. I caught them trying to defend a hierarchy which makes a lungfish and pigeon more similar than a lungfish and tuna. When pressed for the reasons they do this, they point out to the methodical cherry picking of characters (i.e. they ignore the fact pigeons have legs, toes, wings etc.) in order to make their groupings.

    They aren’t even being clear on what nested hierarchy they are defending, much less explaining how common descent explains that hierarchy. When they do attempt to become clear on what hierarchy it is, and why they built the hierarchy that way, they disclose their systematic cherry picking methods (which ignore the fact a pigeon has legs, toes, wings, etc.).

  10. Mung: I would say that I don’t read that Discovery Institute propaganda but it was not published by the DI Press.

    In any case, now you know the template I’m making my case from, it’s from Michael Denton’s chapter on Typology, i.e. a Pigeon is not a fish, it is a bird!

  11. Glen Davidson, I briefly took you off the ignore list briefly to see if you could answer the question about which pair creatures were the most similar:

    1. Lungfish and Tuna
    2. Lungfish and Pigeon
    3. Tuna and Pigeon

    All I seem to recall was something you said about me being some kind of bag. Anyway, you’re back on my ignore list after one comment. Congratulations.

  12. Rumraket,

    For all these factors, were I to make them more realistic, the nested hiearchy would become all the more apparent and undeniable.

    Just like evolution Rum you make a rudimentary example and then claim it explains everything. You did this with small molecules binding to proteins to claim that almost any DNA sequence would work in biology forgetting that proteins often have more then one function.

    I don’t need to make a counter-argument to a blind assertion.

    I explained that there are clearly different computers that all share similarities Laptops desktops and handhelds. Like DNA and Proteins are common to all life, c-mos transistors are common to all these computers. So are D Ram memory, S Ram memory, E prom memory, capacitors, resistors, inductors, PC boards, LCD or OLED displays. The differences are more in mechanical structure except where handhelds have a different operating system and microprocessor architecture.

    My argument is that we can use these computers to build a nested hierarchy which is the result of commonly designed systems and components. We can build the hierarchy structurally and by the commonality of both software and hardware.

    Lets start with laptop which forms its own group where the display is attached to the main computer which contains a keyboard and the display folds on top of the keyboard for easy transportation.

  13. stcordova:
    Glen Davidson,I briefly took you off the ignore list briefly to see if you could answer the question about which pair creatures were the most similar:

    1. Lungfish and Tuna
    2. Lungfish and Pigeon
    3. Tuna and Pigeon

    All I seem to recall was something you said about me being some kind ofbag.Anyway, you’re back on my ignore list after one comment.Congratulations.

    I never wanted to be off of your ignore list, since you’re never anything but dishonest to me.

    Learn to be honest once, or wait until this forum finally insists that dishonesty is worse than someone calling you on your dishonesty, and then you can take me off of “ignore.” Until then you can just fantasize that you’re competent and honest, when you’re neither.

    Glen Davidson

  14. Bill Cole:

    We can build the hierarchy structurally and by the commonality of both software and hardware.

    Exactly, the hierarchy is structural. To the extent the hierarchy is not explainable by the process of reproduction and PHYSICAL rather than conceptual descent with modification, common design is a better explanation than common descent. In the case of man-made objects, common design explains the nested hierarchical structure since common descent clearly would not.

    And as you pointed out, with respect to DNA, if mutation were random, common descent runs the risk of actually erasing the hierarchical pattern completely over time.

    Beyond that, I showed there are different RAM (random access memory) architectures between species at the protein level here:

    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-93/#comment-204934

    But I’m so proud of this diagram I’ll show it again as it vindicates so much of what I said against the model of random mutation to explain the patterns of differences in genes between species. The 1st row is Yeast, the 2nd row is Human. It is the same protein, but the RAM locations (marked with red triangles) are different in the human than in the yeast.

    So we have the common design of the basic protein (in this case Topoisomerase II), but a different RAM architecture in that protein.

