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.

4,650 thoughts on “Common Design vs. Common Descent

  1. Mung,

    Not if Y is obtained by cherry-picking only the data that forms a nested hierarchy.

    One has to pick data somehow, in a trillions-of-bases system.

    In the SINE paper I referenced several derails ago, the authors ‘cherry-picked’ 36 SINE sequences. By a very simple process, assuming that all possessors of a given insert received them from a common ancestor, it was possible to generate a robust tree. In doing so, they discovered instances of incomplete sorting – where a SINE had not become fixed before speciation. These were identifiable by being incongruent. The ambiguities themselves can be resolved by ‘cherry-picking’ some more sites. The data on the broad scale gave trees congruent with those produces on mitochondrial DNA (cherry-picked!). Other researchers have cherry picked haemoglobin, certain intronic sequences, etc etc etc. By a consilient set of instances of so-called cherry picking, we find a tree that consists of little but cherries. I bet one could do the same on the clade that includes … well … cherries. How so?

  2. Corneel: Mung: And if we talk only of single-celled organisms does that still hold?

    We now it works for metazoans, where HGT is negligible. Why are you suddenly using special pleading for microbes? You are like an upside-down creationist; most only get excited when dealing with humans and ignore bacteria.

    It holds even for microbes the vast majority of the time. There are many many more cell divisions for any particular instance of HGTf or a particular gene. And when there is HGT, is is usually restricted to a few genes. The number of nucleotides propagated vertically still massively outweighs the number of nucleotides propagated horizontally for universally conserved genes.
    So much so, that even behind the rampant HGT near the root, a central tree-like trend still stands out:

    Pere Puigbò, Yuri I Wolf, and Eugene V Koonin. Seeing the Tree of Life behind the phylogenetic forest. BMC Biol. 2013 Apr 15;11:46. doi: 10.1186/1741-7007-11-46.

    The concept of ‘horizontal genomics’ involves an internal contradiction because the notion of horizontal gene transfer (HGT) inherently implies the existence of a standard of vertical, tree-like evolution, and most of the existing methods for HGT detection are based on the comparison of gene trees to a standard ‘species tree’, in practice often the rRNA tree [16,17]. If the vertical standard does not exist, the concept of HGT becomes effectively meaningless, so all we can talk about is a network of life, with nodes corresponding to genomes and edges reflecting gene exchange [18]. The stakes here are high because replacement of the TOL with a network graph would change our entire perception of the process of evolution and invalidate all evolutionary reconstruction based on a species tree. However, the tree representation is by no means superfluous to the description of evolution because the very process of the replication of genetic information implies a bifurcating graph – in other words, a tree [19]. Thus, the key question is [1,20]: in the genome-wide compendium of phylogenetic trees, that we denoted the Forest Of Life (FOL), can we detect any order, any preferred tree topology (branching order) that would reflect a consensus of the topologies of other trees?

    We set out to address the above question as objectively as possible, first of all dispensing with any pre-selected standard of tree-like evolution. The analyzed FOL consisted of 6,901 maximum likelihood phylogenetic trees that were built for clusters of orthologous genes from a representative set of 100 diverse bacterial and archaeal genomes [1]. The complete matrix of topological distances between these trees was analyzed using the Inconsistency Score, a measure that we defined specifically for this purpose that reflects the average topological (in)consistency of a given tree with the rest of the trees in the FOL (for the details of the methods employed in this analysis, see [21]). Although the FOL includes very few trees with exactly identical topologies, we found that the topologies of the trees were far more congruent than expected by chance. The 102 Nearly Universal Trees (NUTs; that is, the trees for genes that are represented in all or nearly all archaea and bacteria), which include primarily genes for key protein components of the translation and transcription systems, showed particularly high topological similarity to the other trees in the FOL. Although the topologies of the NUTs are not identical, apparently reflecting multiple HGT events, these transfers appeared to be distributed randomly. In other words, there seem to be no prominent ‘highways’ of HGT that would preferentially connect particular groups of archaea and bacteria. Thus, although the NUTs cannot represent the FOL completely, they appear to reflect a significant central trend, an attractor in the tree space that could be equated with the STOL (Figure ​(Figure11).

