Common Design vs. Common Descent

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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. Rumraket, to Sal:

    This is just the summary and introduction. Read the whole paper, it’s open access. No excuses. Then ask yourself this question: If the phylogenetic methods that you both reject and claim are just some similarity-based fantasy, are not actually correctly inferring historical events, why do they consistently manage to infer functional intermediate and ancestral molecules? How is that even possible if a phylogeny is just some tree with no relation to real historical events and entities?

    Because God is faking the evidence to make it look as if common descent is true. Bizarrely, Sal actually seems desperate enough to make that argument:

    By the way, can an intelligent designer in principle create nested taxnomic hierarchies if he wanted to, like say the nested molecular taxonomy one would find for cytochrome-C or aaRS or whatever.

  2. Sal,

    By the way, can an intelligent designer in principle create nested taxnomic hierarchies if he wanted to, like say the nested molecular taxonomy one would find for cytochrome-C or aaRS or whatever.

    Yes, and the Rain Fairy could in principle create weather of exactly the kind we see. Does that persuade you to believe in the Rain Fairy, Sal?

    Creationism is every bit as stupid as Rain Fairyism.

  4. John Harshman:

    On that we can agree, since you have not yet begun.

    There you go misinterpreting the meaning of what I said. When I said I was only half done, the half I presented was sufficient to make my case. Now it’s time for me to pile on and gloat at your inability to refute my points.

    You started claiming Gish Gallop. Well, that’s a convenient way to make an excuse for your absence of mechanistic explanations to the problems I posed.

    You’ve essentially confirmed to me I have a good enough case you and others can’t give credible rebuttals on regarding the fact “evolution did it” is not an explanation for evolution of complex taxonomically restricted features, which you yourself said is important for creating nested hierarchies. Thank you very much.

  5. keiths: Because God is faking the evidence to make it look as if common descent is true.

    Why would God need to fake evidence to make it look as if common descent is true?

  6. stcordova: There you go misinterpreting the meaning of what I said.When I said I was only half done, the half I presented was sufficient to make my case.Now it’s time for me to pile on and gloat at your inability to refute my points.

    My point is in fact that you have not yet begun, because none of your argument was relevant to common descent vs. common design. As I have tried to explain to you many times now. As others have tried to explain to you many times now. When will you make your attempt to explain the nested hierarchy of life?

    You started claiming Gish Gallop.Well, that’s a convenient way to make an excuse for your absence of mechanistic explanations to the problems I posed.

    I see no need to deal with irrelevant claims.

    You’ve essentially confirmed to me I have a good enough case you and others can’t give credible rebuttals on regarding the fact “evolution did it” is not an explanation for evolution of complex taxonomically restricted features, which you yourself said is importantfor creating nested hierarchies.Thank you very much.

    That’s a complete misunderstanding of everything I said. I wonder if you even read it. The fact that you quote only a single sentence and never refer to any others is suggestive. Please read what I wrote, try to understand it, and then, if you prefer, try to rebut. But don’t skip any of the steps.

    As for the importance of taxonomically restricted features for creating (discovering, really) nested hierarchies, you missed the part where it’s their distribution that counts, not the reasons for their origin. And that was the important part.

  7. Why aren’t the three domains of life in a nice objective nested hierarchy?

    Each of these three domains of life recognized by biologists today contain unique rRNA. This fact in itself forms the basis of the three-domain system. While the presence of a nuclear membrane differentiates the Eukarya domain from the Archaea and Bacteria domains, both of which lack a nuclear membrane, distinct biochemical and RNA markers differentiate the Archaea and Bacteria domains from each other.

    Bacteria and Eukarya nested within Archaea. Nope.
    Bacteria and Archaea nested within Eukarya. Nope.
    Archaea and Eukarya nested within Bacteria. Nope.

    So right off the bat there’s no “objective nested hierarchy.”

    There probably was a nice nested hierarchy, at one time, before we knew what we know now. Or not.

  8. Thus, the eukaryotic cell was not so much the product of a changing lineage of familial descent, but was the result of a series of mergers between diverse families of microbes. To put it another way, the origin of the eukaryotic cell was not so much Darwinian as it was Lamarckian.

    That must play hell with any “objective nested hierarchy.”

  9. Mung: Thus, the eukaryotic cell was not so much the product of a changing lineage of familial descent, but was the result of a series of mergers between diverse families of microbes. To put it another way, the origin of the eukaryotic cell was not so much Darwinian as it was Lamarckian.

