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.

5,163 thoughts on “Common Design vs. Common Descent

  1. So common descent predicts a nested hierarchy if the random sequence generator doesn’t generate random sequences?

    So we get this random gene duplication, and then that sequence diverges from the original sequence due to random changes, until magically it’s expressed and found to be useful (by george!) also at random, but that’s not really random sequence generation, and the data isn’t generated at random.

    Why doesn’t someone just admit that John is wrong?

    John Harshman: Randomized data don’t have a hierarchical structure.

    Sure it does. It’s what comes of “unguided evolution.” And “unguided evolution” is the only reasonable explanation for the hierarchy.

  2. keiths: I know that, Mung. My point, once again, is that you don’t know why common descent is such a solid conclusion:

    Well, I do know though that it’s not because “unguided evolution” “predicts” the very hierarchy that we observe.

  3. Mung actually believes that the only reason genomes aren’t completely uncorrelated is because mutations are guided.

    Wow.

  4. Mung: So you accept that the first template copying process was created?

    How does that follow from anything I’ve said? Please lay that one out in finely-grained detail for me.

    All you have is this post-hoc claim that the initial data is not random therefore the source of the data isn’t random.

    LOL. You’re confused again. No, the claim is that it takes very long time for the random mutations to completely erase phylogenetic signal under most biologically realistic conditions.

    Whether the very first sequence was created, or generated at random, is actually completely irrelevant to the inference of common descent. The fact that it is faithfully copied over and over again, and occasionally a mistake sneaks in, and that divergence happens as populations split up, is the key factors at work.

    You have this initially not random set of data and then everything added to that is random. That’s your story?

    No.

    Admit it. The data comes from a random generator.

    No, the data comes from the copying of templates with occasional mutations.

    Whether those mutations are random is actually not particularly relevant.

    There’s no reason on evolution to expect the actual phylogenies that we see.

    Correct. But a total irrelevancy. The fact that independent phylogenies are significantly congruent with each other is what you expect on common descent.

    All the arguments that you have in their favor are arguments that the data is not random.

    This doesn’t even make sense at all.

    Random changes to sequences are all you have, unless you accept design.

    You’re so throughly confused, and you managed to do it to yourself. Whether the mutations that happen are random or not is actually irrelevant. The only criterion for the inference of phylogeny is that it isn’t the same changes happening in parallel over and over again in independent lineages, and that the rate of mutation isn’t so high that the signal is no longer detectable.

    The nested hiearchy could have been created with a theistic evolution-type designer behind the scene “guiding” the process of selection, or even making some particular mutation happen here and there. As such, it is at least concievable they aren’t random, yet they’d still yield a nesting hiearchy of life.

  5. keiths: Once more into the breach.

    LoL. Little man with finger in a dyke?

    Mung, do you seriously think that if mutations are random, all genomes must be completely uncorrelated?

    No.

    Do you think that John thinks that Salvador thinks that all organisms are specially created with their genomes randomly generated?

    If “randomized data don’t have a hierarchical structure,” and we have before us a hierarchical structure, then it follows that the data is not randomized.

    What is wrong with that logic?

  6. Mung:

    If “randomized data don’t have a hierarchical structure,” and we have before us a hierarchical structure, then it follows that the data is not randomized.

    What is wrong with that logic?

    You’re assuming that if mutations are random, then “the data” must be random. That’s dumb.

    Evolution is more than just mutation.

  7. keiths: You’re assuming that if mutations are random, then “the data” must be random. That’s just dumb.

    I agree that random mutations does not imply random data. The whole point of inferring phylogenies is to make use of patterns of correlation that come from recency of common ancestry. Only if the common ancestor were very long ago, and each present species had evolved independently from that common ancestor (with no more recent common ancestors of any set of species) would we see random data.

    Evolution is more than just mutation.

    Well, actually, even if it were just mutation, with no natural selection, we would be able to infer phylogenies from the pattern of distribution of the mutant alleles.

  8. keiths:

    Once more into the breach.

    Mung:

    LoL. Little man with finger in a dyke?