    Figure 1:
    The central tree-like trend in the phylogenetic forest of life. The circles show genomes of extant species and the grey tree in the background shows the statistical central trend in the data. For the purpose of illustration, the figure shows an ‘FOL’ made of 16 trees with 20 deviations from the central tree-like pattern.

  3. Rumraket: It holds even for microbes the vast majority of the time.

    I suspected as much, thanks. Mung may take issue with “the vast majority of time” though.

  4. Rumraket,

    HGT is itself informative, of course. You detect it by incongruity. But instead of discarding it as not-a-cherry, an HGT event is inherited by all descendants, just as a within-genome transposition or mutation, and therefore becomes a phylogenetic marker for a clade, even if incongruent with the wider clade in which it sits (nests). For the well-known example of the transfer of a retrovirus from primates to cats, we have 3 phylogenetic systems for which detective work was done: the primates, the cats with and without the insert, and retroviruses. From this, one can tell what the element was, the direction of travel, and one also has a small data point to add to the mountain of evidence of relationships among the smaller cats.

    The Design explanation, meanwhile, is … ?

  5. keiths:

    Mung is right on both counts. Cumulative change does not depend on selection, and stochastic processes can be biased.

    Mung:

    I am framing this.

    Even a Mung can be right sometimes. 🙂

    Too bad you had to go and ruin it.

  6. Rumraket,

    More tomorrow, but for now, consider the example I gave Bill:

    A manufacturer could have taken its entire line of devices and added a USB-C port to each of them, leaving the remainder of the design unchanged. All of the resulting devices would have been USB-C compatible, and the ONH would have been hugely violated by the parallel introduction of this functionality across the product line.

    It’s not difficult for a Designer/Guide to mess up the ONH, in this case by what amounts to a massive case of parallel HGT.

  7. GlenDavidson: For you, I think there’s some kind of mystical connection between development and evolution, but it’s really just what you get from common descent.

    There is no mystical connection but similar patterns which are observable. If I compared the path taken by the earth in relation to the sun with the path of the sun in relation to the centre of the galaxy would you say that I believed there was some kind of mystical connection between the two?

    I am not engaging in any mysticism, I am taking a holistic approach rather than the usual reductionist one. If we look at the development of an individual human, the single celled zygote, the embryo, the baby, the adult; these are all complete unitary organisms. Physical substances may come and go but they maintain their unity through metabolic activity. Life on earth has been a unity from the beginning. Species may come and go but life continues by maintaining a balance. Without this overall balance there was nothing to prevent the dominant species being so successful that they suffocated in their own waste and life would have been over before it even had a chance to get going. Living processes ensures the environment is suitable for the continuation of life. This type of feedback cannot be achieved through blind processes from below

    Here is how Malte C. Ebach compares Goethean science to current biological thinking.

    There are currently two fundamentally different ways of thinking influencing comparative biology. The dominating mode of consciousness, herein termed the analytical mind (Bortoft’s intellectual mind [Bortoft, 1998a, p.52]), is predisposed to Cartesian (dualistic) perceptions of the world. This dualistic way of thinking has become the driving force of a mechanised reductivist brand of science widely practised today.

    Goethe remains as one of the few who rejected the ‘objectivity’ of Galilean/Newtonian physics as a misdirected and mechanised way at looking at Nature (Goethe, 1995, p.311). In Goethe’s approach, the science of comparative biology recognised and embraced the involvement of the observer. The assertion of a barrier between the observer and the thing observed is a dualistic concept that was demolished by Goethe in his Morphologie (Goethe, 1981; see Goethe, 1995). Goethe’s approach was influenced by the writings of Benedict de Spinoza who validated experience and thought as a direct way of knowing phenomena. The monistic philosophy of Goethe did not attempt to divide our knowledge of the world between what we think and what we see. To him, knowledge is our experience—an activity of our sensing mind.

    The significance of the holistic application of the mind’s ability to discover something of the world is difficult to appreciate for those who are trained to think analytically. The analytical mind only ‘sees’ phenomena in terms of empirical tests or in reference to how they fit some mechanism or model. Under the analytical mind, our experiences are subjective and must be open to ‘falsification’ to be devoid of opinion. Phenomena are therefore generated as by-products of models, tests and predictions. If we replace our own experiences with models and theories, then the world can only be ‘united’ (i.e. made intelligible) by a general or unifying theory: one which all phenomena obey (i.e. natural selection, dispersal etc.).