    OMG!!! Who wrote this???

  10. J-Mac: OMG!!! Who wrote this???

    This was from the J. Scott Turner book Purpose and Desire that I invited people to discuss.

    I don’t know what on earth compels me to keep bringing up for discussion books that no one else wants to read, lol.

  11. Mung: This was from the J. Scott Turner book Purpose and Desire that I invited people to discuss.

    I don’t know what on earth compels me to keep bringing up for discussion books that no one else wants to read, lol.

    Sorry…I lost my interest in reading it the second time you quoted from it…

    I’m reading Darwin’s Doubt and Shadows of the Mind: A Search for the Missing Science of Consciousness…

  13. What does Luskin’s article have to do with your goofy statement, apart from the fact that both are appallingly dumb?

    Bacteria and Eukarya nested within Archaea. Nope.
    Bacteria and Archaea nested within Eukarya. Nope.
    Archaea and Eukarya nested within Bacteria. Nope.

    So right off the bat there’s no “objective nested hierarchy.”

  14. Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past

    How does that work, given endosymbiosis involving multiple species?

  21. colewd,

    I think you need re look at this. It has shown a causal link between the cc isoform and the action of the apoptosis mechanism especially rate and initiation.

    Cobblers. The fact that there is a different isoform in two organisms is not evidence that the isoform is at the root of any differences between the organisms.

  22. Mung: Bacteria and Eukarya nested within Archaea. Nope.
    Bacteria and Archaea nested within Eukarya. Nope.
    Archaea and Eukarya nested within Bacteria. Nope.

    So right off the bat there’s no “objective nested hierarchy.”

    There probably was a nice nested hierarchy, at one time, before we knew what we know now. Or not.

    Bacteria and archaea nest within the prokaryote clade. They always did, nothing has changed. They both evolved from a common ancestor. There is still a nested hiearchy and there always was.

    What might be in flux is the question of where the root is relative to both. Is it closer to bacteria or is it closer to archaea? This is still quite heavily debated. Nevertheless, they both make up the prokaryote clade.

  23. colewd: I am not trying to extract a trend. I am showing how single mutations can be delirious to complex regulatory structures such as apoptosis.

    I think you are getting “delirious” 🙂

    This is evidence against its evolvability by random change.

    No Bill, deleterious mutations are not evidence against evolvability by random change. All theories of molecular evolution have deleterious mutations as a factor and phenomenon that happens. They neither contradict nor constitute evidence against it.

    These are complex structures that are unlikely built by mutation at all.

    Why?

    This is the hurdle from a single cell to multicellular organisms that bacterial experiments fall short as adequate supporting evidence.

    That is just confused. Nobody claims that any bacterial experiments constitute “adequate supporting evidence” for the origin of multicellularity. Nor is the origin of multicellularity it even relevant to what we are discussing.

  24. Take an alignable sequence and look at the degree of identity between various organisms.

    You have 100% identity – that’s due to common descent.
    You have 99.99% identity – that’s due to common descent.
    You have 99.98% identity – that’s due to common descent.
    You have 99.97% identity – that’s due to common descent.

    [… snip a few steps]

    You have 90% identity – That’s due to ‘common design’. Why? Because you can’t achieve 90% incrementally? Well, obviously, you can. So, where does ‘Common Design’ cut in and become the better explanation?

  26. CharlieM: I believe that in living systems the parts reflect the whole and I have no problem believing in common design (of sorts) and common descent.
    If we focus on the development of an individual human we can see that all the body cells form a nested hierarchy with the zygote at the root. But we also know that the development of the individual follows a regulated, pattern to a predestined outcome under normal circumstances. It is a process of increasing autonomy of the individual from the mother.
    Living nature follows the same general direction where increasingly autonomy is a recognised feature. And increasing autonomy leads to greater self awareness and the flexibility to consciously begin to take control of ones own actions and destiny.

    Mmmmmmmno doesn’t cut it, I think. If you explain species change and divergence as a process analogous to cell differentiation in individual development, you are simply describing the phylogenetic process. Even though the derived characters are arising from design (of sorts), the vertical inheritance along lineages still make it 100% common descent.
    Perhaps I am missing something. Where does common design come in?

  27. John Harshman mentioned coalescence. If he was referring to Coalescent theory:

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

    How well does that apply to bacterial populations spread across the globe?

