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 Replies to “Common Design vs. Common Descent”

  1. Mung Mung
    Ignored
    says:

    Allan Miller: I dug out the original paper

    I visited that page and it said “You are viewing the new design.”

    So there you have it.

  2. Mung Mung
    Ignored
    says:

    Entropy: For example, Carlitos Linnaeus’ taxonomic classification, which he made on the basis of morphological traits (shared and unshared, otherwise we would get all organisms into a single taxonomic species, rather than the hierarchy that Carlitos came up with).

    Yes, I already pointed this out.

    …the process of evolution would explain how that hierarchy might be produced by natural processes.

    Isn’t this the same as what I have been saying? It is the process of evolution that explains the nested hierarchy.

    So, now that we agree on that, can’t we agree that it is evolution that explains the differences?

  3. Mung Mung
    Ignored
    says:

    Entropy: I know the concepts have been mixed and remixed in the conversation and in the literature, that common descent is used when people mean evolution, that evolution is used when people mean common descent, etc.

    Right. You even do it right there in the same post.

    Thus common descent is confirmed, since it predicted that we would get very similar nested hierarchies, and that’s that.

    You should have said evolution is confirmed, because you were talking about evolution.

    …the process of evolution would explain how that hierarchy might be produced by natural processes.

    Did you mean to say that the process of common descent would explain how that hierarchy might be produced by natural processes?

  4. GlenDavidson
    Ignored
    says:

    Sal can complain about the genetic evidence of the nested hierarchy all he wants, but it hardly matters. He can explain any of the evidence for the nested hierarchy using common design (not illegitimate assumptions, like if evolution didn’t do it his favorite fantasy did) if he wants design to be taken seriously. Morphologic evidence will do.

    Of course he will never explain why the “designer” can’t think across separate lineages of organisms. Because it simply doesn’t make any sense at all.

    Glen Davidson

  5. John Harshman John Harshman
    Ignored
    says:

    Mung: Isn’t this the same as what I have been saying? It is the process of evolution that explains the nested hierarchy.

    No, that isn’t what you’ve been saying. The problem here is that “evolution” covers a broad ground. It includes common descent, natural selection, speciation, genetic drift, and other things. Common descent is the bit that explains why similarities and differences follow a nested hierarchy. Other bits explain how differences arise and become fixed within species and how speciation happens. While it’s necessary differences to arise in order to provide the evidence for common descent and it’s necessary for speciation to happen in order to produce the branching descent that forms the nested hierarchy, common descent doesn’t have to explain either of these things. It’s enough that they occur.

    So, now that we agree on that, can’t we agree that it is evolution that explains the differences?

    I expect so, though not the element of evolution known as common descent, but other elements like mutation and selection. And even if evolution didn’t explain the differences, common descent would remain the explanation for nested hierarchy.

  6. stcordova
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    says:

    Corneel:

    So why did you ask?

    The question of Neighbor Joining is better resolved, imho, to the extent we can dispense with gene by gene comparisons and go to large scale chromosome comparisons where synteny is important. Large scale chromosome comparisons are not too bad if we’re comparing human vs. human. We can see huge sections shoved from one place to another.

    The point? I was trying to understand how we can account for these facts as we try to aggregate and decide which organism is to be neighbored with the next, or how we group them together.

    The D4Z4 repeat came to mind because the Lungfish has soooooooo many repeats. Shouldn’t the non-coding regions count for something? How could we factor stuff like that in. The variability between lungfish genomes is between 100 and 200 gigabases. So it seems there is an orderly variability to all this, lest the poor creature die. In humans D4Z4 has a mean of about 100 repeats, but if it goes below 11, there is muscular dystrophy.

    But where this is going? If the kind and repeat number are controlled for individual repeats this is a POOF-omorphy. 🙂

    Telomeric repeats are one example. There are some species specific telomeric repeats, and it is mechanistically controlled. It’s not rote copying. How about the centromeric repeats?

    The reason synteny is important is TRANSCRIPTION FACTORIES. How is synteny preserved, or how is it re-ordered. Transcription factories require 3-dimensional positioning that is dependent on the 1-dimensional synteny in chromosomes.