    As I have repeatedly said, but cannot too much emphasize, the actual value and invincible strength of the Theory of Descent does not lie in explaining this and that single phenomenon, but in the fact that it explains all biological phenomena, that it makes all botanical and zoological series of phenomena intelligible in their relations to one another (Haeckel, 1925, p 363 original italics).

    Those, like Ernst Haeckel, who champion their unifying model or theory, see the world by generating explanations rather than experiencing phenomena. A giraffe, for instance, is no longer observed as an interaction of qualities, but as a quantification of parts that fulfill the requirements of a theory or model.

    Holistic comparative biology, a small developing field and a remnant from Goethe’s day, has remained sidelined. Goethean science should not remain a footnote to science, but rather it should become an important and active approach. Comparative biology will be greatly enhanced by extending the holistic approach that was initiated by Goethe, rediscovered by Agnes Arber and defended by many contemporary scientists and philosophers, in particular Ronald Brady.

    The premise of comparative biology is the discovery of homology, namely, the relationship of the parts, called homologues. The analytical approach assumes evolution has occurred and seeks a mechanism to explain its history. Organisms are therefore subjected to mathematical and statistical scrutiny, divided into infinitesimal parts, calculated as probabilities and expressed as units or even in terms of ‘DNA barcodes’.

    Our own experiences of the organism however are deemed subjective, and thus a barrier between our minds and the world is raised. Homologies are no longer seen as a multiplicity of relationships that express the unity of form, but rather as scenarios that infer direct paths of descent. The further comparative biology moves towards a general model, the further it removes the scientist and the science from the ability to appreciate multiplicity in unity within the organic whole. In order to re-discover homology as an intuitive association of homologues, we need to investigate the significance of the organic whole and extend our ability to see and to perceive intuitively and re-assert the importance of classification in comparative biology.

    The liver cell does not become a liver cell because it is descended from the zygote, it becomes a liver cell in order to ensure the viability of the organic whole. DNA does not cause the liver cell to develop, it is only the means by which its constituent substances are produced.

  8. CharlieM: DNA does not cause the liver cell to develop, it is only the means by which its constituent substances are produced.

    The cells that become liver cells do so because of the local conditions the cells find themselves in, which cause particular gene expression patterns of DNA to differentiate the cell down the pathway to “liver cells”.
    It is the extracellular conditions that influence the gene-expression of the cell that determine it’s pathway of differentiation. It is basically the interaction of the DNA, through gene expression, with the surroundings, that produce differentiation in cell-lines.

  9. Rumraket: It is the extracellular conditions that influence the gene-expression of the cell that determine it’s pathway of differentiation. It is basically the interaction of the DNA, through gene expression, with the surroundings, that produce differentiation in cell-lines.

    I consider this a step in the right direction 🙂

  10. keiths: The fact that there’s only one assumption hardly makes these hypotheses reasonable.

    Sure. Let’s just forget all about Ockham’s Razor.

  11. Corneel: We now it works for metazoans, where HGT is negligible. Why are you suddenly using special pleading for microbes? You are like an upside-down creationist; most only get excited when dealing with humans and ignore bacteria.

    Why are you special pleading for metazoans?

    Yes, I could hardly care if primates share a common ancestor and we can fit primates into a nested hierarchy. I am not denying, for instance, that a nested hierarchy can be constructed for metazoans.

    Rumraket’s source seemed to indicate that the same cannot be said for microbes.

    If that’s the cased then to say that evolution predicts a nested hierarchy is only the case given special pleading. Under some conditions it does. Under other conditions it doesn’t. Sometimes it do, sometimes it don’t.

    When does it? In the cases where we see that it does.

    Is anyone going to make the case that evolution predicts a nested hierarchy for microbes?

    Evolution predicts a nested hierarchy unless the vertical signals are lost and unless the branching signals are lost. Evolution predicts a nested hierarchy except when it doesn’t. Unless there is something in place that forbids these “signals” from being lost this is what we are left with.

  12. keiths:

    The fact that there’s only one assumption hardly makes these hypotheses reasonable.

