Phylogenetic Systematics

Posted on by

Let’s have a serious discussion about phylogenetic systematics.

What are the assumptions, the methods, and the inferences that can be drawn from phylogenetic analysis.

For example, is there anything to the creationist claim that phylogenetic systematics assumes common ancestry and does it even matter?

I’ll be using a number of different references such as Molecular Evolution: A Phylogenetic Approach and Molecular Evolution and Phylogenetics.

This thread will not be password protected, but it will be protected by angels.

1,034 thoughts on “Phylogenetic Systematics”

  1. Rumraket,

    Two things are known that can do this:
    1. Common descent.
    2. A designer that is deliberately forcing the genes to exhibit a similar genealogical branching pattern.

    3. An efficient design strategy that uses similar components across the designs.

  2. Rumraket: But why would the designer be deliberately forcing the genes to exhibit a similar genealogical branching pattern?

    That is a nonsensical question.

  3. Rumraket: That would be extremely deceptive, because it makes it look like the organisms really did go through a branching genealogical process.

    What deception? If the process you describe does not in fact exist how can some other process be “deceptive” with respect to this other process that does not exist?

  4. colewd:
    Rumraket,

    3. An efficient design strategy that uses similar components across the designs.

    You know very well that an efficient design strategy uses the same components across the designs, as in Macs. It’s evolution (common descent) that ends up with similar, yet different, components across the “designs.”

    Glen Davidson

  5. Part 1 of 3.

    At present the methodology of phylogenetic reconstruction is quite controversial. There seem to be at least three reasons for this controversy, putting aside personal preferences. First, some workers were originally trained as systematicists using morphological characters, and they tend to be suspicious about any methods that are based on mathematical models of evolutionary changes, because the evolutionary change of morphological characters is so complex that it does not obey any simple rule. They therefore prefer parsimony methods, which require a minimum number of assumptions. Another group of workers has been trained as geneticists or molecular biologists and tends to prefer using analytical approaches but does not trust highly sophisticated mathematical models. A third group of workers is primarily trained as mathematicians or statisticians and tries to understand the construction of phylogenetic trees as a mathematical problem rather than a practical problem, using abstract mathematical concepts. Since the approaches used by the three groups of workers are quite different, controversies naturally occur.

    – Molecular Evolution and Phylogenetics (2000). p. 84.

    Any thoughts on whether this state of affairs still exists?

    Also, if the methods of all three groups produce the same results, why would there be any need for controversy? My inference is that the differing methods produced differing results. Why is that inference wrong?

  6. GlenDavidson,

    You know very well that an efficient design strategy uses the same components across the designs, as in Macs.

    Nonsense. The Mac air uses a silicon mass storage system. The Mac Book uses disc mass storage. Their can be variation in other components as well.

  7. colewd:
    Rumraket,

    Why do you believe there are so many possible changes if the design is efficient?

    For two reasons. I see the diversity of possible functional sequences in life that exists, and many more have been created in the laboratory and found to work. Even without the laboratory creations, the number of similar (but not identical) and functional sequences used in life makes it extremely improbable that multiple independent sequences designed to have different functions, but which are not being deliberately designed to yield a particular branching topology, would happen to converge on the same phylogeny.

    As I directly demonstrated to you in the common design vs common descent thread. If a designer is creating multiple genes, and wants those genes to be slightly different for each species she creates, but is making them slightly different because they need to be different for reasons of function, it is extremely unlikely that each set of such similar but different genes, will yield a similar tree if analyzed by the same phylogenetic algorithm.

    Every different animal contains nucleotides and amino acids and the genetic code.There are many ways to make a nand gate but designers use standards to make designs more efficient. Efficient design restricts choices as evidenced by Mac designs and forms a hierarchy of similarity and differences.

    Yes it does Bill, but it doesn’t restrict choises such that it forces the changes to converge on a similar tree topology.

    How many times do you need this already proven fact repeated to you?

  8. Mung: I did explain why. Let me try again. You cannot mimic something that cannot be mimicked. Would you at least agree with that?

    Yes, with the premise “it cannot be mimicked” taken to be an established fact, then it follows that it cannot indeed be mimicked. Well done Mung.

    And what sorts of things cannot be mimicked? Things that do not exist. Would you also agree with that?

    No, I would not agree with that as it is superficial and simplistic.