    My take on coalescent theory is that it involves species where a mother and father are required for reproduction. Even though there is genetic exchange possible between bacteria, bacteria don’t have genders that are needed to reproduce. Therefore coalescence is not a good explanation for the lack of diversity in the aaRS genes of E. Coli. A better explanation is MRCA of all E Coli aaRS genes on the planet was not a billion years old, maybe not even a few hundred million years old, maybe less than that!

  28. stcordova: (to John) You’ve essentially confirmed to me I have a good enough case you and others can’t give credible rebuttals on regarding the fact “evolution did it” is not an explanation for evolution of complex taxonomically restricted features, which you yourself said is important for creating nested hierarchies.

    Let’s assume for a moment that everything you wrote here is correct, and that you were right about everything and all biologists were wrong. Then we are still missing the little puzzle piece we are looking for for well over 1600 comments:

    The designer restricted his brilliant exquisitely crafted orphan features to selected subsets of certain larger taxonomic groups because …
    or:

    The designer decided not to distribute his brilliant exquisitely crafted orphan features over several taxonomic groups because …
    That would be the beginning of a case for common design.

  29. stcordova: A better explanation is MRCA of all E Coli aaRS genes on the planet was not a billion years old, maybe not even a few hundred million years old, maybe less than that!

    I am not really familiar with coalescence theory, so may be wrong, but isn’t that exactly how the theory explains the limited variation at genetic loci?
    Also, the time of the MRCA can be a long time after the lineage branched off of other extant lineages, right?

  30. Corneel: Let’s assume for a moment that everything you wrote here is correct, and that you were right about everything and all biologists were wrong. Then we are still missing the little puzzle piece we are looking for for well over 1600 comments:

    The designer restricted his brilliant exquisitely crafted orphan features to selected subsets of certain larger taxonomic groups because …
    or:

    The designer decided not to distribute his brilliant exquisitely crafted orphan features over several taxonomic groups because …
    That would be the beginning of a case for common design.

    Because He is the Designer…When, or rather if, you design anything even remotely resembling “the simplest of life forms”, like say prokaryotic cell, then, and only then,you will have the idea as to why the designer did it…

    It’s just hit me; you can’t design even the simplest of life forms…because you can’t even define what life is…and even if you did do it, that achievement would definitely meant that life originated on its own…

    Bravo! Aplausos!

    Who can argue with that?

  31. J-Mac: Because He is the Designer…When, or rather if, you design anything even remotely resembling “the simplest of life forms”, like say prokaryotic cell, then, and only then,you will have the idea as to why the designer did it…

    So you don’t know, which means you don’t have an explanation at all, so you don’t have an explanation to replace common descent. So common descent is still the best scientific theory that actually explains the nested hiearchy. Thank you.

    It’s just hit me; you can’t design even the simplest of life forms…because you can’t even define what life is…and even if you did do it, that achievement would definitely meant that life originated on its own…

    Bravo! Aplausos!

    So let’s see: We, intelligent designers, can’t design life, and we don’t know of any other reason for why there would be a nested hiearchy of life other than common descent, therefore life must have been designed for reasons we can’t figure out.

    Great logic J-mac. Just sublime.

    Who can argue with that?

    Not me, that’s for sure.

  32. J-Mac: Because He is the Designer…When, or rather if, you design anything even remotely resembling “the simplest of life forms”, like say prokaryotic cell, then, and only then,you will have the idea as to why the designer did it…

    I am feeling very accommodating today, so I will grant you your argument and see where that leads us.

    So you are saying that nobody here can fathom why the Designer created a nested hierarchy, until we create living cells ourselves?

    First: How do you know that? Can’t we discover those reasons through careful study? Not even devote students like Sal? Why not?

    Second: Most creationists here claim that certain designed characters of species are best understood as adaptations to their envirnonment. So what exactly is preventing us from learning why some adaptations must be nested within others?

    Please enlighten me.

  33. stcordova:
    John Harshman mentioned coalescence.If he was referring toCoalescent theory:

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

    How well does that apply to bacterial populations spread across the globe?

    My take on coalescent theory is that it involves species where a mother and father are required for reproduction.

    That’s not correct. If anything, the math underlying coalescent models is simpler when dealing with haploid, clonal reproduction. There are lots of example in the literature of coalescent theory applied to bacteria. Here’s a nice (free) book chapter that goes over some of the theory:
    http://www.math.ku.dk/~wiuf/journalWiuf/coal_bac_2010.pdf

  34. stcordova,

    My take on coalescent theory is that it involves species where a mother and father are required for reproduction.