    Mung:

    Sure. Let’s just forget all about Ockham’s Razor.

    That isn’t Ockham’s Razor. It’s Mung’s Rusty Razor Blade:

    Any hypothesis that can be supported by a single assumption, no matter how ridiculous, is a reasonable hypothesis.

  13. Mung,

    If that’s the cased then to say that evolution predicts a nested hierarchy is only the case given special pleading. Under some conditions it does. Under other conditions it doesn’t. Sometimes it do, sometimes it don’t.

    When does it? In the cases where we see that it does.

    Inheritance with branching predicts that a nested hierarchy will occur. It doesn’t predict that we will always be able to recover it from a given data set.

    Is anyone going to make the case that evolution predicts a nested hierarchy for microbes?

    Yeah – why not? HGT can scrub the phylogenetic signal from vertical descent, but vertical descent is still by far the dominant mode of genetic transmission in microbes. Furthermore, when HGT occurs, evolution predicts a nested hierarchy from then on.

  14. Corneel,

    A few comments upthread, you rejected the nested hierarchy of life. Why are you trying to concoct explanations for something you don’t believe exists?

    I think Mung makes the right point. We see a pattern that looks like a hierarchy and then it gets violated. Examples are Sal’s flower where genes skip generations and convergent evolution where complex features don’t continue through generations. This type of hierarchy is what I would expect from design.

    Harshman is right. I don’t completely understand all the rules of an objective nested hierarchy. I have read Theobald and some other explanations however they have yet to make complete sense to me.

  15. keiths: More tomorrow, but for now, consider the example I gave Bill:

    A manufacturer could have taken its entire line of devices and added a USB-C port to each of them, leaving the remainder of the design unchanged. All of the resulting devices would have been USB-C compatible, and the ONH would have been hugely violated by the parallel introduction of this functionality across the product line.

    It’s not difficult for a Designer/Guide to mess up the ONH, in this case by what amounts to a massive case of parallel HGT.

    That’s true keiths but then we’re not talking about guided evolution. You’re talking about a *POOF* theory of ID.

    As I understand the term guided evolution, it’s still evolution, but there is some sort of intelligent agent selecting towards certain outcomes. If you want to posit a designer that intervenes to insert complete systems simultaneously across the diversity of life, that’s not guided evolution by any common sense interpretation.

  16. colewd,

    We see a pattern that looks like a hierarchy and then it gets violated. Examples are Sal’s flower where genes skip generations and convergent evolution

    “Sal’s flower” does not tell you what you think it tells you. Much effort has been spent trying to get this across, to no avail. Convergent evolution, meanwhile – again, done to death. It does not indicate the non-existence of the hierarchic background – quite the reverse.

    The fundamental point here is that any ‘anomaly’ is only an anomaly because of the hierarchy. The hierarchy provides a context. If there were nothing but anomaly, there would be no standard against which a feature could be judged anomalous. It is only because the prediction of the nested hierarchy is confirmed at non-anomalous sites that the anomalies you cherish are even detectable. You cannot destroy common descent by features whose status depend on it.

  17. colewd: This type of hierarchy is what I would expect from design.

    You’re good at saying that, never able to say why.

    With Mac designers, complex “organs” (better designs) are taken in new from unrelated sources, like from Toshiba and Intel. With life, ancestry prevents this, which is why we don’t have bird optics and birds don’t have our earbones. Birds get better lungs, mammals get lactation. Mac designers aren’t so limited, and you constantly fail to deal with this point.

    You don’t and can’t explain why this is the case. Merely restating that you’d expect what we see doesn’t change the fact that it is not what reasonable people would expect of designers. You’ll have to do a lot better than just show how biased you are on the matter.

    Glen Davidson

  18. Allan Miller,

    “Sal’s flower” does not tell you what you think it tells you. Much effort has been spent trying to get this across, to no avail. Convergent evolution, meanwhile – again, done to death. It does not indicate the non-existence of the hierarchic background – quite the reverse.

    Maybe kieths can explain how inserting a ubs port violates a nested hierarchy and genes skipping generations does not. I think you are sweeping contradictory data under the rug.

  19. Rumraket,

    That explains our disagreement, then. You have a much more restrictive view of what “guided evolution” is than I do. And than most guided evolutionists do.