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

  15. If individual proteins have RAM it should not be surprising then that learning and cognition are affected by the phospho proteomic RAM in proteins. This again highlights the difference in protein architecture between species is functionally coordinated, not the result of random mutation as phylogeneticists model it.

    https://www.ncbi.nlm.nih.gov/pubmed/24509310

    Protein phosphorylation is a well-known and well-documented mechanism in memory processes. Although a large series of protein kinases involved in memory processes have been reported, information on phosphoproteins is limited. It was therefore the aim of the study to determine a partial and differential phosphoproteome along with the corresponding network in hippocampus of a wild caught mouse strain with excellent performance in several paradigms of spatial memory. Apodemus sylvaticus mice were trained in the Barnes maze, a non-invasive test system for spatial memory and untrained mice served as controls. Animals were sacrificed 6h following memory retrieval, hippocampi were taken, proteins extracted and in-solution digestion was carried out with subsequent iTRAQ double labelling. Phosphopeptides were enriched by a TiO2-based method and semi-quantified using two fragmentation principles on the LTQ-orbitrap Velos. In hippocampi of trained animals phosphopeptide levels representing signalling, neuronal, synaptosomal, cytoskeletal and metabolism proteins were at least twofold reduced or increased. Furthermore, a network revealing a link to pathways of ubiquitination, the androgen receptor, small GTPase Rab5 and MAPK signaling as well as synucleins was constructed. This work is relevant for interpretation of previous work and the design of future studies on protein phosphorylation in spatial memory.

    1. Introduction

    Learning and memory (L&M) are processes by which organisms acquire, retain and retrieve information. There is a complex network, a cellular machinery, underlying memory processes and many different chemical signaling messengers are involved. Among them, protein phosphorylation and dephosphorylation events are playing a key role. Dynamic regulation of protein phosphorylation is critically controlling various forms and stages of memory [1–5] and mediate chromatin remodelling and gene transcription that in turn is mediating synaptogenesis [6], cytoskeletal changes that modulate and enable learning and memory [7] and contribute to the activity and localization of synaptic proteins [8]. Phosphorylation/dephosphorylation controls receptor assembly and activities [9] and exerts synaptic transmission [10]. It has also been reported that autophosphorylation of the Ca(2+)/calmodulin(CaM)-dependent protein kinase II (CaMKII) generates partially Ca(2+)/calmodulin (CaM)-independent autonomous activity, which is thought to be required for long-term potentiation (LTP), a form of synaptic plasticity proposed to underlie learning and memory [11].

    John Harshman & co. exemplify how their theories are built on increasingly obsolete (and false) views of biology. This in addition to systematic cherry picking that so underlies the industry they don’t even realize they are cherry picking.

  16. GlenDavidson: The difference is that I understood what Rum was saying there, which was that we can infer from the present into the deep past. He didn’t say that all of the processes are the same, merely that they involve deep time.

    Anything that exists “involves” deep time.

    He was implying that non-Darwinists were hypocritical in that we treat evolution differently than things like weathering.

    If you are granting that there is no reason we should expect biology to be in an any way similar to the processes he mentioned over deep time you are on my side.

    But that renders his entire point mute

    peace

  17. fifthmonarchyman: Anything that exists “involves” deep time.

    He was implying that non-Darwinists were hypocritical in that we treat evolution differently than things like weathering.

    If you are granting that there is no reason we should expect biology to be similar to the processes he mentioned over deep time you are on my side.

    But that renders his entire point mute

    peace

    To you, apparently.

    Glen Davidson

  18. GlenDavidson: To you, apparently.

    Not at all.

    I was just using a handy analogy to explain that we don’t normally expect nature to carve sharp edges that persist over time and if the claim is that Darwinism does this we would expect to see some evidence.

    On the other hand if the Darwinist’s claim is that we see no sharp edges between species then it’s just false.

    peace

  19. Allan Miller: 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.

    Well, I’ll just say that I don’t know why you think it is strong evidence, nor do I know what you think would qualify as only weak evidence.

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

    What is the logic of the inference?

    You understand that there is a decided absence of extensive genetic identity among various groups of organisms yet we still believe they share a common ancestor. So I don’t find the inference to be at all based on extensive genetic identity.

    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.

    I was attempting to put your claim to the test. So in the case of siblings we cannot infer common descent based on extensive genetic similarity?

  20. colewd:
    Rumraket,

    Just like evolution Rum you make a rudimentary example and then claim it explains everything.

    Explains everything? My example explains what it is supposed to explain: Why common descent predicts convergence of independent phylogenies.