    More like “The cat threw up, and someone’s got to clean it up. I guess I will.”

  9. Joe:

    Well, actually, even if it were just mutation, with no natural selection, we would be able to infer phylogenies from the pattern of distribution of the mutant alleles.

    Except that Mung seems to be unaware that parents pass genes to their offspring. He thinks that if mutation is random, then every genome should be random:

    Admit it. The data comes from a random generator. There’s no reason on evolution to expect the actual phylogenies that we see. All the arguments that you have in their favor are arguments that the data is not random.

    It’s hard to fathom, I know. But Mung actually believes that.

  10. Rumraket: No, the claim is that it takes very long time for the random mutations to completely erase phylogenetic signal under most biologically realistic conditions.

    So you could have this sequence of DNA, totally random, and it gets copied and inherited, and that sequence now becomes your “signal” that you will try to track over time. And this is why you can create hierarchies from “junk” DNA.

    So randomized data can have a hierarchical structure. Is that what you’re saying?

  11. keiths: It’s hard to believe, I know. But Mung actually believes it.

    It’s far, far, more likely that you are just making stuff up again. 🙂

  12. keiths: More like “The cat threw up, and someone’s got to clean it up. I guess I will.”

    That’s what I’ll be doing in a few minutes, lol.

  13. It’s far, far, more likely that you are just making stuff up again.

    It was a direct quote, Mung.

  14. Here’s what you’re missing, Mung.

    Let’s say you insert a junk sequence into an E. coli cell. The sequence might be random, but the copies will not be uncorrelated. A daughter E. coli cell will get an accurate copy from its parent, with the occasional error. It’s the combined pattern of similarities and differences that establishes the phylogeny. The fact that the initial sequence is random does not matter, and whether the errors are random does not matter either,

    Your statement is obviously incorrect:

    Admit it. The data comes from a random generator. There’s no reason on evolution to expect the actual phylogenies that we see.

    On the other hand, if parents didn’t pass copies to their offspring, and if you truly generated each genome randomly, then they would be uncorrelated, and no objective nested hierarchy could be inferred.

  15. Mung [to keiths]: So you could have this sequence of DNA, totally random, and it gets copied and inherited, and that sequence now becomes your “signal” that you will try to track over time. And this is why you can create hierarchies from “junk” DNA.

    So randomized data can have a hierarchical structure. Is that what you’re saying?

    Given the historical pattern of inheritance, yes.

  16. Rumraket:

    And by the way what you say is demonstrably false, as common descent predicts statistically significant levels of congruence between indpendent phylogenies. And you can even put numbers on it. Read Theobald.

    Mung, have you ever read 29+ Evidences? If so, did it baffle you as it did Bill?

  17. keiths: Mung, have you ever read 29+ Evidences? If so, did it baffle you as it did Bill?

    It’s been around a while right? Didn’t talkorigins used to be a newsgroup? How long ago was that? I probably read at least some of it. Maybe not all that is currently available:

    http://www.talkorigins.org/faqs/comdesc/

    But since I accept common descent I don’t get your point. If you have one. What on earth do you think “baffles” me about common descent?

    By the way, could you save me some time and point out where Theobald covers unguided evolution vs. guided evolution? Thanks

  18. keiths: On the other hand, if parents didn’t pass copies to their offspring, and if you truly generated each genome randomly, then they would be uncorrelated, and no objective nested hierarchy could be inferred.

    The claim wasn’t that no objective nested hierarchy could be inferred if each genome was generated randomly.

    A daughter E. coli cell will get an accurate copy from its parent, with the occasional error. It’s the combined pattern of similarities and differences that establishes the phylogeny.

    So it’s all “signal.”

    The fact that the initial sequence is random does not matter, and whether the errors are random does not matter either

    What a relief. So where does “noise” enter the picture?

  19. keiths,

    Says Bill, who by his own admission doesn’t understand Theobald’s 29+ Evidences for Macroevolution.

    I have read it. Where in this document is the contradictory evidence? This document is about common descent independent of a mechanism.