    More on this later.

  20. colewd,

    Maybe kieths can explain how inserting a ubs port violates a nested hierarchy and genes skipping generations does not. I think you are sweeping contradictory data under the rug.

    As we keep explaining and explaining and explaining to you, genes don’t “skip generations.” That is just your goofy misinterpretation of the data.

  21. GlenDavidson,

    With Mac designers, complex “organs” (better designs) are taken in new from unrelated sources, like from Toshiba and Intel. With life, ancestry prevents this, which is why we don’t have bird optics and birds don’t have our earbones. Birds get better lungs, mammals get lactation. Mac designers aren’t so limited, and you constantly fail to deal with this point.

    And whales get echo location and humans and share zebrafish genes that mice and chickens don’t have. The designer is limited to making changes to the DNA code and the splicing code. The initial architecture creates the constraint which creates a partial hierarchy.

  22. keiths,

    As we keep explaining and explaining and explaining to you, genes don’t “skip generations.” That is just your goofy misinterpretation of the data.

    It’s an exact description of what the data is showing.

  23. Rumraket: That’s true keiths but then we’re not talking about guided evolution. You’re talking about a *POOF* theory of ID.

    As I understand the term guided evolution, it’s still evolution, but there is some sort of intelligent agent selecting towards certain outcomes. If you want to posit a designer that intervenes to insert complete systems simultaneously across the diversity of life, that’s not guided evolution by any common sense interpretation.

    Yes, but what do you understand about the term “guided evolution”? As used for anything but selective breeding or something of the kind, it’s just a fluid concept that could have a “designer” operating very sparingly and in a manner impossible to distinguish from the other processes of evolution, or it could be more like computer or auto evolution, where there is legacy, but rather too much change to produce a nested hierarchy.

    On the one hand, of course we have to consider that we can’t rule out Behe’s designer, the sparing designer, since it’s a logical possibility. However, I don’t like granting that much credit because we’ve never ever seen anything like it, and, really, a designer tweaking life for billions of years while leaving the nested hierarchy intact seems a tad incredible. Suspiciously close to God. An alien species presumably could do it, in theory, but does it really seem at all likely?

    On the other hand, we do have design evolution quite visible, and it almost never produces a visible nested hierarchy of product.

    That’s why I think keiths has a point, even though theoretically one could imagine a kind of guided evolution that would leave behind a nested hierarchy. I don’t think that we should grant the IDists just any ad hoc “save the hypothesis” scenario. If it’s evolution by design, the evidence only gives us design evolution sans nested hierarchy. Bare possibility says that it’s not impossible for guided evolution to give us nested hierarchies, but it has no evidence in favor of it. Evidenceless possibilities are trumped by examples that have evidence in favor.

    One might say, well, what of selective breeding? But that involves humans who are not highly capable designers of life, almost not at all analogous with the Designer who supposedly can design the extreme complexities of molecular biology.

    So on the one hand I think that Harshman’s right to at least consider the possible “tweaker of life,” but on the other hand, he seems to give too much credit to a possibility for which no examples are found. Keiths is right that one is a much more credible scenario than the other, the case with design that doesn’t leave nested hierarchies, but seems too willing to throw away even the logical possibility of Behe’s tweaker. Yet Behe’s tweaker is certainly far too unlikely a being to give it much credit.

    Glen Davidson

  24. colewd:
    keiths,

    It’s an exact description of what the data is showing.

    No, it’s an exact description of your misunderstanding of the data. The data show a pattern, and you explain the pattern in a nonsensical way. The correct explanation is that mouse and chicken (or some ancestor in each case, which we could determine by looking at a lot more species) independently lost or, more probably, inactivated a gene. Since gene loss happens all the time, it isn’t surprising that a few genes are lost twice, no more surprising than multiple occurrences of any other single mutation.

  25. colewd:
    GlenDavidson,

    And whales get echo location

    You mean that they vocalize and sense sound in a particular manner? Yes, I can’t imagine how that might evolve (even we are capable of a very crude sort of echolocation).

    and humans and share zebrafish genes that mice and chickens don’t have.

    Yeah, just like you’d expect from common descent.