    These are also potential POOF-omorphies. How do we put the POOF-omorphies into our recipe of Neighbor Joining?

    Transcription factories are related to Topologically Associating (DNA) Domains which change configuration based on cell type.
    https://upload.wikimedia.org/wikipedia/commons/b/be/Structural_organization_of_chromatin.png

    Corneel:

    So why did you ask?

    I’m fishing for POOF-omorophies. 🙂

  7. Mung Mung
    Ignored
    says:

    poofamorphies. i like it. 🙂

    An apomorphy is a character that is different from the form found in an ancestor, i.e., an innovation, that sets the clade apart (“apo”) from other clades.

    A theory that does not explain the apomorphies does not explain the nested hierarchy.

  8. stcordova
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    says:

    I mentioned the centromeric regions. Ah yes, on my fishing expedition for POOF-omorphies, I found evidence of a mechanism that maintains Alpha Satelite repeats! Bwahaha!

    This is the sort of POOF-omporphy Phylogeneticists can’t seem to make their statistical phylogenies digest. In their statistical phylogenies, it’s just a repeat of DNA. How does their phylogenetic method capture the complex machinery associated with the tandem repetitive DNA? It doesn’t. Their methods are behind the times and inadequate to caputure the POOF-omporphies in their Nieghbor Joining algorithms. That’s again one reason they conclude giraffes are fish!

    You know, I learned a giraffe isn’t a fish when I was in elementary school. Nothing evolutionary biologists have done or said has changed that perception. And now as we’re seeing POOF-omorphies which their phylogenetic methods can’t account for, it only highlights the inadequacy and systematic cherry picking of data from a highly simplistic viewpoint — as in “repetitive DNA, no big deal.” Yes big deal baby, yes big deal.

    From the prestigious National Academy of Sciences:
    http://www.pnas.org/content/114/8/1928.full.pdf

    Centromeres are highly specialized chromatin domains that enable chromosome segregation and orchestrate faithful cell division. Human centromeres are composed of tandem arrays of α-satellite DNA, which spans up to several megabases. Little is known about the
    mechanisms that maintain integrity of the long arrays of α-satellite DNA repeats.
    ….
    Our study points toward the presence of a centromere-specificmechanism that actively
    maintains α-satellite repeat integrity during human cell proliferation.

    and what is an important of the mechanism? Histones baby, histones! Yes those Random-Access-Memory devices that help implement massively parallel computation.

    You can see the two classes of histones described in the diagram below: H3 and CENP-A.

    the mechanism(s) that maintains centromere integrity, we examined the contribution of the centromere-specific histone variant CENP-A

    CENP-A protects α-satellite repeats from extensive rearrangements.

    Creating a functional histone variant CENP-A , not to mention the Alpha-satellite repeat it maintains, is a POOF-omorphy.

    Kudos to the team that did some friggin awesome lab work that explores God’s creation. Amazing! It was a wonderful paper. One of the nicer ones that I’ve read in a long time. That diagram alone is worth celebrating as it shows God’s genius.

    Fig. 1. CO-FISH application to monitor human centromeric α-satellite repeats.

    (A) Diagram of the human centromere. (Left) The centromere locus of metaphase sister chromatids is depicted in red or green due to hybridization
    by unidirectional PNA probes, differentially labeled to detect the forward or reverse strands of one sister chromatid. Each black arrow symbolizes a HOR in the α-satellite array. The blue box gives a zoom in into a schematic example of the HOR tandem repeat monomers arranged head to tail. Represented on each monomer are black lines indicating divergence of sequence, teal box where the CENP-B box sequence is found, and the regions where
    the probes hybridize. (Above) The localization of CENP-A nucleosomes shown at the core centromere repeats, interspersed with canonical H3 nucleosomes. Outside of the core domain into the pericentromeric heterochromatin (HC), only H3 nucleosomes are found.