    Why do you think it was necessary to create a document that separated a mechanism out of evolutionary theory?

  20. Rumraket,

    They weren’t “created by inheritance”. They evolved by mutation, natural selection and genetic drift. The “feature” you are so impressed by in whales is really just adaptations to the hearing system, and in so far as convergence exists between bats and whales it is really just in the broadest sense of “navigating by sound in the dark”, while the convergence in implementation is only observed at the level of less than 10 amino acid substitutions in a particular gene.

    So evolving echolocation is easy just like evolving proteins. At what point are you going to start taking a fresh look at your assumptions?

  21. colewd: This document is about common descent independent of a mechanism.

    Say it isn’t so Bill. keiths so needs for the mechanism to be unguided that he’s willing to lay his lowly reputation on the line over it.

    Help us out here keiths. If mechanism is irrelevant to the evidence, how can the evidence tell us that the mechanism was unguided?

    Theobald:

    Evolution, the overarching concept that unifies the biological sciences, in fact embraces a plurality of theories and hypotheses.

    Say it isn’t so boys. Evolutionary theories.

    Theobald:

    Common Descent Can Be Tested Independently of Mechanistic Theories

    Well ain’t that just a shot to the old nutsack.

  22. colewd: So evolving echolocation is easy just like evolving proteins.

    But not as easy as evolving an eye! Given the sheer number of times that eyes have independently evolved it is certainly much easier to evolve an eye.

    Right Rumraket?

  23. Douglas Theobald:

    Universal common descent is a general descriptive theory concerning the genetic origins of living organisms (though not the ultimate origin of life).

    Descriptive? As opposed to what, prescriptive?

    Thus, universal common ancestry entails the transformation of one species into another and, consequently, macroevolutionary history and processes involving the origin of higher taxa.

    How does a theory that is “a general descriptive theory” entail anything at all?

  24. Mung,

    And when pressed about a convergent feature Rum brings out the old mechanism as the explanation.

    They weren’t “created by inheritance”. They evolved by mutation, natural selection and genetic drift.

  25. Joe Felsenstein: Given the historical pattern of inheritance, yes.

    Given that there is an historical pattern of inheritance, there is an historical pattern of inheritance, yes.

  26. colewd: And when pressed about a convergent feature Rum brings out the old mechanism as the explanation.

    It would appear that Rumraket has not read Theobald. I’m beginning to think that keiths hasn’t read Theobald either.

  27. It’s cute how excited Bill and Mung get when they think they’ve finally found a significant flaw in their opponents’ positions. It almost seems a shame to spoil their fantasy, but I will.

    Mung:

    Help us out here keiths. If mechanism is irrelevant to the evidence, how can the evidence tell us that the mechanism was unguided?

    Who said mechanism is irrelevant to the evidence? Certainly not Theobald.

    What he said is quite different:

    Common Descent Can Be Tested Independently of Mechanistic Theories

    In this essay, universal common descent alone is specifically considered and weighed against the scientific evidence. In general, separate “microevolutionary” theories are left unaddressed. Microevolutionary theories are gradualistic explanatory mechanisms that biologists use to account for the origin and evolution of macroevolutionary adaptations and variation. These mechanisms include such concepts as natural selection, genetic drift, sexual selection, neutral evolution, and theories of speciation. The fundamentals of genetics, developmental biology, molecular biology, biochemistry, and geology are assumed to be fundamentally correct—especially those that do not directly purport to explain adaptation. However, whether microevolutionary theories are sufficient to account for macroevolutionary adaptations is a question that is left open.

    Therefore, the evidence for common descent discussed here is independent of specific gradualistic explanatory mechanisms. None of the dozens of predictions directly address how macroevolution has occurred, how fins were able to develop into limbs, how the leopard got its spots, or how the vertebrate eye evolved. None of the evidence recounted here assumes that natural selection is valid. None of the evidence assumes that natural selection is sufficient for generating adaptations or the differences between species and other taxa. Because of this evidentiary independence, the validity of the macroevolutionary conclusion does not depend on whether natural selection, or the inheritance of acquired characaters, or a force vitale, or something else is the true mechanism of adaptive evolutionary change. The scientific case for common descent stands, regardless.