    The designer is limited to making changes to the DNA code and the splicing code.

    I guess you decided that.

    The initial architecture creates the constraint which creates a partial hierarchy.

    Just like with evolutionary processes.

    Only I’m not sure why God would be so akin to evolutionary processes.

    Of course you explained nothing at all about why Macs get large infusions of new information, while life is stuck with ancestral information plus tweaking.

    Glen Davidson

  26. colewd: The designer is limited to making changes to the DNA code and the splicing code. The initial architecture creates the constraint which creates a partial hierarchy.

    Why would a designer be limited to make just changes to existing DNA? What do you know about the abilities or motivations of the designer to justify that conclusion? If the designer created the initial architecture,what would constrain it from creating another architecture?

  27. GlenDavidson: So on the one hand I think that Harshman’s right to at least consider the possible “tweaker of life,” but on the other hand, he seems to give too much credit to a possibility for which no examples are found.

    That isn’t my purpose. I merely wish to disentangle two arguments that ought to be separate: the cause of the hierarchy of life and the cause of innovations. The hierarchy of life implies common descent regardless of the cause of innovations. There is no purpose in discussing the cause of innovations when arguing about the explanation for the hierarchy of life. Whether that hierarchy argues against guided evolution or whether guided evolution is expected to produce a hierarchy is irrelevant to the matter under discussion. To think otherwise, incidentally, is to admit that all of Sal’s nonsense is on-topic.

  28. Mung: Rumraket’s source seemed to indicate that the same cannot be said for microbes.

    Not really.

    If that’s the cased then to say that evolution predicts a nested hierarchy is only the case given special pleading. Under some conditions it does. Under other conditions it doesn’t. Sometimes it do, sometimes it don’t.

    This is too general and vague to be meaningful. The way you express yourself here it could apply to literally all predictive theories in science. Under some conditions X, outcome Y is predicted. Under other conditions it doesn’t. Sometimes it do, sometimes it don’t.

    Gravity predicts that what you throw up, must come down. Except if you throw it at escape velocity or above.

    When does it? In the cases where we see that it does.

    That’s not the actual answer anyone gives to that question. It’s an answer you just sat there and made up.

    The actual answer is quite complicated and depends on different factors for different conditions, but limits can be calculated. To pick an example (character reversals) from Theobald’s list of caveats with phylogenetics: Over sufficiently long time scales, the continued accumulation of mutations can erase phylogenetic signal. Any particular gene is of finite length, and if mutations continue to accumulate over billions and billions of generations, eventually the entire gene-sequence could be replaced several times over. The amount of time required of course also depends on mutation rate and the length of the sequence. While statistically very unlikely, it could even fully revert to the ancestral state.

    The shorter the sequence, the more likely it is that it could have been fully replaced and therefore phylogeny has been erased. But this very fact also suggests the solution: Use a longer sequence (or just more loci, or slower evolving ones) to construct a (consensus) phylogeny from.

    Is anyone going to make the case that evolution predicts a nested hierarchy for microbes?

    I believe I cited a paper up above in this very thread that shows that even at the deepest nodes evolution is still significantly tree-like.

    One could make many detailed predictions about nested hiearchy evolution for microbes involving mutation rates and generation times. All twelve independent lineages in Lenski’s evolution experiment yield nesting hiearchies. Despite the fact that there has also been convergence observed for some loci.

    Look, the statement “evolution predicts a nested hiearchy” is not to be confused with “evolution always and only predicts a nested hiearchy for all loci under all possible conditions”. The latter isn’t the case and nobody has claimed it is. If that is what you take the statement “evolution predicts a nested hiearchy” to mean, you have been fighting a straw-man.

    Evolution predicts a nested hierarchy unless the vertical signals are lost and unless the branching signals are lost. Evolution predicts a nested hierarchy except when it doesn’t.

    Oh back to this dumb shit again. You’re not somehow saying something that isn’t true for all predictive theories in science. They predict what they do under some range of conditions, which if violated, the prediction no longer holds.

    Unless there is something in place that forbids these “signals” from being lost this is what we are left with.

