Miracle of Evolution – The Appendix

In a recent thread here at TSZ the question was raised as to whether naturalism is comfortable with highly typical events. My answer to that question was quite so. Exhibit: the appendix.

Although it is widely viewed as a vestigial organ with little known function, recent research suggests that the appendix may serve an important purpose. In particular, it may serve as a reservoir for beneficial gut bacteria. Several other mammal species also have an appendix, and studying how it evolved and functions in these species may shed light on this mysterious organ in humans.

But wait. There’s more…

Heather F. Smith, Ph.D., Associate Professor, Midwestern University Arizona College of Osteopathic Medicine, is currently studying the evolution of the appendix across mammals. Dr. Smith’s international research team gathered data on the presence or absence of the appendix and other gastrointestinal and environmental traits for 533 mammal species. They mapped the data onto a phylogeny (genetic tree) to track how the appendix has evolved through mammalian evolution, and to try to determine why some species have an appendix while others don’t.

They discovered that the appendix has evolved independently in several mammal lineages, over 30 separate times, and almost never disappears from a lineage once it has appeared.

Evolved independently over 30 separate times! Now that’s right up there in miracle territory if you ask me. I mean, what are the odds!?

For those who have access to this paper, do they really explain how the appendix evolved 30 or more times?

Of course, I’d also love to hear from all the fans of the miraculous powers of evolution just how they think it came to pass that the appendix evolved 30 independent times.

Source:

https://www.sciencedaily.com/releases/2017/01/170109162333.htm

214 thoughts on “Miracle of Evolution – The Appendix

  1. Frankie,

    If you assert that you have a process that can produce such a thing then you need to demonstrate it. If you want to make a claim you have to support it.

    So you can demonstrate Design producing appendixes? I’ll pull up a chair.

    It isn’t up to us to show there is a boundary. It is up to you to show that you have a mechanism capable of doing what you say.

    You are the one saying there is a boundary, chum.

  2. colewd:
    Rumraket,

    How many mutations do you think are required to build an appendix?

    What difference does it make? If it were 100 or 10,000 the evidence still shows evolution over deep time.

    Why do YECkies love to argue if science can’t provide every last detail then science knows absolutely nothing?

  3. Allan Miller:
    Frankie,

    Word-gaming on Darwin’s choice of word: providing comfort to Creationists for 160 years and counting.

    Darwin was the one word-gaming, Allan. Nature doesn’t select and he knew it. But he needed something catchy even though it meant stretching the truth.

  4. Allan Miller: You are the one saying there is a boundary, chum.

    That is incorrect. I am saying that you don’t have any way to test your claims. And all you can do is try to talk about some boundary. Obviously the boundary is your inability to show that you have a mechanism capable of producing the changes required of universal common descent.

    I can show you design producing insulin with bacteria. I can show you design with GMOs. I can show you design with an entire bacterial genome. Can you show us blind and mindless processes doing any of that?

  5. Is macroevolution just an accumulation of microevolution? With the advent of developmental biology that answer is no as genes that influence traits are not the same as the genes that influence body plans.

    Loci that are obviously variable within natural populations do not seem to lie at the basis of many major adaptive changes, while those loci that seemingly do constitute the foundation of many if not most major adaptive changes are not variable.- John McDonald, “The Molecular Basis of Adaptation: A Critical Review of Relevant Ideas and Observation”, Annual Review of Ecology and Systematics: 14, 1983, p77-102

    I am not using the quote to say that macroevolution is impossible or has been refuted. Just that it isn’t an accumulation of micro evolutionary changes. And apparently that has been known for several decades.

  6. newton: What is the alternative,somehow it was designed and caused 41 times?

    There is no alternative to evolution, therefore it evolved, even if we don’t know how.

    Is that the logic?

  7. dazz: Is it correct to conclude that the appendix is not a vestigial organ then…

    That is one conclusion of the paper.

    Thus, we can confidently reject the hypothesis that the appendix is a vestigial structure with little adaptive value or function among mammals.

  8. Frankie,

    Nature doesn’t select and he knew it.