  28. colewd,

    Why do you think it was necessary to create a document that separated a mechanism out of evolutionary theory?

    It wasn’t. He didn’t do it out of necessity, Bill.

  29. Another keeper from Mung:

    How does a theory that is “a general descriptive theory” entail anything at all?

    Derp.

  30. Mung:

    We have better access to The Designer than you have to “unguided evolution,” whatever that is.

    keiths:

    Well, then by all means ask him “What’s up with the evolution mimicry?” Let us know what he says.

    Did you get an answer, Mung? Or did the Designer do his customary “Mung’s at the door! Everyone be quiet and pretend we’re not home.”

  31. Mung,

    But since I accept common descent I don’t get your point. If you have one. What on earth do you think “baffles” me about common descent?

    I told you already. You don’t understand the very best evidence for it:

    My point, once again, is that you don’t know why common descent is such a solid conclusion:

    He has no idea why common descent is such a slam dunk.

    You just don’t get it. You seem to be as lost as Sal and Bill.

    Hence my question about whether you had read Theobald.

    By the way, do you finally understand why the following statement of yours is wrong?

    Admit it. The data comes from a random generator. There’s no reason on evolution to expect the actual phylogenies that we see.

  32. Allan,

    I think if you perceive someone as arguing with themselves, you have to be alert to the possibility that you may not have grasped their point.

    I considered that possibility, and I double- and triple-checked what you wrote. It still looks like a blatant contradiction.

    You objected to the exclusion of HGT from ‘common descent’…

    You appear to want to restrict the term ‘common descent’ to vertical inheritance.

    …but then you agreed with it:

    I don’t want HGT to be an ‘instance of descent’.

    If you don’t consider HGT to be descent, then why did you object when I excluded it from ‘common descent’?

    In the second [statement], I am pointing out that HGT itself is not ‘descent’ at all.

    Right. So again, if you agree that HGT is not descent, why did you object when I excluded it from ‘common descent’?

    And how is it not contradictory to both include and exclude HGT as part of ‘common descent’?

    (I even considered the possibility that you had some relevant distinction in mind between ‘descent’ and ‘common descent’, but couldn’t come up with a plausible one. Note the word ‘relevant’ there.)

    ETA: And in any case, you ruled that out with the following:

    I’m definitely not saying that HGT is a form of common descent.

  33. Allan,

    Corneel and DNA_Jock seem to have got my drift; you seem to be trying to pursue some kind of definitional insistence.

    I’m using ‘common descent’ in the standard way. You are the one urging a broader definition that doesn’t exclude HGT.

    Allan:

    You can define common descent as anything you like of course; I am more interested in the mechanics of the situation.

    We’ve never disagreed, as far as I can tell, on the mechanics. The disagreement has always been over the scope of the term ‘common descent’.

    I think you may be hung up on the ‘vertical/horizontal’ thing.

    I’m not “hung up” on it. I just think it’s a useful distinction, and by all indications, so does the biological community. Why drop a useful distinction, and why redefine a standard term?

    The reason you gave is poor:

    That’s a semantic preference to which you are entitled, but I don’t see the point of making life easy for the Creationist, here, and giving them an entire arena they can exclude from explanation as per the thread title.

    My response:

    You’re granting way too much power to the creationists if you think we should redefine ‘common descent’ on account of their potential exploitation of a thread title.

    Besides, excluding HGT from common descent doesn’t help them. The phenomenon is still there, just as I described it:

    Nothing is lost by doing so, and an important distinction is maintained.

    We can still discuss the full history of a sequence that experiences HGT. It descends with modification in the donor lineage; then the HGT event occurs; then it descends with modification in both donor and recipient lineages. The HGT event itself is not an instance of descent.

    None of that gets creationists off the hook or allows them to “exclude an entire arena from explanation”.