    Any given point of data can be lost due to loss of the conditions that yield the nested hiearchy, but given the total amount of data to which this would have to happen simultaneously, it is simply too unlikely to be able to fully erase the signal. Life will not be able to exist on this planet long enough for the phylogenetic signal detected in universally conserved ribosomal sequences to be lost. In 5 billion years or so the Sun will have swelled to a red giant, boiled away the oceans and scorched every square-inch of rock sterile, while all geological strata that contained traces of life will have been remelted and replaced. Then there will be no nested hiearchy any more.

  29. John Harshman: That isn’t my purpose. I merely wish to disentangle two arguments that ought to be separate: the cause of the hierarchy of life and the cause of innovations.

    I guess I think that they’re properly entangled, due to pragmatically limited sources of innovation.

    Conceptually the two may be disentangled, of course, especially for didactic purposes. However, I’m not sure that it really helps in getting anything across to the creationists/IDists. But then, what does?

    Glen Davidson

  30. This thread has now over 2,133 comments. Thanks to all the participants. I hope we can continue this lively and compelling discussion.

  31. stcordova:
    This thread has now over 2,133 comments.Thanks to all the participants.I hope we can continue this lively and compelling discussion.

    And yet not one of those comments from you or any other creationist is actually on topic. That doesn’t seem very lively or compelling to me.

  32. I myself have learned several things from this thread actually. Some of my own misconceptions about phylogenetic methods have been (I hope) corrected. So at least it hasn’t all been totally wasted effort.

  33. Those of us who know Sal can imagine how he will try to spin this thread for his “subscribers”.

    Just send them here, Sal, so they can see your ass being handed to you while you attempt to avoid the key question.

  34. Rumraket: This is too general and vague to be meaningful. The way you express yourself here it could apply to literally all predictive theories in science. Under some conditions X, outcome Y is predicted.

    It’s hilarious that you think that evolution is predictive science.

  35. Rumraket: Gravity predicts that what you throw up, must come down.

    You’re so close to understanding. If your prediction sounds like nonsense abandon the your prediction. Evolution doesn’t even predict branching, much less a nested hierarchy.

  36. Mung: It’s hilarious that you think that evolution is predictive science.

    It’s ironic that you think it’s not. Weren’t you all up in arms about how it was obvious what would follow in the many weasel-related. threads given certain conditions?

  37. colewd,

    Maybe kieths can explain how inserting a ubs port violates a nested hierarchy and genes skipping generations does not. I think you are sweeping contradictory data under the rug.

    Give me an example – a biological example – in which a convergent feature calls into question common descent.

  38. colewd,

    It’s an exact description of what the data is showing.

    Again, give an actual example of a gene that ‘skips generations’.

  39. keiths,

    Just send them here, Sal, so they can see your ass being handed to you while you attempt to avoid the key question.

    Sadly, they, like colewd, will see Sal as the hero. Much as J-Mac was backslapped despite rampant incoherence. I hope no-one thinks they will get anywhere with this.

  40. Mung: You’re so close to understanding. If your prediction sounds like nonsense abandon the your prediction. Evolution doesn’t even predict branching, much less a nested hierarchy.

    Branching is inevitable for any situation where more than one offspring survives. Mung, please just step back and try to think for a moment. Let’s take the microbe evolution which you think doesn’t yield a nested hiearchy. One bacterium exists, it divides so there’s two. That’s branching right there. One cell division, two independent lineages now exist. They each divide again. Four branches. Every bacterium in the history of life that established a colony somewhere, whether on a rotting carcass on an agar-plate in the laboratory, produced it’s very own tree of life from itself as the common ancestor of all it’s billions of descendants.

  41. Rumraket,

    Even lower-level, it’s an inevitable consequence of semiconservative replication of DNA. When a DNA molecule replicates, the two new molecules are commonly descended from the first. When each of those replicates … hard to draw without drawing a tree.

  42. keiths:

    Just send them here, Sal, so they can see your ass being handed to you while you attempt to avoid the key question.

    Allan:

    Sadly, they, like colewd, will see Sal as the hero.

    That’s probably true for anyone dumb enough to sign up as one of Sal’s paid “subscribers”. On the other hand, it might create at least a smidge of cognitive dissonance to see their hero running away from a simple and obvious question.

    They’ll get that if they come here, but not if they rely on Sal’s notoriously dishonest accounts of his debates.

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