    We all know it. Genes aren’t selfish either. Makes no difference to the phenomena to which the terms are attached.

  9. Frankie,

    That is incorrect. I am saying that you don’t have any way to test your claims. And all you can do is try to talk about some boundary. Obviously the boundary is your inability to show that you have a mechanism capable of producing the changes required of universal common descent.

    Why do you lot insist on seeing the word UNIVERSAL in front of any mention of Common Descent? colewd does the same. I didn’t put it there.

    Nonetheless, you have decided, with no apparent rationale, that a CommonDescent/Common Design boundary exists at approximately the family level – the ‘baramin’. I have no reason to accept that this boundary exists.

  10. Mung,

    What pathetic level of detail do you want?

    Absolutely none. A fully-formed Designed appendix would be quite sufficient.

  11. Allan Miller: Why do you lot insist on seeing the word UNIVERSAL in front of any mention of Common Descent? colewd does the same. I didn’t put it there.

    So there isn’t any equivocation to what I am talking about. By not putting it there it becomes unclear what you mean by it.

    Nonetheless, you have decided, with no apparent rationale, that a CommonDescent/Common Design boundary exists at approximately the family level – the ‘baramin’.

    The rationale is body plans and what accounts for them.

    I have no reason to accept that this boundary exists.

    Besides the fact that different genes are involved? Look you don’t have a mechanism capable of accounting for the anatomical and physiological differences observed between two allegedly related organisms like chimps and humans.

  12. Allan Miller:
    Frankie,

    We all know it. Genes aren’t selfish either. Makes no difference to the phenomena to which the terms are attached.

    We know the power of artificial selection. Natural selection is impotent with that regard. Why not call it what it is- the culling of the not good enough to survive and reproduce.

  13. Mung: There is no alternative to evolution, therefore it evolved, even if we don’t know how.

    Is that the logic?

    Nope, just would like your alternative

  14. If an appendage A is currently functional, presumably its loss or reduction in function would be detrimental. That would include the back-mutation B. When the current state A arose, what is now the back mutation B was once the norm – A was a single copy in a sea of Bs. Clearly in that situation, selection would be expected to fix the improvement, just as now it acts to prevent deterioration or reversal. A is fitter than B, throughout, driving both fixation and retention.

    Detriment and benefit are the yin and yang of population frequency change through selection – the one is inevitably accompanied by the other, while polymorphism exists and there is a selective differential between variants. I don’t quite see how people think that a beneficial organ can only arise in one step, which is all that remains if the above generalised argument is accepted. Is a change to the invagination of the gut that hard?

  15. Adapa:

    Why do YECkies love to argue if science can’t provide every last detail then science knows absolutely nothing?

    Number 3 of Schopenhauer’s 38 ways to win an argument:

    Ignore your opponent’s proposition, which was intended to refer to a particular thing. Rather, understand it in some quite different sense, and then refute it. Attack something different than that which was asserted.

  16. Frankie,

    Why not call it what it is- the culling of the not good enough to survive and reproduce.

    It already has a name – natural selection.

    If you cull the ‘not good enough’, inevitably you enrich the population in the remainder. If you start with 50/50 red and blue balls, and cull the blue, inevitably you have ‘selected’ red to remain, even if that was not your intent.

  17. Frankie,

    So there isn’t any equivocation to what I am talking about. By not putting it there it becomes unclear what you mean by it.

    It is entirely clear what I mean by it. What should I put in front of ‘Common Descent’ to stop people like you and colewd reading ‘Universal’ when it isn’t there?

    Allan: Nonetheless, you have decided, with no apparent rationale, that a CommonDescent/Common Design boundary exists at approximately the family level – the ‘baramin’.

    Frankie: The rationale is body plans and what accounts for them.

    That is meaningless.

    Allan I have no reason to accept that this boundary exists.

    Frankie: Besides the fact that different genes are involved?

    There is a steady, not a sudden, increase in the extent of genetic divergence as one goes up the taxonomic series. If there were a boundary, I would expect to see it as a genetic discontinuity – a sudden leap. It is not there.