    Given

    a) that your rationale fails, and
    b) that the vertical/horizontal distinction is useful, and
    c) that the current terminology doesn’t hobble us in describing HGT events interspersed with descent;

    what incentive is there for the biological community to redefine ‘common descent’ per your wishes?

  34. Rumraket:

    I’m beginning to understand why Nick Matzke was so dismissive in his 2-part review of Meyer’s Darwin’s Doubt crackpottery

    Oh, Nick the guy with a PhD in evolutionary biology who couldn’t even answer a basic statistics question, yeah that Nick:

    A Statistics Question for Nick Matzke

    Here was the question I had Barry Arrington pose to Nick:

    The Fundamental Law of Intelligent Design

    Any wagers whether Nick will answer this simple question. Now, Barry, you’ve been really trying to put the screws to Nick about Niles Eldridge. Nick has been so generous and quick to respond. You might consider you post this question to Nick:

    Dr. Matzke,

    If you found 500 fair coins all heads on a tray, would you reject chance as an explanation. If yes, explain why. Thank you.

    And predictably Nick folded:

    A Statistics Question for Nick Matzke

    Yeah, that Nick. Hahaha!

  35. Just a stray thought, but this “disagreement” might be why Dawkins wrote a whole book about the survival of genes.

    One can get hung up on definitions, but there is a point of view in which descent is about genes (or sequences) rather than about organisms.

    This is not incompatible with the notion that sequences come in large packages that usually stick together.

  36. stcordova,
    Looking through that thread, it seems Nick Matzke’s cloak fell on Mark Frank who in the most polite way shredded your argument. To me anyway.

  37. Mung: So you could have this sequence of DNA, totally random, and it gets copied and inherited, and that sequence now becomes your “signal” that you will try to track over time.

    As it mutates, yes.

    And this is why you can create hierarchies from “junk” DNA.

    Yes, that too. Both functional and junk DNA.

    So randomized data can have a hierarchical structure. Is that what you’re saying?

    No because now you’re trying to smuggle that whole explanation you gave into that single word “randomized”. Which is extremely deceptive. And you’re doing that deliberately to mask the iterative copying and make it appear as if a random sequence generator could just generate, say ten sequences, and then those ten sequences would just so happen to yield hiearchical structure.

    That’d be extremely, extremely unlikely. Sorry Mung, not falling for your silly rhetorical trick here.

  38. colewd: I have read it.

    No you haven’t. You’ve tried to read it, and it went okay until you came to that sentence about it being independent of mechanism, which is where you stopped. And you’ve never picked up where you left off. Rather than read the rest of the article, so that you would come to understand why the evidence of common descent is indpendent of mechanism and in what way that is meant, you instead decided you’d found something disagreeable long before you comprehended it, and then came here to start an argument about it instead.
    We’ve been over this at least five times as far as I can remember.

    Where in this document is the contradictory evidence?

    There isn’t any contradictory evidence.

    This document is about common descent independent of a mechanism.

    Why do you think it was necessary to create a document that separated a mechanism out of evolutionary theory?

    Because it really is independent of mechanism. There’s no reason to start blathering about the relative contributions of selection or drift, or multi-level selection, or mutation biases or anything of the sort, because none of that really affects the evidence for common descent.

  39. Rumraket, Alan Fox:

    If you found 500 fair coins all heads on a tray, would you reject chance as an explanation. If yes, explain why. Thank you.

    A simple “yes” or “no” would suffice. If not, explain it like you would to college students.

    I would say, “yes”, I reject chance as an explanation. Now, why would all disagree with my answer.

  40. colewd:
    Rumraket,

    So evolving echolocation is easy just like evolving proteins.

    What does that even mean? Echolocation evolved regardless of how difficult you think it is.

    At what point are you going to start taking a fresh look at your assumptions?

    When you bring something up that merits such an endeavour. You still haven’t.

    When are you?

  41. Now onto matter more weighty than Dr. Nick Matzke, PhD Evoutionary biology’s misunderstandings of basic statistics…..