    Do things which are imagined, for example in books (like science fiction novels), exist or not exist?

    Take Darth Vader from the Star Wars franchise. Does Darth Vader exist? I would say no. But I do believe Darth Vader can be mimicked. There is some novel that describes the imagined character Darth Vader. This character can be mimicked by an actor playing the part of Darth Vader.

    In this way Darth Vader is an idea, or a concept. It exists as an idea, or as a concept.

    Common descent could exist as an idea, or a concept, and can thus be mimicked in the same way. What would Darth Vader do? What would happen if Darth Vader were to exist?

    In the same way, what would follow if common descent really happened? What would happen if species went through common descent?

    This is basically what is known in philosophy as a hypothetical.

    If “common descent” does not exist it cannot be mimicked.

    It sure as hell can.

    Q.E.D.

    FIFY.

  9. colewd:
    Rumraket,

    3. An efficient design strategy that uses similar components across the designs.

    Yeah Bill that doesn’t actually yield consilience of independent phylogenies. For reasons explained to you now like, what, twenty times?

  10. Rumraket: But why would the designer be deliberately forcing the genes to exhibit a similar genealogical branching pattern?

    No, it’s an extremely pertinent question.

    I know of a designer who did exactly that. His name is Sal Cordova. He deliberately designed a set of genes to exhibit a similar genealogical branching pattern. And we even know the answer to my question (why did he do that?) – to prove that he could.

    So not only is it an entirely sensible question, in some situations it is even answerable.

    But for those of you who reject common descent, but nevertheless have to contend with the fact that independent genes converge on a similar branching topology, the question stands: Why would your designer be deliberately forcing the genes to exhibit a similar genealogical branching pattern?

    And if you do not believe your designer is actually doing that, then why do they exhibit a similar genealogical branching pattern?

  11. Rumraket,

    Even without the laboratory creations, the number of similar (but not identical) and functional sequences used in life makes it extremely improbable that multiple independent sequences designed to have different functions, but which are not being deliberately designed to yield a particular branching topology, would happen to converge on the same phylogeny.

    We don’t see convergence with different functions. We see it with modifications of the same function. Modification of the beta catenin sequence requires modification of probably 10 proteins it interacts with. Convergence is what I would expect with intentional design change.

  12. Rumraket,

    But for those of you who reject common descent, but nevertheless have to contend with the fact that independent genes converge on a similar branching topology, the question stands: Why would your designer be deliberately forcing the genes to exhibit a similar genealogical branching pattern?

    If designed gene change to gene A makes a required compatible change to gene
    B,C,D and E we would expect convergence.

    Design would be a much better explanation for multiple compatible changes in nuclear proteins.

  13. Mung: Any thoughts on whether this state of affairs still exists?

    I believe it still does. I can even see their respective points.

    Also, if the methods of all three groups produce the same results, why would there be any need for controversy?

    They don’t always produce the exact same results. They’re almost always very similar, and similar enough for it not to be a probem in the broader sense that they are still significantly similar, but I think the controversy arises from the fact that we are human and we’re just not satisfied with approximate truthes.

    From the quote you gave I can see at least two major camps. The people to whom method trumps results, and the people with the opposite inclination. And I’m sure everything in between, and that they sometimes go back and forth.

    In one camp there are methodological purists who want to minimize assumptions (which basically guarantees inaccuracies, but at least you can’t be charged with having “poisoned” your result with potentially unfounded assumptions), and in another camp there are precision fetishists who aren’t that afraid of how they get there, as long as they get it done.

    My inference is that the differing methods produced differing results. Why is that inference wrong?

    It’s largest failure is it’s superficiality and vagueness.

    There are lots of data sets for which the different methods give exactly identical results under most reasonable parameters. But even in the cases where they don’t, they’re still highly similar. In the same way that the same algorithm on a number of independent genes will give a similar but not exactly identical tree, using different algorithms on the same dataset can give similar but not exactly identical trees.
    The differences are important in the sense that they it more difficult to estimate what the true phylogeny might be, but in the greater scheme of things it’s not like they throw the whole field into doubt.

  15. Rumraket: No, I would not agree with that as it is superficial and simplistic.

    Given that you believe that it is possible to mimic something that does not exist I don’t see much reason to continue. One last attempt. How would one go about mimicking something which does not exist? What would they mimic?