    You did this with small molecules binding to proteins to claim that almost any DNA sequence would work in biology forgetting that proteins often have more then one function.

    I have not claimed that “almost any DNA sequence would work in biology. Rather, I have explained that the number of known functional DNA sequences are still so numerous that interdependent function cannot be a prediction of the kinds of “common design” rationalizations you made up.

    I explained that there are clearly different computers that all share similarities Laptops desktops and handhelds.

    Actually you asserted this, which is different from explaining. Nevertheless, yes there are similarities between electronic devices. That’s not what you’re supposed to explain, you’re supposed to explain why there is convergence of independent phylogenies.

    Just because some properties are shared among electronic devices, like computers of various sorts, does not mean they yield convergence of independent phylogenies.

    Bill, what property of computers can we use to build a phylogenetic tree from? Once you have decided on one, what other property can we then use to make another tree from? And will those trees then be similar?

    The trees are similar, Bill. The phylogenetic trees which we infer from shared derived characteristics, like DNA sequences.

    Like DNA and Proteins are common to all life, c-mos transistors are common to all these computers.So are D Ram memory, S Ram memory, E prom memory, capacitors, resistors, inductors, PC boards, LCD or OLED displays.The differences are more in mechanical structure except where handhelds have a different operating system and microprocessor architecture.

    And yet none of those yield phylogenetic trees that are similar Bill.

    My argument is that we can use these computers to build a nested hierarchy which is the result of commonly designed systems and components. We can build the hierarchy structurally and by the commonality of both software and hardware.

    That’s not your “argument”, that is your claim. You claim we can do this. Then do it. Pick a computer manufacturer and build me a nested hiearchy of computers.

    Lets start with laptop which forms its own group where the display is attached to the main computer which contains a keyboard and the display folds on top of the keyboard for easy transportation.

    Yes, laptops are a group. But what is the defining characteristic of laptops? You say the display is attached to the main computer, and contains a keyboard that folds onto the display so it is easy to transport. Is that your defining characteristic of laptops?

    Here’s a mountable server-rack with a display that folds down on the keyobard.

  21. Mung: See, you’re not as ignorant as you think. But if the shape of the skull or spine is different can’t that qualify as a derived/advanced character rather than a primitive one and thus be used for cladistic classification?

    I’m really no the man to ask but yes, I think it can. I don’t know how that is done in practice.

  22. Rumraket: Here’s a mountable server-rack with a display that folds down on the keyobard.

    That is obviously not a laptop. It appears to be a tabletop but looks like it could also be classified as a floortop, groundtop or perhaps even hoodtop.

  23. stcordova: Oh, so why then would you say a Lungfish is more similar to a Pigeon than a Lungfish to a Tuna?

    Again with this “more similar to”. They’re not grouped by similarity Sal.

    The Pigeon has legs, toes, feathered wings… I don’t see them in the Lungfish and Tuna.

    Congratulations, you’ve found a true tetrapod of the avian clade .

    The Lungfish and Tuna have gills to breathe with, the Pigeon does not.

    Lungfish and pigeon also have lungs, the Tuna does not.

    NOTE to colewd: the phylogeneticists here aren’t being very clear about what nested hierarchy the are actually defending. I caught them trying to defend a hierarchy which makes a lungfish and pigeon more similar than a lungfish and tuna.

    You didn’t catch anyone trying to define members of a clade by similarity.

    When pressed for the reasons they do this

    But they DON’T do this.

    You need to start asking yourself this question: If my fundamentalist religious beliefs really are true, why do I have to lie to support them?

    they point out to the methodical cherry picking of characters (i.e.they ignore the fact pigeons have legs, toes, wings etc.) in order to make their groupings.
    No, those are all fully accepted characters, which make it a tetrapod and an avian. They define subdivisions within vertebrates.

    They aren’t even being clear on what nested hierarchy they are defending

    The one with a clade called vertebrates, which contain (among others) two clades called sarcopterygii and actinopterygiii, and inside sarcopterygii you find another clade called tetrapods, and inside tetrapods you find avians.

    This has been crystal clear throughout.

    much less explaining how common descent explains that hierarchy.