    Look you don’t have a mechanism capable of accounting for the anatomical and physiological differences observed between two allegedly related organisms like chimps and humans.

    And you do?

  18. Allan Miller: If you cull the ‘not good enough’, inevitably you enrich the population in the remainder.

    The best you get is possibly having more resources to go around.

    If you start with 50/50 red and blue balls, and cull the blue, inevitably you have ‘selected’ red to remain, even if that was not your intent.

    Actually it would be the intent by intentionally culling the blue in favor of the red. Artificial selection.

  19. Allan Miller: It is entirely clear what I mean by it.

    Not to me.

    The rationale is body plans and what accounts for them.

    That is meaningless.

    No it isn’t. You just don’t have any idea what it means.

    There is a steady, not a sudden, increase in the extent of genetic divergence as one goes up the taxonomic series. If there were a boundary, I would expect to see it as a genetic discontinuity – a sudden leap. It is not there.

    That may be true but that steady increase in extent of genetic divergence is in part of the genome that has nothing to do with body plans.

    As I posted above and you ignored:

    Is macroevolution just an accumulation of microevolution? With the advent of developmental biology that answer is no as genes that influence traits are not the same as the genes that influence body plans.

    Loci that are obviously variable within natural populations do not seem to lie at the basis of many major adaptive changes, while those loci that seemingly do constitute the foundation of many if not most major adaptive changes are not variable.- John McDonald, “The Molecular Basis of Adaptation: A Critical Review of Relevant Ideas and Observation”, Annual Review of Ecology and Systematics: 14, 1983, p77-102

    I am not using the quote to say that macroevolution is impossible or has been refuted. Just that it isn’t an accumulation of micro evolutionary changes. And apparently that has been known for several decades.

  20. Look you don’t have a mechanism capable of accounting for the anatomical and physiological differences observed between two allegedly related organisms like chimps and humans.

    And you do?

    Intelligent Design.

  21. OMagain:

    What makes them not good enough?

    Contingent serendipity. That is one reason natural selection is impotent with respect to universal common descent.

  22. Frankie,

    Actually it would be the intent by intentionally culling the blue in favor of the red. Artificial selection.

    Not if you didn’t even cull the blue intentionally …

    You can’t do one without the other. You can’t enrich in red without impoverishing in blue. You can’t cull the blue without enriching the red. You can’t say, whichever result people point to: “oh yeah … I meant to do that”. You can’t not-do-it! If you do one you do the other.

    And that applies to your definition of natural selection. It can’t not-keep the survivors, and hence enrich the population, precisely as if it were an act of intentional selection. Which is why Darwin chose the word.

  23. Frankie,

    That may be true but that steady increase in extent of genetic divergence is in part of the genome that has nothing to do with body plans.

    Prove it.

    [eta – actually no, we are broadly in agreement. Most of the differences are not related to development. The remainder, therefore are Common Descent, no?]

  24. Frankie,

    As I posted above and you ignored:

    Is macroevolution just an accumulation of microevolution?

    The fraction of a genome involved in developmental differences between these metazoan taxa is tiny. You still have the vast amount of genetic commonality to account for. And no, Common Design is not it. Not when it is digitally aligned, al la Common Descent. (Note – I left off the qualifier ‘Universal’, because I do not mean ‘Universal’).

  25. Allan Miller:
    Frankie,

    Not if you didn’t even cull the blue intentionally …

    You can’t do one without the other. You can’t enrich in red without impoverishing in blue. You can’t cull the blue without enriching the red. You can’t say, whichever result people point to: “oh yeah … I meant to do that”. You can’t not-do-it! If you do one you do the other.

    And that applies to your definition of natural selection. It can’t not-keep the survivors, and hence enrich the population, prescisely as if it were an act of intentional selection. Which is why Darwin chose the word.