  16. DNA_Jock: That is an idiotic lampoon of evolution.
    For a linguist, you sure find comprehension a challenge.

    How is it possible to lampoon evolution? Lampoon a theory that says, well, random things happened, luckily, and some of those random things, well, they turned out to be pretty good at living. One can lampoon that? By making it sound even MORE ridiculous?

    One can lampoon the idea that an egg shell came about by lucky accidents that just so happened to have a reproductive advantage?

    One can lampoon the idea that if you have a light sensitive patch SOMEWHERE on an organisms body, and that happens to get a random mutation which causes a dent right in the middle of that patch, well, it better than no dent, so you will probably have more babies then those without the dent. One can lampoon THAT??

    The lampoon surely can’t be as funny as the real proposal.

  17. colewd:
    GlenDavidson,

    Nonsense.The Mac air uses a silicon mass storage system.The Mac Book uses disc mass storage.Their can be variation in other components as well.

    Oh please, I was responding to what you said about “similar components,” not to different parts, which are also possible (and which may show up in quite unrelated machines as well). Don’t pull a subject switch in order to avoid the issue.

    You keep on playing with words in order to avoid dealing properly with the evidence.

    Glen Davidson

  18. GlenDavidson,

    You keep on playing with words in order to avoid dealing properly with the evidence.

    Not playing with words at all. The “brains” or microprocessors of different Macs can have slight variations. Also changes in generations can have fundamental changes to architecture while still holding to the basic transistor and gate design.

    The logic that connects from a solid state drive to main memory is similar to the logic that connects to disc memory.

    If Rum looked at the logical output of one’s and zero’s (represented by voltage levels) he would claim common ancestry and phylogenetic convergence and argue that adult Macs can have babies 🙂

  20. Mung: But the designer would not be mimicking common descent.

    What would the designer be doing, then? What would be the point of creating new species modeled on the old ones with just the number and type of differences that would be generated by random mutation?

    I do however believe he used a process of descent with modification where the modifications were not “mistakes” or “errors” in copying..

    What is your evidence that he used descent with modification, if you don’t think the nested hierarchy is such evidence?

  21. colewd:
    John Harshman,

    The tree is how the data is arranged.The data does not require a conclusion of loss of flight because there is so much sequence variation.

    I still have no idea what this emphasis on sequence variation means to you. Could you tell me?

    What is driving the mutation?

    Are you asking for a primer on mutation? Most mutations result from errors during replication.

  22. colewd: I think 1% or less difference in both sequence variation, phosphorylation patterns and alternative splicing patterns would support common descent. Anything greater would create the mine field dilemma especially with complex nuclear proteins. Based on this my tentative conclusion is that crocks share a common ancestor but flightless birds do not.

    But that’s a number you just made up, based on nothing. Also you should note that most of the data doesn’t involve proteins; they’re mostly intron sequences that have no actual function. You believe what you want to believe.

  23. Mung:
    And what sorts of things cannot be mimicked? Things that do not exist. Would you also agree with that?

    Good try. But no. It isn’t necessary for common descent to exist in order to mimic it. All you have to do is to produce the sort of data it would produce if it existed.

  24. colewd to Glen Davidson:

    Nonsense. The Mac air uses a silicon mass storage system. The Mac Book uses disc mass storage. Their can be variation in other components as well.

    Well said. Merry Christmas.

    The gene can be thought of as a basic mother board or chassis for miniaturized RAM. The RAM patterns of phosphorylations of amino acids are different between species.

    Depicted below are 3 species with segments of the TopoIsomerase IIA homologs. I sent this recently at the request of a professional biochemist researching TopoIsomerases in connection with chemotherapy research. Since I’m a bit of a data clerk, it was a natural task for me.

    A publication in the mid 1990’s showed that we can insert human TopoIsomerase II into a yeast, and as far as chromosome segregation, it works fine for the yeast. Would anyone dare think of doing the reverse considering the importance of phosphorylation in the process of memory and cognition?

    Phosphorylation in the brain can change rapidly by factors of 2 in the process of learning based on a study where they trained rats in a maze and then examined the phosyphorylation degree in their brains compared to a control group that weren’t trained. The phosphorylation acts like a miniature RAM.