    Clade-defining traits aries in populations, which split, and inside those subpupulations there is descent where along the way, new clade-defining traits arise independently in different lineages. These kinds of branching genealogical lines of descent from common ancestors immediately predicts nesting hiearchical groupings (clades) defined by such characters having arisen along the way.

    How does creationism explain it? And I mean actually explain why there should be such subdivisions? Better yet, explain how creationism of any sort would result in convergence of independent phylogenies?

    Meanwhile, keep asking yourself: If my fundamentalist creationist religious beliefs really are true, why do I have to lie to support them?

  24. Mung: That is obviously not a laptop. It appears to be a tabletop but looks like it could also be classified as a floortop, groundtop or perhaps even hoodtop.

    I agree, it’s not a laptop. So the defining characteristic of the “laptop clade” can’t be what Bill Cole suggested.

  25. Rumraket: So the defining characteristic of the “laptop clade” can’t be what Bill Cole suggested.

    Incorrect definition and characterization is a defining characteristic of the “human clade”.

    That does not mean that definition and characterization are not useful or are futile endeavors.

    It only means that our efforts in these regards are never the final authority.

    peace

  26. Alan Fox:
    Has anyone linked to this paper?

    I like how they constructed a phylogeny using 251 genes. An alignment of 251 genes from 22 species was used, and this tree resulted:

    “Multiple sequence alignments of 251 genes with a 1:1 ratio of orthologues in 22 vertebrates and with a full sequence coverage for both lungfish and coelacanth were used to generate a concatenated matrix of 100,583 unambiguously aligned amino acid positions. The Bayesian tree was inferred using PhyloBayes under the CAT + GTR + Γ4 model with confidence estimates derived from 100 gene jack-knife replicates (support is 100% for all clades but armadillo + elephant with 45%)48. The tree was rooted on cartilaginous fish, and shows that the lungfish is more closely related to tetrapods than the coelacanth, and that the protein sequence of coelacanth is evolving slowly. Pink lines (tetrapods) are slightly offset from purple lines (lobe-finned fish), to indicate that these species are both tetrapods and lobe-finned fish.”

  27. Rumraket:

    I like how they constructed a phylogeny using 251 genes. An alignment of 251 genes from 22 species was used, and this tree resulted:

    Cherry picked genes, I showed a gene that gave a different phylogeny, and if we throw in orphan genes, you know where that will go… it won’t give that diagram.

  28. Rumraket:

    They’re not grouped by similarity Sal.

    Why? Why does it bother you and other Darwinists that a lungfish (Sarcopterygii) and a tuna (Actinopterygii ) are more physically similar to each other than a pigeon is to either of them? I tell you why, it emphasizes the mechanistic gap which evolution must overcome, and which Darwinists pretend isn’t there by saying a lungfish is very similar to a pigeon.

  29. Rumraket: The fossil record and comparative genetics exhibit the sorts of patterns we would expect if evolution and common descent was the explanation for life’s diversity.

    You mean the fossil record shows that both poodles and Great Danes can be dogs? Who disagrees with that?

    Rumraket: If you are fine accepting such transformations in physiology can happen within species (as long as we don’t call it evolution), it just makes it all the more hypocritical and perplexing that you reject such transformations between distinct species can happen over deep geological time.

    What do you mean by transformations? Have I “transformed” from my father? is a goldfish “transformed” from every other goldfish?

    You are using the word transformed to mean everything that is not the other thing. A horse is a transformation of a horse. A cat is a transformation of a cat. An elephant is a transformation of an elephant. That elephants tend to look more similar to each other than dogs do is irrelevant. They are all just transformations.

  30. Rumraket,

    Explains everything? My example explains what it is supposed to explain: Why common descent predicts convergence of independent phylogenies.

    You did this with small molecules binding to proteins to claim that almost any DNA sequence would work in biology forgetting that proteins often have more then one function.

    This does not include other requirement that Sal has mentioned like phosphorylation.

    I have not claimed that “almost any DNA sequence would work in biology. Rather, I have explained that the number of known functional DNA sequences are still so numerous that interdependent function cannot be a prediction of the kinds of “common design” rationalizations you made up.

    Small molecules binding to proteins simulate very little of real biological function. If you take your genetic simulation out 12 generations you will get garbage trees due to your high mutation rate.