    Yes, Allan, in your simple model that has nothing to do with real world populations elimination and selection are the same. However there is a difference between selection and elimination as Mayr elucidates:

    Do selection and elimination differ in their evolutionary consequences? This question never seems to have been raised in the evolutionary literature. A process of selection would have a concrete objective, the determination of the “best” or “fittest” phenotype. Only a relatively few individuals in a given generation would qualify and survive the selection procedure. That small sample would be only to be able to preserve only a small amount of the whole variance of the parent population. Such survival selection would be highly restrained.
    By contrast, mere elimination of the less fit might permit the survival of a rather large number of individuals because they have no obvious deficiencies in fitness. Such a large sample would provide, for instance, the needed material for the exercise of sexual selection. This also explains why survival is so uneven from season to season. The percentage of the less fit would depend on the severity of each year’s environmental conditions.

    I know Allan doesn’t care about Mayr but find a mistake in the message if you don’t like the messenger- which you should as he is one of the giants of evolutionary thought

  26. Frankie:
    Look you don’t have a mechanism capable of accounting for the anatomical and physiological differences observed between two allegedly related organisms like chimps and humans.

    Intelligent Design.

    How is the design implemented?

  27. Allan Miller: The fraction of a genome involved in developmental differences between taxa is tiny.

    Evidence please. You seem unable to account for the anatomical and physiological differences observed. Why is that?

    You still have the vast amount of genetic commonality to account for. And no, Common Design is not it. Not when it is digitally aligned, al la Common Descent. (Note – I left of the qualifier ‘Universal’, because I do not mean ‘Universal’).

    Common design is not it cuz you say so? Really? So what do you mean by “Common Descent”? And I already said Common Design doesn’t explain all of the similarities.

    I would think that given recombination that over the illions of form transforming generations genetic signals should be scrambled- why would we see such similarity given CHANGE is what made all of the difference?

  28. Allan Miller:
    Frankie,

    So if I say ‘Evolution’, we’re quits?

    Intelligent Design is not anti-evolution and we had just established that your position didn’t have a mechanism capable of explaining those differences. We see what intelligent designers can do around a common theme- powered engines. From that we get cars, trucks, motorcycles, planes- one common thing and many variations from it.

    So no, you already gave up the farm.

  29. newton: How is the design implemented?

    I don’t know. That question is for another time.

    However, thanks to Darwin and never superseded, yours is the position that claims to have a mechanism of numerous slight successive modifications. We are just asking for that. And if you don’t have it that is OK. What needs to be done is we start teaching the kids that we really don’t know how we evolved or even if humans could have non-humans as common ancestors. That way someone starts really looking and the mystery gets solved.

    One of them will figure out how the design was implemented but that cannot happen until they are allowed to look

  30. dazz:
    Rumraket,
    Is it correct to conclude that the appendix is not a vestigial organ then Mikkel? Because if a vestigial organ is explained by the disappearance of the selective pressure to keep it / evolve it, then it seems to me positive selective pressure is the opposite to that

    In my scenario, I took it for granted that the appendix has a postitively selected function that is useful to the organism. In that view yes, the appendix would not be vestigial.

    But if you read the article by PZ Myers it seems to conflict with that assumption and, in contrast to Mung’s source, says the appendix only evolved 4-5 times while most lineages didn’t evolve one (depending on how you define an appendix, it’s not so straightforward as there are many strange variations of that whole area) and is more like a neutral structure that exists as a byproduct of the developmental pathways that differentiate the different sections of the digestive tract.

    Incidentally I’m more inclined to believe the appendix is adaptive. That hypothesis seems to explain the data better.

  31. colewd: How many mutations do you think are required to build an appendix?

    It’s hard to quantify something like that without knowing anything about the developmental pathways that are responsible for formation of the appendix. From what little i know of basic evo-devo and evolution of gene-regulatory networks (hox genes and all that), I’m guessing very few, probably less than 30. These things are usually the result of very few genetic changes.

  32. Rumraket,

    From what little i know of basic evo-devo and evolution of gene-regulatory networks (hox genes and all that), I’m guessing very few, probably less than 30. These things are usually the result of very few genetic changes.

    I think this is a reasonable approximation. It does, however, seem like a low probability that a trial and error process could find these mutations more than once. In addition I think Hox genes are mutationally sensitive. This is an interesting op by Mung.