    See:
    https://www.sciencedirect.com/science/article/pii/S0166432814000618

    But back to the diagram of this amazing Random Access Memory machine that is species specific on the TopoIsomerase IIA protein:

    Row 1: yeast
    Row 2: chicken
    Row 3: human

    The Red triangles are the phosyphorylation marks on the human, the green on the yeast. I omitted the chicken because UNIPROT has no reports on the chicken. The purple stars are the lysine acetylation positions. I omitted the huge amount of ubiquitination positions effected by SUMO (that’s a whole nother story).

    http://theskepticalzone.com/wp/wp-content/uploads/2017/12/human_1295_1377_yeast_1252_1272_mhy.png

    http://theskepticalzone.com/wp/wp-content/uploads/2017/12/human_1387_1449_yeast_1353_1356_mhy.png

    http://theskepticalzone.com/wp/wp-content/uploads/2017/12/human_1469_1525_yeast_1408_1423_mhy.png

    In human Topoisomerase IIA, 11 of the 25 positions involving S (Serine) are followed by a D (Aspartic acid). So we have the “SD” motif over represented. A rough calculation using the binomial distribution indicates the odds of that happening by chance are 1 in 80 million. That difference is not consistent with random mutation changing genes in the evolution of higher eukaryotes, it suggests the differences have functional significance for the molecular Random Access Memory specific to the architecture of the species.

  25. colewd:
    GlenDavidson,

    Not playing with words at all. The “brains” or microprocessors of different Macs can have slight variations.Also changes in generations can have fundamental changes to architecture while still holding to the basic transistor and gate design.

    Yes, and the changes to architecture need not be derivative at all. Unlike with life.

    The logic that connects from a solid state drive to main memory is similar to the logic that connects to disc memory.

    How else would it work? But a solid state drive has no relation to a hard drive. You simply don’t get that in life.

    If Rum looked at the logical output of one’s and zero’s (represented by voltage levels) he would claim common ancestry and phylogenetic convergence and argue that adult Macs can have babies

    Hardly. Did you already forget your earlier statement?

    Nonsense. The Mac air uses a silicon mass storage system. The Mac Book uses disc mass storage. Their can be variation in other components as well.

    How are silicon storage and disc storage related? Not at all. That’s what you simply don’t get out of life, completely novel organs or systems appearing out of the blue. I have no idea why you keep dancing around such a colossal difference between life and designed entities.

    Glen Davidson

  26. Mung: Given that you believe that it is possible to mimic something that does not exist I don’t see much reason to continue. One last attempt. How would one go about mimicking something which does not exist? What would they mimic?

    They would mimick what would happen if common descent did exist.

    Here let me copy and paste the answer you already recieved:

    “Do things which are imagined, for example in books (like science fiction novels), exist or not exist?

    Take Darth Vader from the Star Wars franchise. Does Darth Vader exist? I would say no. But I do believe Darth Vader can be mimicked. There is some novel that describes the imagined character Darth Vader. This character can be mimicked by an actor playing the part of Darth Vader.In this way Darth Vader is an idea, or a concept. It exists as an idea, or as a concept.What would Darth Vader do? What would happen if Darth Vader were to exist?

    Common descent could exist as an idea, or a concept, and can thus be mimicked in the same way. What would follow if common descent really happened? What would happen if species went through common descent?

    This is basically what is known in philosophy as a hypothetical.”

    I’m honestly rather astonished that you’d try to weasel out of this with such a pathetic semantical trick as arguing you can’t mimick something that doesn’t exist. How absolutely ridiculous.

  27. stcordova: The RAM patterns of phosphorylations of amino acids are different between species.
    (…)
    That difference is not consistent with random mutation changing genes in the evolution of higher eukaryotes, it suggests the differences have functional significance for the molecular Random Access Memory specific to the architecture of the species.

    What is the implication for the “baramins” or biblical “kinds” of this statement?

    Don’t you need pretty much all extant species on the Ark then, if “RAM patterns” are different between species and simultaneously is a barrier to evolution?

    This doesn’t bode well for your Young Earth Creationist Great Flood story.

  28. By the way Sal, your whole argument from “RAM” here is completely nonsensical. RAM can only function as RAM if it is editable and rewritable. It has to be possible to change it basically on the fly, as memories are stored, deleted, rewritten and so on.