    Living organisms have genomes of which only 2% are coding genes and certain segments of the genome can be more susceptible to mutations. Living organisms have proteins that may have to bind with several other proteins or become part of a multi protein complex.

    Your experiments have not really addressed the common design argument as they are too dissimilar from multicellular organisms cellular function.

    Actually you asserted this, which is different from explaining. Nevertheless, yes there are similarities between electronic devices. That’s not what you’re supposed to explain, you’re supposed to explain why there is convergence of independent phylogenies.

    What if I were to say to you that in order to show a living nested hierarchy you had to show convergence of c mos gates 🙂

    None the less, the gate type and count nicely converges between similar laptops. If I were to show memory gate similarity and logic gate similarity the trees should agree. If I were to stratify by weight and battery life vs logic and memory gate similarity again the trees would agree. Common design can build a nested hierarchy.

    Yes, laptops are a group. But what is the defining characteristic of laptops? You say the display is attached to the main computer, and contains a keyboard that folds onto the display so it is easy to transport. Is that your defining characteristic of laptops?

    They can be defined by
    -size
    -weight-
    -battery
    -portability
    -power consumption
    -keyboard screen and computer single foldable unit

    If we nest the mac laptop that would include a group of laptops that most simulate common design as they are built by the same company.

  31. phoodoo,

    Rumraket: If you are fine accepting such transformations in physiology can happen within species (as long as we don’t call it evolution), it just makes it all the more hypocritical and perplexing that you reject such transformations between distinct species can happen over deep geological time.

    In species variation tells you very little about transformation. To have a transformation you need a 5 to 100 times greater change in DNA sequences then in species variation. You also need epigenetic changes that Sal can address.

    Or we may transform the skeptical zone into the hypocritical zone 🙂

  32. stcordova: The definition used “and/or” for notochord, you can’t even mince words properly in your petty objection.

    How is it “structural” to present two characters, either of which you consider enough, and one of which diagnoses a much wider group? Vertebrates have vertebrae (or arcualia, which we can consider homologous), while chordates have notochords, or don’t. How can this “structural classification” work if some of the members of a group don’t have the structure in question? Are snakes tetrapods? Are whales? I think your notions have problems.

  33. stcordova: a pigeon is structurally and geometrically more similar to a lungfish than a tuna to a lungfish. He needs to provide his answers in terms of geometry, not phylogenetic phantasies and sophistry.

    It’s not about similarity. It’s about special similarity, i.e. nested hierarchy. Pigeons aren’t necessarily more similar overall to lungfish than to tuna, but they have derived characters in common with lungfish. You can tell this by assembling a tree. Doesn’t have to be a phylogenetic tree; as you note you can do the analysis without assuming phylogeny. Now, lungfish don’t have humerus, radius, ulna, and metapodials; those diagnose a narrower group than Sarcopterygii, but that group includes Eusthenopteron, Panderichthys, and Tiktaalik. Since you can’t actually address these fossils and their characters, you choose shameless ridicule instead.

    Now since John recommended I re-read Joe Felsenstein’s book, this is what I recommend to John from first grade science:

    https://i.pinimg.com/736x/92/59/40/9259406266a87c6baaec75b37581d518–classifying-animals-classroom-charts.jpg

    Now it’s not 100% accurate, but close. Lungfish breathe with a lung but also have some respiration with gills. Whales and dophins also live in water, etc. But it’s a lot better than what John is trying to teach.

    Well, your abilities have finally graduated from kindergarten to first grade level, but that isn’t much of an improvement. Thanks for the insults, though.

  34. Mung: It depends on who you ask.

    True. If you ask Sal, you get one answer. If you ask anyone who knows anything about systematics, you get another answer. Which would you consider more likely?

  35. stcordova: Why?Why does it bother you and other Darwinists that a lungfish (Sarcopterygii) and a tuna (Actinopterygii ) are more physically similar to each other than a pigeon is to either of them?I tell you why, it emphasizes the mechanistic gap which evolution must overcome, and which Darwinists pretend isn’t there by saying a lungfish is very similar to a pigeon.

    No, your “mechanistic gap” is once again confusing the origin of novelty with the origin of nested hierarchy.