  33. Frankie:
    I don’t know. That question is for another time.

    Actually no, you are demanding an answer right now.

    However, thanks to Darwin and never superseded, yours is the position that claims to have a mechanism of numerous slight successive modifications. We are just asking for that.

    Yes that is how it is implemented, how is design implemented?

    And if you don’t have it that is OK. What needs to be done is we start teaching the kids that we really don’t know how we evolved or even if humans could have non-humans as common ancestors. That way someone starts really looking and the mystery gets solved.

    Since design is not anti- evolution , what is ID’s explanation to those questions? Did the designer use common descent? How are any limits to evolution designed?

    One of them will figure out how the design was implemented but that cannot happen until they are allowed to look

    Look away, but if lack of a mechanism is a problem for one theory it is for any theory lacking a mechanism.A cynical view might be there is no way to know what an unknown designer with unknown capabilities would choose.

  34. newton: Actually no, you are demanding an answer right now.

    Darwin made the claim over 150 years ago. And if you don’t have the answers then tat needs to be said to the students

    Yes that is how it is implemented, how is design implemented?

    What Darwin said is too vague, useless and as such untestable

    Look away, but if lack of a mechanism is a problem for one theory it is for any theory lacking a mechanism.

    ID isn’t a mechanistic claim but design is a mechanism

    A cynical view might be there is no way to know what an unknown designer with unknown capabilities would choose.

    We don’t have to know that. We just have to be able to use our knowledge of cause and effect relationships to come up with a scientific inference.

  35. colewd: It does, however, seem like a low probability that a trial and error process could find these mutations more than once.

    I don’t believe they’re the same mutations in each lineage where an appendix independently evolved. Rather there’s probably many different combinations that lead to roughly the same result.

    In addition I think Hox genes are mutationally sensitive.

    They are, that’s sort of the whole point. It takes only a few mutations in the regulator networks to have large-scale morphological effects.

  36. Rumraket,

    I don’t believe they’re the same mutations in each lineage where an appendix independently evolved. Rather there’s probably many different combinations that lead to roughly the same result.

    Agree that different mutations can lead to an appendix. Probably significantly more combinations that lead to a different result then an appendix. Does an appendix result in reproductive advantage?

  37. Frankie:
    How do blind and mindless processes account for regulatory networks which require planning?

    You will never get a good answer for this one.

    What you will get is, “Well, just because we don’t know every little detail…”

    or

    “Nature just so happens to do that, what’s the problem?”

  38. phoodoo: “Well, just because we don’t know every little detail…”

    Worse. We shouldn’t expect any detail at all.

    Changes in the genotype can lead to changes in the phenotype. Changs in the phenotype can cause some organisms to leave more offspring than others. And that’s a good enough “explanation” for any and every scenario you can imagine.

    We don’t need any stinking details.

  39. colewd: Does an appendix result in reproductive advantage?

    Of course! Or its neutral. Or nearly neutral! Or not detrimental enough to not exist. But by definition beneficial, because it exists you see!

    Say it in a exaggerated hackney British accent and it sounds even more fanciful.

  40. dazz: perhaps you want to know every single mutation that led to the formation of the appendix of each of the species? That’s fucking ridiculous.

    You have something that’s actually testable or you don’t. What’s ridiculous is people asserting their skepticism but then suddenly kicking it to the curb when it comes to a position they favor.

  41. phoodoo: Think niche!

    Niche the blind designer? Oh look, here’s a niche that designs appendixes. Except when it doesn’t. How testable is that, pray tell?

  42. Frankie:
    How do blind and mindless processes account for regulatory networks which require planning?

    You haven’t shown they require planning.

  43. Frankie

    ID isn’t a mechanistic claim but design is a mechanism

    If just saying “design” counts as a mechanism then just “evolution” is a mechanism too. Of course science has a lot more details than just saying “evolution”. We have a timeline, and the known processes which produce genetic variation, and the empirically observed results of natural selection. The IDiots have nothing beyond “it looks designed to me!”.

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