  29. Erik,

    Amen. a formal valedidation of the tree is not a formal valedition of common descent!
    Exactly. The tree existing, as far as it does, is only evidence of this tree.
    The hypothesis for it must be open. to any possible option.
    INSTEAD evolutionism insisted there was only one option and NO creationist option.
    even though the creationist one was first in history, and they claim they were overthrowing it.!
    Its careless science thinking or extreme prejudice. (also not science).
    If evolutionism in this issue wants intellectual credibility THEY must allow for a creaor option for likeness in biology. A common Design hypothesis.
    They must beat that or admit they only allow one option. sop one conclusion.
    Why? Are they admitting common descent has no evidence except no other option?!
    Is this a Christmas gift??

  30. Mung,

    What deception? If the process you describe does not in fact exist how can some other process be “deceptive” with respect to this other process that does not exist?

    You don’t think genealogical processes exist, now? Or is this some kind of hypothetical not applicable to our present world?

  32. DNA_Jock: See Erik, this is how you come across.

    Agreed. That same unwillingness to put aside whatever that is in favour of some humble open mindedness is awesome in it’s way.

    What I find fascinating is the asymmetry. They are simply trying to convince you that you are wrong without simultaneously trying to convince you of what is right. They don’t actually know what is right (beyond “god did it”), but they sure know what is wrong….

  33. DNA_Jock:
    See Erik, this is how you come across.

    Yes Erik, you come across as not lampooning evolution, but rather as reiterating evolution.

    Who needs mocking, when you have evolutionists.

  35. Rumraket:

    By the way Sal, your whole argument from “RAM” here is completely nonsensical. RAM can only function as RAM if it is editable and rewritable. It has to be possible to change it basically on the fly, as memories are stored, deleted, rewritten and so on.

    Well, well, well…..
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415845/

    Phosphorylation sites are formed by protein kinases (‘writers’), frequently exert their effects following recognition by phospho-binding proteins (‘readers’) and are removed by protein phosphatases (‘erasers’). This writer–reader–eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.

    “Major inventions”? Like new designs on a species specific level. Yep.

    I proved my point.

  36. John Harshman: Good try. But no. It isn’t necessary for common descent to exist in order to mimic it. All you have to do is to produce the sort of data it would produce if it existed.

    But we do not know what sort of data common descent would produce if it existed. Rather, what we do know is what sort of data would be produced by an intelligent designer who creates species from scratch by copying existing species and making changes in the copying process.

    You can’t then take that data and claim that it is the same sort of data that common descent would produce. Well, you could, but there is no evidence for that claim.

  37. DNA_Jock:
    phoodoo will be here all week. Veal . Waitress.

    I am pretty funny, I admit. But a lucky light sensitive patch, getting a lucky indentation, which makes you better at getting laid. And then a lucky liquid filled cavity shows up, which makes you even better at getting laid. And then a lucky iris, which makes you incredibly even better at getting laid? That’s fucking hilarious. I ain’t that dam funny.

    And then the same thing happens for a million other things?

    I don’t care what kind of lucky joke telling mutation you get, which makes you great at getting laid, NOBODY is THAT funny!

  38. Allan Miller: You don’t think genealogical processes exist, now? Or is this some kind of hypothetical not applicable to our present world?

    We’re discussing a world where common descent does not exist. For all we know it could be this world. It is described in this post:

    Phylogenetic Systematics

  39. phoodoo: I am pretty funny, I admit.

    😀

    ETA:

    phoodoo: I don’t care what kind of lucky joke telling mutation you get, which makes you great at getting laid, NOBODY is THAT funny!

    What about asexual organisms? Is that why they never evolved an eye?

  41. Rumraket: I’m honestly rather astonished that you’d try to weasel out of this with such a pathetic semantical trick as arguing you can’t mimick something that doesn’t exist. How absolutely ridiculous.

    Darth Vader exists as a fictional character. By analogy, common descent is a fictional process.

    Now let’s take a concrete example, the fictional process of turning lead into gold. Any thoughts on how to mimic that process?

  42. John Harshman: What would the designer be doing, then?

    The designer would be creating new things from existing things. Just like designers are known to do.

    What would be the point of creating new species modeled on the old ones…?

    Diversity. Just like designers are known to do.

    … with just the number and type of differences that would be generated by random mutation?

    The claim that random mutations can do what a designer can do is in dispute. 🙂

  43. stcordova: Well, well, well…..
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415845/

    “Major inventions”?Like new designs on a species specific level.Yep.