    (B) Unidirectional PNA probe set 1 against α-satellite or (C) PNA probe set 2 against the CENP-B box. White box indicates zoomed-in Insets. (D) Diagrammatic figures and example images of c-CO-FISH using probe set 1 in hTERT-RPE1 cells showing separated signal, where only one probe hybridizes on each sister chromatid (normal) and aberrant c-CO-FISH pattern, where the signal has exchanged between the two sister chromatids and probes overlap. (All scale bars, 1 μm.)

    click to enlarge:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/12/alpha_satelite_centrome_v2.png

  9. stcordova
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    says:

    Mung:

    poofamorphies. i like it. 🙂

    Thanks!

  10. John Harshman John Harshman
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    says:

    Mung: A theory that does not explain the apomorphies does not explain the nested hierarchy.

    Why?

  11. stcordova
    Ignored
    says:

    The paper uses the term Higher Order Repeat using the acronym HOR. Did they have to call it that word? It sounds too much like, you know, something not family friendly — as in wHORe.

    Look at all them HORs.

  12. Entropy Entropy
    Ignored
    says:

    Mung: Isn’t this the same as what I have been saying? It is the process of evolution that explains the nested hierarchy.

    I was explaining this to Salvador to see if we could get the terms right. But Salvador doesn’t seem too interested, Confusion works better for him. Otherwise he’d have no complains. I don’t know either if you’ve been trying to clarify concepts. I haven’t read your comments in this “thread.”

    Mung: So, now that we agree on that, can’t we agree that it is evolution that explains the differences?

    Evolution is not just about the processes, but also about the relationships. Which is why I made the distinction between the processes of evolution, and the relationships (common descent).

    Mung: Right. You even do it right there in the same post.

    Nope. I didn’t. You forgot to check the main point of my comment: distinguishing between the relationships and the processes.

    Mung: You should have said evolution is confirmed, because you were talking about evolution.

    One aspect of evolution Mung, the common descent aspect. I was focusing there on the relationships (common descent), not on the processes.

    Mung: Did you mean to say that the process of common descent would explain how that hierarchy might be produced by natural processes?

    Seems like you missed the point Mung. I meant what I wrote, that the processes of evolution explain how the hierarchy might be produced. Common descent is not a process, is the relationships that we expect from the evolutionary processes. A relationship is not the same as the processes that produce the relationship, even though they’re so intimately intertwined.

  13. Rumraket Rumraket
    Ignored
    says:

    Entropy: As the copies increase, so does the opportunity to further mis-recombinations and further increase of the copies. You end up with several versions of the “locus” with different numbers of copies of the gene.

    This is also similar to how CAG repeat expansions increase the opportunity for more CAG repeat expansions, as the very fact that there are repeats makes it possible for the error that results in more repeats, to occur.

  14. John Harshman John Harshman
    Ignored
    says:

    Just to note: Sal is using “neighbor-joining” as a buzzword. He seems not to know quite what it is or how it works. Though he’s capable of repeating by rote the explanation I once gave him, I don’t think he knows what it means, based on his other statements about it. I suspect the same statement would apply to most if not all of his other buzzwords.

  15. stcordova
    Ignored
    says:

    Entropy:

    The story for D4Z4 might be out there somewhere, but I don’t have time to look for it, or check for places where recombinations can occur besides the obvious.

    Thanks for the response.

    Does this happen for non-coding DNA? How does it recognize a discrete unit like an long repeat (say over 200 bases) over some arbitrary unit?

    Would this mechanism work for a non-coding alpha satellite repeat? As I showed, there is evidence the alpha satellite repeat is a discrete unit that has machinery specifically targeting it as a unit. The generation of the repeats could not be by some arbitrary copy and paste where some arbitrary stretch of DNA of arbitrary length is copied to a random location on the chromosome generation after generation.

    For a repeat to be actually nicely copied, somehow the repeated unit needs to have a means of identifying the start and stop of the repeat.

  16. stcordova
    Ignored
    says:

    John Harshman:

    Just to note: Sal is using “neighbor-joining” as a buzzword. He seems not to know quite what it is or how it works.

    Sure I know how it works. I just push a button on the phylogeny software called “Neighbor Joining”, and it pumps out the phylogeny like the one Rumraket wanted to see on his hypothetical genealogy. No problem.

  17. Mung Mung
    Ignored
    says:

    John Harshman: Why?