    Your take is wrong. Second sentence in in your own source: “In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. “.

    And then, to say coalescence is irrelevant, it’s all about the MRCA! That’s funny. MRCAs are coalescents.

  35. stcordova: My take on coalescent theory is that it involves species where a mother and father are required for reproduction.

    Your take is wrong. Why would you imagine that gene exchange is necessary for coalescence?

  36. Why would you imagine that gene exchange is necessary for coalescence?

    I don’t but some of your words appeared to suggest it. Maybe I misread since you were complaining there are no unstirred populations of bacteria and I thought you said something about information exchange.

    But why do you even invoke coalescence? Most stuff drifts out of populations if the population size is constricted. Even though Patrick Moran’s processes are some tough math, the essential concept is there. But obviously some stuff doesn’t drift out of the descendant lines, otherwise you wouldn’t have divergence in the genes at all!

    But lets get to the crux of the matter. Suppose you have some species of bacteria that eventually grew and spread around the globe and then the lines lived for a billion years. Why do you think the lines will have no detectable divergence in their aaRS genes after a billion years?

  37. And this just in from a supposedly top 100 university in the world:

    http://www.biology.lu.se/research/research-groups/microbial-ecology/research-projects/reductive-evolution-of-microbial-genomes

    Reductive evolution of microbial genomes

    We study the evolutionary links between the three cellular domains: Archaea, Bacteria and Eukaryotes. In contrast to conventional wisdom, all the available phylogenomic, proteomic and paleontological data suggest that Eukaryotes are the ancestors of both Archaea and Bacteria. The embarrassing fact is that the characteristic features of eukaryotic cells cannot be explained by the traditional endosymbiotic theory, which postulates the evolution of eukaryotes from a fusion of Archaea and Bacteria. Rather, it appears that stringent selection for maximal growth rates has supported the metabolic specializations and correlated reductive evolution of Archaea and Bacteria from their Eukaryote ancestors.

    The data demonstrate that the intensity of that reductive selection depends on large population sizes, but this same selective pressure is inversely proportional to the complexity of proteomes. As a consequence small populations of complex Eukaryotes in general are less intensively driven by stringent reductive pressure than are the large populations of Archaea and Bacteria, with their numerically simpler proteomes. In addition to minimization of proteome complexity (genome coding capacity) reductive evolution in Archaea and Bacteria is expressed at the level of individual protein sequences, which are shorter than their eukaryote homologues.

    Our current research focuses on large-scale phylogenomic methods to further define the deep phylogenetic relationships between domains of organisms. We also explore the ecological adaptations of modern organisms that support reductive evolution among some eukaryotes such as fungi and protozoa.

    And so where did eukaryotes come from then? POOF! Like I said evolution doesn’t have mechanistic explanations when it counts. “It happened but we don’t know exactly how” isn’t much of a mechanistic explanation.

  38. Dave Carlson:

    That’s not correct. If anything, the math underlying coalescent models is simpler when dealing with haploid, clonal reproduction. There are lots of example in the literature of coalescent theory applied to bacteria. Here’s a nice (free) book chapter that goes over some of the theory:
    http://www.math.ku.dk/~wiuf/journalWiuf/coal_bac_2010.pdf

    Hey thanks for setting me straight on that. That right there made it worth my time to start this thread.

  40. stcordova: And so where did eukaryotes come from then? POOF! Like I said evolution doesn’t have mechanistic explanations when it counts. “It happened but we don’t know exactly how” isn’t much of a mechanistic explanation.

    So glad you’re fixing that with “God did it.”

    Of course much is known, and, more importantly, the leads are out there in the relationships that are visible to those who will see. Unlike ID, science is about actually working out what happened.

    I guess since we know so little about Stphen Paddock, we never can know any more. Or, could it be that further investigation might tell us something?

    Your desire to stick with knowing nothing isn’t really helping.

    Glen Davidson

  41. There are at least 3 levels of functional constraint on gene sequence:

    constraint on the DNA
    constraint on the RNA
    constrain on the coded protein

    For example, it has been long suspected DNA in eukaryotes is optimized to be wound into nucleosomes. It also needs to have binding sites for molecular machines. Hence we see lots of enhancer sites up to milliions of base pairs away from the regulated genes on the same chromosome, and now with the 4D nucleome project we see potential enhancer sites between chromosomes!