    As for similarity, note that, in the tree Rumraket showed above, the coelacanth and lungfish are more similar (genetically) to each other than either is to the birds, and yet the lungfish is more closely related to the bird than to the coelacanth. (Notice also that the coelacanth is more similar to the bird than the lungfish is.) Mere similarity doesn’t cause the nested hierarchy; it’s shared derived similarity that counts.

    We’re really racking up a long list of things you don’t understand about biology.

  36. stcordova: Cherry picked genes, I showed agene that gave a different phylogeny, and if we throw in orphan genes, you know where that will go… it won’t give that diagram.

    Once again you accuse scientists of fraud. Will you at least admit that’s what you’re doing? You showed a mitochondrial gene that, if provided with a much poorer taxon sample than the study Rumraket referenced, produces one different node. How is that relevant? Why isn’t preferring one mitocondrial gene to a couple hundred nuclear genes cherry picking?

    And I bet that if you threw in lots of orphan genes you would get the same tree as in Rumraket’s cited study. I’ve already told you two ways to deal with the data: treat missing genes as missing data and create a binary presence/absence matrix. Either one would give you the standard tree.

  37. Sal

    Lungfish breathe with a lung but also have some respiration with gills

    Insufficient for survival for some since they drown if deprived of assess to the atmosphere. Kinda like a pigeon.

    Their circulatory system also separates pulmonary and systemic blood flow. More like a pigeon than a tuna.

  38. John Harshman:

    It’s not about similarity.

    and

    Rumraket:

    They’re not grouped by similarity Sal.

    So, ladies and gentleman, the pattern of similarity isn’t what they are talking about when they are talking about nested hierarchy.

    John Harshman:

    they have derived characters in common with lungfish.

    What is a derived character? Is that something defined in terms of common descent? It’s otherwise meaningless without the assumption of common descent. If so, there you go again John, demonstrating you are using circular reasoning to describe geometric structural and physiological relationships.

    You have, as I pointed out in the OP, are conflating what people intuitively in their minds consider the real nested hierarchy, which is structural, not phylogenetic.

  39. John Harshman:

    Once again you accuse scientists of fraud

    No, just being mistaken and in the case of evolutionary biologists, rather self-delusional and illogical. Sorry, your professed field of expertise is rather low in science’s pecking order compared to other scientific disciplines. The way you’ve argued your case, the amount of circular reasoning and equivocation and cherry picking on display confirms what Jerry Coyne said:

    In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to [the pseudo science of] phrenology than to physics

    Jerry Coyne
    World Famous Evolutionary Biologist

    I don’t have any arguments with chemists about chemistry, almost no arguments with physicists about physics, no arguments with biochemists about biochemistry, no arguments about physiologists about physiology, NEVER an argument with mathematicians about mathematics. But when it comes to evolutionary biology, it just never ends. Is that because of my religious belief? Partly, but when guys say, “we’re Sarcopterygiian fish” your going to be called on saying stupid stuff especially if you’re promoting it as science. It’s not science, it’s story telling, circular reasoning, equivocation, cherry picking, etc.

    What would be more straight up on your guys part if you simply admitted all you have is a belief system that only pretends to be on par with other scientific disciplines.

  40. John Harshman:

    I bet that if you threw in lots of orphan genes you would get the same tree as in Rumraket’s cited study.

    So you’re making a bet, you actually don’t know! It doesn’t even bother you mammals have a different immune system than any fish.

    You can’t show skeletal structure of tetrapods is similar to fish. So you punt and say the argument isn’t about similarity.

    You can’t show the immune systems of mammals are similar to fish.

    You can’t show the thermo regulation of birds and mammals are similar to fish.

    You obviously can’t show orphan genes that are unique to mammals and birds and not in lungfish and coelecanths are similar (obviously).

    So you punt and say the evolutionary groupings are about similarity. So evolutionary groupings are about evolutionary groupings, not about grouping according to similarity. It’s circular reasoning and the only pattern that is explained is circularly-reasoned patterns explained by circular reasoning.

    Common descent doesn’t explain the structural patterns that are deduced purely in terms of structural relationships. Well done John.

  41. stcordova: Cherry picked genes, I showed agene that gave a different phylogeny, and if we throw in orphan genes, you know where that will go… it won’t give that diagram.

    Oh, the irony, Sal!

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