    Because the apomorphies define the clades and the clades are what are nested. more simply, it is the apomorphies that are nested and if you have not explained them then you have not explained the nesting.

  18. John Harshman John Harshman
    Ignored
    says:

    Mung: Because the apomorphies define the clades and the clades are what are nested. more simply, it is the apomorphies that are nested and if you have not explained them then you have not explained the nesting.

    Your conclusion doesn’t follow from your premise. In order to explain the Great Pyramid, do you have to know how limestone forms?

  19. Mung Mung
    Ignored
    says:

    John Harshman: Your conclusion doesn’t follow from your premise. In order to explain the Great Pyramid, do you have to know how limestone forms?

    I was wondering who would be the first to resort to analogy. 🙂

    You could argue that the distribution of the stones explains the Great Pyramid, because of course a pyramid is defined by the distribution of it’s component stones. But would you accept that as an explanation for the pyramid?

    The stones form a pyramid, therefore that explains the pyramid.

  20. John Harshman John Harshman
    Ignored
    says:

    Mung: I was wondering who would be the first to resort to analogy. 🙂

    Is there something wrong with analogy?

    You could argue that the distribution of the stones explains the Great Pyramid, because of course a pyramid is defined by the distribution of it’s component stones. But would you accept that as an explanation for the pyramid?

    The stones form a pyramid, therefore that explains the pyramid.

    OK, that’s what’s wrong with analogies. Someone else can take them and bend them out of shape. Now of course the great pyramid is explained by the fact that somebody took a lot of limestone blocks and piled them up in a particular pattern. The pattern is explained by the piling. You don’t have to know where the blocks game from or how the stone formed. The only difference between that and common descent is that the nested hierarchy can arise naturally; nobody has to pile it up. We can infer from the pattern of blocks in the pyramid that somebody piled them up, and we can infer from the nested hierarchy of characters that there is common descent. There’s your analogy.

  21. Entropy Entropy
    Ignored
    says:

    stcordova: Would this mechanism work for a non-coding alpha satellite repeat?

    It would work for any repeats. It’s called homologous recombination because it happens between almost identical-to-identical sequences. Repeats recognize each other because they have complementary strands. Each “unit” is identical or almost identical to the other, so, when recombination happens, it could happen against any of the repeats.

    stcordova: For a repeat to be actually nicely copied, somehow the repeated unit needs to have a means of identifying the start and stop of the repeat.

    It only needs to align, by complementarity, anywhere within any of the copies. In my example, I used (D2b/1a) to denote a “hibrid” repeat of a piece of D2b, and D1a. That means that it’s a mixture of two repeats. I used that notation just so that the explanation could be followed. However, for identical repeats, we would not be able to tell where within the sequences the “break-and-recombination” points might be. They only need to be long enough to recombine. Doesn’t matter where each repeat starts and ends, other than being the limits for where the recombination can occur.

    I have assumed that you know about DNA, double helix, and complementarity between the strands. If not, then it would be a good idea to check what that means in order to understand the explanations.

  22. Mung Mung
    Ignored
    says:

    John Harshman: Is there something wrong with analogy? … OK, that’s what’s wrong with analogies. Someone else can take them and bend them out of shape.

    🙂

    Would you say that the stones in the Great Pyramid form a nested hierarchy? I don’t see how they do, but maybe you see something I don’t. And even if they do form a nested hierarchy, in what what are the nestings within it defined by something analogous to apomorphies?

    For an analogy to hold, it needs to be analogous. I hope we can agree on at least that much!

  23. stcordova
    Ignored
    says:

    Enrtropy:

    I have assumed that you know about DNA, double helix, and complementarity between the strands. If not, then it would be a good idea to check what that means in order to understand the explanations.

    Actually I had a couple of semesters of biochem. Was top of the class. Thanks for the attempted explanation, but it doesn’t seem coherent. Sorry.

    I have a colleague who is professor bio biochemistry from Vanderbilt, in light of your explanation I will discuss with him, so please don’t invest time assuming I don’t know enough or don’t have adequate contacts. Thanks anyway. I appreciate the time you invested to make a response. No offense intended, but what you said doesn’t capture the issue very well.