    RNA has to be constrained for RNA folding and micro-RNA interference regulation.

    Proteins are poly functional and need constraints for binding sites and sites for post translational modification and glycol conjugation, etc.

    It boggles the mind how these levels of constraint are simultaneously achieved!

    Anyway, people don’t seem to appreciate DNA’s Brownian motion can shepard molecular machines and components with pin-point accuracy. This is partly due to binding site specificity, but then maybe stuff we’re only beginning to appreciate. All this to say, we can’t just assume stuff is free to mutate merely because functionally similar proteins between species may only have 12% sequence similarity.

    Some of what applies to the non-coding regions as described in my article below applies to the coding regions as well.

    Pinpoint Navigation and Propulsion in a Seemingly Random Soup

    Pinpoint Navigation and Propulsion in a Seemingly Random Soup

    Non-coding sequences of DNA, sometimes considered genetic junk, may actually function to help navigate proteins to their target genes.

    by Sal Cordova

    Think of the difficulty of sending a package from one location to another when there are a billion possible destinations. To make this process efficient it requires infrastructure and machines that can propel themselves and navigate. It’s even more amazing if this happens in an ever changing soup of molecules within a cell.

    In 2007, John Rinn discovered a lncRNA (long non-coding RNA) transcribed from DNA on human Chromosome 12 that would somehow navigate and land at a specific location on human Chromosome 2 by riding a molecular “bus” known as the Suz12 protein. It was the first example of a transcript from one chromosome influencing the expression of a gene on another chromosome. This epigenetic action, he found, was a crucial part of cell signaling for differentiating skin cells in the body. It’s why the skin cells in the sole of the foot, for instance, have different qualities than skin cells in the lid of the eye.

    Amazingly, Rinn began his research suspecting all he would come up with was “hotair” rather than a real discovery. He thus named this amazing RNA molecule HOTAIR. When his research was published, the journal editors hailed it as the greatest article in their history, but the name HOTAIR was retained. It stands for ‘HOX transcript antisense RNA’.

    How this feat of navigation and propulsion by the SUZ12 protein that shuttles the HOTAIR lncRNA from a specific location on Chromosome 12 to a specific location on Chromosome 2 could be accomplished in a seemingly random soup of chemicals boggles the mind. After all, there are over a billion locations in the nucleus to park HOTAIR on a particular stretch of DNA, not to mention the additional challenge that DNA is a moving target!

    What Rinn’s research demonstrated is that many parts of DNA formerly thought to be junk could serve as navigational markers, like street signs as well as highways that allow molecules to sail the winds of Brownian motion and deliver molecular packages with pin-point accuracy.

    Frame from simulation of DNA shuttling an enzyme. Credit: Georgia Tech / Edmond Chow / Jeffrey Skolnick

    It intuitively suggests a very well conceived system of highways and shuttles where DNA plays a role. We tend to think of DNA solely as a blueprint, but DNA could also serve multiple roles as a means of navigation and propulsion!

    The hypothesis that DNA serves multiple roles is furthered by a recent related development regarding proteins known as transcription factors. According to Phys.org, “Rattling DNA hustles transcribers to targets” –

    New simulations of DNA as a transport conduit could shatter the way scientists have thought about how large molecules called transcription factors diffuse on their way to carry out genetic missions, according to a study by researchers at the Georgia Institute of Technology. The simulations add important brush strokes to our picture of elusive inner mechanics of cells.

    The simulations strongly support the hypothesis that, in a live cell, DNA is in constant motion, making it the dominant mover of transcription factors, to their target sites on DNA. There, the factors regulate the transcription of genetic code into life-sustaining action.

    A video clip of the simulation shows how DNA motion “shuttles” transcription factors through a thicket of DNA strands. What is not mentioned is how the transcription factors are efficiently transported to their proper destination. This research only goes to show that when the popular press gives the impression we’ve got life figured out, nothing could be further from the truth.

    It’s certainly possible, in fact increasingly believable, that much of the so-called junk DNA in humans is part of an elaborate 3-dimemsional structure necessary for shuttling molecules to and fro. If so, then we are indeed fearfully and wonderfully made rather than the piles of junk Darwinists would prefer to have us believe.

    Here is the video clip:

  42. stcordova: But why do you even invoke coalescence? Most stuff drifts out of populations if the population size is constricted. Even though Patrick Moran’s processes are some tough math, the essential concept is there. But obviously some stuff doesn’t drift out of the descendant lines, otherwise you wouldn’t have divergence in the genes at all!