    I proved my point.

    Additionally, and piling on:
    http://www.cell.com/molecular-cell/pdf/S1097-2765(03)00139-4.pdf

    Contingent Phosphorylation/Dephosphorylation Provides a Mechanism of Molecular Memory
    ….

    and

    https://www.ncbi.nlm.nih.gov/pubmed/26980786

    Phosphorylation of K+ channels at single residues regulates memory formation.

    Vernon J1, Irvine EE2, Peters M3, Jeyabalan J1, Giese KP4.

    Phosphorylation is a ubiquitous post-translational modification of proteins, and a known physiological regulator of K+ channel function. Phosphorylation of K()channels by kinases has long been presumed to regulate neuronal processing and behavior. Although circumstantial evidence has accumulated from behavioral studies of vertebrates and invertebrates, the contribution to memory of single phosphorylation sites on K+ channels has never been reported. We have used gene targeting in mice to inactivate protein kinase A substrate residues in the fast-inactivating subunit Kv4.2 (T38A mutants), and in the small-conductance Ca2+ -activated subunit SK1 (S105A mutants). Both manipulations perturbed a specific form of memory, leaving others intact. T38A mutants had enhanced spatial memory for at least 4 wk after training, whereas performance in three tests of fear memory was unaffected. S105A mutants were impaired in passive avoidance memory, sparing fear, and spatial memory. Together with recent findings that excitability governs the participation of neurons in a memory circuit, this result suggests that the memory type supported by neurons may depend critically on the phosphorylation of specific K+ channels at single residues.

    So phosphorylation of a single amino acid residue can be important to regulating memory. Thus the molecular RAM is important for our ability to remember and learn!

    If I’m not mistaken the K+ channel in eukaryotes is analogous to this K channel in bacteria, except the K+ channel in eukaryotes has a memory device attached to it to improve regulation:

    But in any case, Rumraket, you can probably guess from the studies cited, the RAM metaphor isn’t going away, and we’re only going to learn more about God’s mind boggling molecular designs if civilization stays viable for the next few decades….

  44. John Harshman: What is your evidence that he used descent with modification, if you don’t think the nested hierarchy is such evidence?

    Not sure I understand the question. I think descent with modification serves as an explanation for the nested hierarchy. I find it superior to “common descent” as an explanation because it at least attempts to explain the origins of the innovations that lead to the nesting pattern. The twiddling bits that the supporters of “common descent” are trying to avoid lest they have to explain what they cannot explain.

  45. Part 2 of 3:

    At present the methodology of phylogenetic reconstruction is quite controversial. There seem to be at least three reasons for this controversy…

    Second, some scientists are primarily interested in short-term evolution within species or between closely related species, whereas others are interested in long-term evolution dealing with different orders, phyla, or kingdoms. The methodologies used by these two groups of scientists are quite different, and one group tends to feel wary of the approach used by the other group.

    – Molecular Evolution and Phylogenetics (2000). p. 84.

    I hope to discover why “the methodologies used by these two groups of scientists are quite different” and whether that is still the case.

    ETA:
    Part 1

  46. Mung: The claim that random mutations can do what a designer can do is in dispute. 🙂

    And its also a punchline.

  48. keiths: Imagine trying to get through life using Mung logic.

    With God, all things are possible.

    Merry Christmas keiths.

    ETA: Hope you have fun mimicking Santa Claus tonight.

  49. Mung: Not sure I understand the question. I think descent with modification serves as an explanation for the nested hierarchy.

    If both common descent and descent with modification explain a nested hierarchy what are differences?

    I find it superior to “common descent” as an explanation because it at least attempts to explain the origins of the innovations that lead to the nesting pattern.

    How is the implementation of these innovations explained beyond someone did something ,somehow?

    The twiddling bits that the supporters of “common descent” are trying to avoid lest they have to explain what they cannot explain.

    In my experience design advocates take the backseat to no one when comes to avoidance .

  50. I have a few questions if anyone is interested

    1)Are there any possible systematics that would allow us to place organisms in ever smaller groupings and at the same time rule out common decent?

    2) Does this nested hierarchy suggest common decent?

    https://www.thinglink.com/scene/494574238494097410

    3) What about the one found in the image below?

    Thanks in advance
    peace

Leave a Reply