  24. Mung Mung
    Ignored
    says:

    stcordova: Actually I had a couple of semesters of biochem. Was top of the class.

    I bet if you took a course in phylogenetics you’d come in top of the class there too. But don’t tell Entropy.

  25. Entropy Entropy
    Ignored
    says:

    stcordova: Actually I had a couple of semesters of biochem. Was top of the class. Thanks for the attempted explanation, but it doesn’t seem coherent. Sorry.

    So you didn’t find it coherent that DNA strands from identical repeats would recognize each other by complementarity? This should be straightforward for someone who was top of the class in a course that included DNA structure. But who am I to judge? I don’t have a friend who’s a professor of biochem in Vanderbilt.

    I hope your friend will be able to help you understand this incredibly difficult concept.

  26. John Harshman John Harshman
    Ignored
    says:

    Mung: 🙂

    Would you say that the stones in the Great Pyramid form a nested hierarchy?

    No. That isn’t the point of the analogy.

    For an analogy to hold, it needs to be analogous. I hope we can agree on at least that much!

    The analogy is quite a simple one, and I’m surprised that yo can’t see it. Here’s a little table:

    Pyramid::Life
    Arrangement of blocks::Pattern of character distribution
    Somebody piled it up::Common descent
    Formation of limestone::Origin of character states

    The lesson too is a simple one: you don’t need to know the origin of the elements of a pattern to explain the pattern. Would you agree that’s true in the case of the pyramid? Why not, then, in the case of the nested hierarchy?

    All analogies break down if carried too far; that’s why they’re analogies instead of identities. This is not a problem of the analogy but a problem of the person who carries it too far.

  27. stcordova
    Ignored
    says:

    Entropy:
    from identical repeats would recognize each other by complementarity

    The problem isn’t finding a complimentary strand on the corresponding homologous chromosome. That’s why your response was incoherent, it answered a question that wasn’t being asked. Thanks anyway. No need to settle the issue today. If I remember, I’ll report back what I find. I’ll be talking to my colleague in about a week as we’re working on a project together.

  28. Entropy Entropy
    Ignored
    says:

    stcordova,

    So you think that tandem repeats in a chromosome won’t find tandem repeats in their sister chromosome? You asked about tandem repeats. I answered about tandem repeats. Then you asked if the same would occur to things other than genes (non-coding DNA). Obviously it would, because all you need is for the regions to be repeats, then they’ll have complementary strands by definition, they’re repeats!

  29. Mung Mung
    Ignored
    says:

    stcordova: I’ll be talking to my colleague in about a week as we’re working on a project together.

    Ask your colleague how short a strand of DNA or RNA needs to be before it will not fold upon itself and how long a strand of DNA or RNA needs to be before it will almost assuredly fold upon itself.

    And how much more likely it is (or is not) that the strand will fold up on itself before finding a complementary strand to pair with.

    Entropy keeps trying to avoid this as if it’s a non-issue. I’m not sure he understands biochemistry at all.

  30. DNA_Jock
    Ignored
    says:

    [Corneel cites unequal cross-over, and Entropy describes it. Sal’s response]
    stcordova: Thanks for the response.

    Does this happen for non-coding DNA? How does it recognize a discrete unit like an long repeat (say over 200 bases) over some arbitrary unit?

    Would this mechanism work for a non-coding alpha satellite repeat? As I showed, there is evidence the alpha satellite repeat is a discrete unit that has machinery specifically targeting it as a unit. The generation of the repeats could not be by some arbitrary copy and paste where some arbitrary stretch of DNA of arbitrary length is copied to a random location on the chromosome generation after generation.

    For a repeat to be actually nicely copied, somehow the repeated unit needs to have a means of identifying the start and stop of the repeat.

    This response betrays a complete and utter lack of understanding of the most basic aspects of DNA dynamics AND, furthermore, a total failure at reading comprehension.
    When called on this, Sal responds.

    stcordova: Actually I had a couple of semesters of biochem. Was top of the class. Thanks for the attempted explanation, but it doesn’t seem coherent. Sorry.