    Whatever can you be talking about? Clearly different things drift out of different descendant lines. And all population sizes are constricted, right?

    But lets get to the crux of the matter. Suppose you have some species of bacteria that eventually grew and spread around the globe and then the lines lived for a billion years. Why do you think the lines will have no detectable divergence in their aaRS genes after a billion years?

    I don’t know what aaRS genes are. I doubt there would be no detectable divergence unless there had been recent coalescence within the lineage. Does anyone claim that individuals in that lineage, whatever it is, have been separated for a billion years, or are you just making that part up? And whatever can this possibly have to do with common descent vs. common design?

  44. stcordova: And so where did eukaryotes come from then? POOF! Like I said evolution doesn’t have mechanistic explanations when it counts. “It happened but we don’t know exactly how” isn’t much of a mechanistic explanation.

    That isn’t even a publication, and if it were it would be a fringe claim. “Paleontological evidence”? Seriously? Just because you can google, that doesn’t mean you should adopt random cut & paste as your primary means of argumentation. And it still has nothing to do with common descent vs. common design.

  45. What? So soon? No no no, let’s first have ANOTHER diversion shall we?

    Diversion? You’re the guys needing diversions. I put all this stuff about mechanistic problems for common descent, and not one rebuttal that involves substantive mechanistic details! You represent common descent as physically feasible through ordinary process. Well, where are the details. You can start with this problem:

    prokaryote
    XXXXXXX

    vs.

    eukaryote
    iiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiii

    and explain how does Theobald’s (or whoever’s) cherry picking of the exons square with reality.

    How do the claims of mostly random walks in the non-similarities in the same protein between species square with the constraints I’m describing. You guys don’t even consider these difficulties, much less address them. When I point them out, you claim DIVERSION. No, these are relevant, you only claim diversion because you claim it isn’t relevant. And that’s the problem.

    Anyway, you don’t seem to appreciate there is a difficulty in claiming universal common ancestry when all the creatures seem to trace their MRCA to something recent relative to geological time. You don’t find that disconcerting?

  46. Rumraket: Bacteria and archaea nest within the prokaryote clade.

    What prokaryote clade? If there’s a prokaryote clade, aren’t eukaryotes part of it? According to current data, the original eukaryote host cell was most closely related to a group within Archaea. If there’s a prokaryote clade, it’s a junior synonym of “life”.

  47. stcordova: Diversion?You’re the guys needing diversions.I put all this stuff about mechanistic problems for common descent, and not one rebuttal that involves substantive mechanistic details!

    Yes, because none of those are problems for common descent. They are at most problems for the natural origin of certain features of some organisms. That isn’t relevant to the question of common descent. How many times has this been brought to your attention?

    Anyway, you don’t seem to appreciate there is a difficulty in claiming universal common ancestry when all the creatures seem to trace their MRCA to something recent relative to geological time.You don’t find that disconcerting?

    I would if it were true. What evidence do you have for a recent universal common ancestor? Or if that isn’t what you mean, please state your claim clearly. Do you mean that the most recent common ancestor within a given species isn’t as old as all life? Why should it be? Why in fact should it be as old as the species’s divergence from its closest relative? And this after supposedly reading a Wikipedia page on coalescence!

  48. And whatever can this possibly have to do with common descent vs. common design?

    If the MRCAs of all species look recent, you wouldn’t find that disconcerting?

  49. stcordova: If the MRCAs of all species look recent, you wouldn’t find that disconcerting?

    Define “recent”. And no, because I understand coalescence. Of course there are exceptions, mostly due to frequency-dependent selection. That’s why humans and chimps share HLA alleles, for example. The coalescence of HLA alleles is deeper than the human-chimp split. Would you find that disconcerting?

  50. Rumraket,

    No Bill, deleterious mutations are not evidence against evolvability by random change. All theories of molecular evolution have deleterious mutations as a factor and phenomenon that happens. They neither contradict nor constitute evidence against it.

    Deleterious mutations are a problem for the theory. Especially mutations that can stop a proper birth from occurring. I know the theory acknowledges deleterious mutations however it underestimates their effect in complex functional protein groups.

    Deleterious mutations that can halt embryo development are like land mines. If there is only one and the field is large you are probably ok. As the number goes up your odds of finding new function through a random walk approaches zero.

    Design avoids the walk through the mine field.

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