    The PHYLIP format (created by our own Joe Felsenstein) is a little hard to use because it is so persnickety — I can’t even put a space in the wrong place without it shooting me down.

    I would suppose PHYLIP was the beginning of many good things and since then there have been more forgiving formats and tools.

    For sequences of varying length, I want to create radial diagrams like this without having to use the PHYLIP format. Any suggestions?

  42. stcordova:
    Rumraket, Alan Fox:

    A simple “yes” or “no” would suffice. If not, explain it like you would to college students.

    I would say, “yes”, I reject chance as an explanation. Now, why would all disagree with my answer.

    I don’t know what “chance” even means as an explanation. Please elaborate.

  43. Rumraket:

    I don’t know what “chance” even means as an explanation.

    Hmm, that’s unfortunate, because to use Gene searches it’s good to know. For example at the NIH NCBI website:

    https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect

    The Expect value (E) is a parameter that describes the number of hits one can “expect” to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise. For example, an E value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance.

    Note the bolded words “chance”.

    So you’ve used blast a lot here at TSZ. You don’t know what they mean by “chance” in that FAQ? Is that right? 🙂

  44. Mung:
    So common descent predicts a nested hierarchy if the random sequence generator doesn’t generate random sequences?

    So we get this random gene duplication, and then that sequence diverges from the original sequence due to random changes, until magically it’s expressed and found to be useful (by george!) also at random, but that’s not really random sequence generation, and the data isn’t generated at random.

    Why doesn’t someone just admit that John is wrong?

    Sure it does. It’s what comes of “unguided evolution.” And “unguided evolution” is the only reasonable explanation for the hierarchy.

    and

    Mung:[to Rumraket] So you could have this sequence of DNA, totally random, and it gets copied and inherited, and that sequence now becomes your “signal” that you will try to track over time. And this is why you can create hierarchies from “junk” DNA.

    So randomized data can have a hierarchical structure. Is that what you’re saying?

    Let’s try to untangle this. If we start from a random sequence, and then after a few million generations find that (say) 3% of the sites, chosen at random, have changed to other bases, will both of these sequences be random?

    Yes, each will be a random sequence.

    Will they be two independent random sequences?

    No, they will show considerable similarity, because they are not independently derived.

    If we look at a region of junk DNA, where the sequence is random, and we look at it in different species, then each sequence would be random, but they are not independent of each other, so there is a signal there which can be used to reconstruct a phylogeny.

    And if we look at another region of the genome, one which is also junk DNA, we see different random sequences, and again, the sequences that we see in those same species are not independent of each other. But each looks like a random sequence if considered by itself.

    So we can look at the sequences in that second region and infer a phylogeny from them. And then we can see whether the two phylogenies are noticeably similar. That is what Theobald is talking about.

    So yes, Mung, even “random” sequences can be used to reconstruct phylogenies. As long as the random sequences in different species are not independent of each other, as they have not diverged so much that the signal of similarity between them is lost. You expressed incredulity, though in typical Mungish fashion you did not actually say that this was not believable.

    It works, both in junk DNA and also in non-junk sequences. It is what Theobald is talking about (and he is following the lead of David Penny and Peter Lockhart in their 1982 paper which did similar things but with less data).

  45. And revisiting last year’s winner of a Darwin Award, DNA_Jock speaking of Thermodynamics and Entropy:

    In Slight Defense of Granville Sewell: A. Lehninger, Larry Moran, L. Boltzmann

    And once we start talking about scientists, then dQ/T is rarely informative:

    What a howler!!!

    If you search for “dQ/T is rarely informative” a frequent number one hit for that statement is by DNA_Jock at TSZ. Why is that?

    Gee DNA_Jock, why is your claim so unique? Could it be, that you’re the only one who swears by such nonsense.

  46. FWIW,

    I and other creationists believe there is some random variation and that phylogenetic tools can be used to trace back MRCAs, especially those of Noah’s Ark and from the original creation.

    Nathaniel Jeanson and Rob Carter are the primary researchers on these topics. I visited with Nathaniel this past June at the Lipscomb University conference.

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