    I have a colleague who is professor bio biochemistry from Vanderbilt, in light of your explanation I will discuss with him, so please don’t invest time assuming I don’t know enough or don’t have adequate contacts. Thanks anyway. I appreciate the time you invested to make a response. No offense intended, but what you said doesn’t capture the issue very well.

    No Sal, whatever grades you claim to have gotten in your biochemistry class, Corneel’s citation of unequal cross-over, let alone Entropy’s description of it, makes your questions irredeemably stupid.
    I have a friend who is a high school student, in light of your questions I will discuss with her, and see if she thinks your questions betray complete ignorance. No offense intended, but what you said is moronic.

    Your credentialism is hi.lar.i.ous.

  31. Mung Mung
    Ignored
    says:

    Entropy: So you think that tandem repeats in a chromosome won’t find tandem repeats in their sister chromosome?

    No, I believe in magic.

  32. Entropy Entropy
    Ignored
    says:

    Mung,

    I’m not avoiding anything Mung. You’re displaying deep ignorance that won’t go away easily. The worst of it is that you still think you’ve got it right, that once folded into themselves, these things won’t unfold. that once in a double strand, those strands won’t separate. You don’t understand that those things are dynamic. Constantly going from one state to another, with equilibriums dependent on several factors, from the DNA composition, to their concentrations, their lengths, the temperature, salt concentrations, pH, other molecules, etc. These things are, I repeat, dynamic, not static. They’re not lego pieces.

  33. Mung Mung
    Ignored
    says:

    DNA_Jock: This response betrays a complete and utter lack of understanding of the most basic aspects of DNA dynamics…

    So, right in my wheelhouse then!

    What prohibits a lone strand of DNA from folding on itself rather than pairing with some other strand of DNA?

  34. Entropy Entropy
    Ignored
    says:

    Mung,

    Read my answer and stop ridiculing yourself!

  35. Mung Mung
    Ignored
    says:

    Entropy: They’re not lego pieces.

    Lego pieces, once connected, can be disconnected. Any child knows this. So yet another failed analogy.

  36. Mung Mung
    Ignored
    says:

    Entropy: Read my answer and stop ridiculing yourself!

    Go buy some lego pieces and play with them. You’ll find that even though you joined them together you can still disconnect them.

  37. Mung Mung
    Ignored
    says:

    Entropy: The worst of it is that you still think you’ve got it right, that once folded into themselves, these things won’t unfold. that once in a double strand, those strands won’t separate.

    This is utterly hi.lar.i.ous. You’ve just accused me of denying one of the most fundamental processes of living organisms. So maybe you’re wrong. You’re probably wrong.

  38. Entropy Entropy
    Ignored
    says:

    Mung: This is utterly hi.lar.i.ous. You’ve just accused me of denying one of the most fundamental processes of living organisms. So maybe you’re wrong. You’re probably wrong.

    Not the most fundamental processes of living organisms, the most fundamental processes of chemical dynamics, which is what would be hilarious if it didn’t make you look so pathetically ignorant.

  39. stcordova
    Ignored
    says:

    I peaked at DNA_jock might have to say by temporarily removing him from ignore since he represents himself as an expert. Turns out, one view of repetitive elements isn’t what Entropy nor DNA_jock suggested:

    https://en.wikipedia.org/wiki/Slipped_strand_mispairing

    Slipped strand mispairing (SSM), (also known as replication slippage), is a mutation process which occurs during DNA replication. It involves denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases. Slipped strand mispairing is one explanation for the origin and evolution of repetitive DNA sequences.[1]

    You just gave another of your errant bloviations as if you know what you’re talking about.

    Have you figured out yet slip strand mis-paring isn’t the same thing as homologous recombination.

    Oh, Well DNA_Jock, you remain on my ignore list for good reason. No Christmas clemency for your scrooge like nastiness in your last comment.

    As far as your claims against my credentialism, I have high school diploma, and I figured out slip strand misparing isn’t the same as homolgous recombination, which is more than I can say for you. 🙂

  40. Mung Mung
    Ignored
    says:

    I got my high school diploma as a junior. I must be smarter than Entropy.

  41. DNA_Jock
    Ignored
    says:

    Mung: So, right in my wheelhouse then!

    What prohibits a lone strand of DNA from folding on itself rather than pairing with some other strand of DNA?

    Absolutely nothing. A single-stranded NA longer than about 10 bases is guaranteed to “snap back” on itself. This process is spontaneously reversible (and a function of the variables that Entropy described). If it wasn’t, then DNA hybridization wouldn’t work. DNA hybridization does work.
    Right in your wheelhouse, indeed.

  42. Entropy Entropy
    Ignored
    says:

    Mung: I wasn’t the one who used lego pieces as an example of things that could be joined but not separated.

    The point was to represent what you imagine, that once self-folded, or paired in double strands, there’s a need for some “help” to separate them, preferably by a tiny “intelligent designer.” It represents your fantasy very well.

    So, if that’s what made you happy, your misunderstanding of the analogy, rather than understanding the explanation about the dynamics, it truly must be miserable to be you.

  43. DNA_Jock
    Ignored
    says:

    stcordova,

    ROFL
    SSM is the cause of di- and tri- (and occasionally tetra-) nucleotide repeats, and NOT the cause of D4Z4 repeats (which are 3,300 bases long), which was the topic under discussion.
    You really can’t stop yourself from the GSW’s to the foot, can you?

  44. Mung Mung
    Ignored
    says:

    DNA_Jock: If it wasn’t, then DNA hybridization wouldn’t work. DNA hybridization does work.

    DNA hybridization does not appear to be something employed by cells for carrying out the process of DNA replication. It appears to be an artificial process introduced by intelligent humans.

    Does DNA hybridization occur in natural populations?

  45. Entropy Entropy
    Ignored
    says:

    stcordova: Slipped strand mispairing is one explanation for the origin and evolution of repetitive DNA sequences

    Sal, That’s exactly the very same idea during a different process. Copy number variation can happen during recombination of sister chromosomes, or when repairing broken DNA strands, which can “slip” and recognize the “wrong” repeat. I never said there was only one way. Your very citation says that’s one explanation, not that it is the only one.

    But slippage is more of the explanation for small repeats (several of one nucleotide are the most common due to slippage, then the small repeat in Huntington disease’), than for tandem duplications of large regions.

  46. stcordova
    Ignored
    says:

    With all that I just said, I still see a problem assuming any of the suggested replication mechanisms. I’ll have to think on it.

  47. Entropy Entropy
    Ignored
    says:

    stcordova,

    But slippage is more of the explanation for small repeats (several of one nucleotide are the most common due to slippage, then the small repeat in Huntington disease’), than for tandem duplications of large regions.

  48. stcordova
    Ignored
    says:

    Sal, That’s exactly the very same idea during a different process. Copy number variation can happen during recombination of sister chromosomes, or when repairing broken DNA strands, which can “slip” and recognize the “wrong” repeat. I never said there was only one way. Your very citation says that’s one explanation, not that it is the only one.

    But there’s still a problem and you obviously don’t see it. You can get one duplication, you have no guarantee what the next round will hold. The next duplication after several generations is not bound to duplicate the first tandem repeat in away that makes contiguous tandem repeats like D4Z4. If it arbitrarily finds some other set of DNA that aligns that may only contain the tandem repeat, it may not duplicate only the tandem repeat in the next round.

    You’re missing the point.

  49. John Harshman John Harshman
    Ignored
    says:

    Mung: Does DNA hybridization occur in natural populations?

    Constantly. Short stretches of DNA are always coming unzipped and re-annealing. It’s also how hairpins form.

  50. Mung Mung
    Ignored
    says:

    Entropy: The point was to represent what you imagine, that once self-folded, or paired in double strands, there’s a need for some “help” to separate them, preferably by a tiny “intelligent designer.” It represents your fantasy very well.

    Your story is changing, don’t you see that?

    It’s changed from cannot separate once joined to needs some help to separate once joined. But even you admit that it needs some help to separate once joined.

    And I never said that a tiny intelligent designer was needed to separate them. Once joined, they cannot be separated, even by a large intelligent designer. At least that’s what you originally claimed is what I imagined.

    Shouldn’t your claims reflect reality?

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