Sunday, July 21, 2013

The Many Faces of Sal Cordova

The IDiots are getting all excited about Nick Matzke because he dared to criticize Darwin's Doubt, a book about evolution written by a philosopher.

The latest post is by Salvador Cordova (scordova) on Uncommon Descent [Two-faced Nick Matzke].

I don't think I can do full justice to the stupidity in this post, you have to read it yourself. Here's the gist ...

Matzke said, quite correctly, that phylogenetic methods can only detect sister groups, not ancestors. This is pretty obvious in the case of sequences because, in most cases, we don't have access to DNA or proteins from extinct ancestors.

Salvador Cordova thinks he was the first one to realize this ...
Not much difference between what Matzke said and I said! I’ve been telling him that since 2006, and now he finally acknowledges it publicly.
Now that's good for a laugh at the expense of IDiots but it gets even funnier. The IDiots think that the absence of living ancestors proves that god(s) created modern species.
I’ve said that it was creationists (like Linnaeus) before Darwin’s time who lumped humans along with the primates, and the primates along with the mammals, etc. The creationists perceived the “sister groups” with no physical ancestor (which suggests the “parent” was an idea in the mind of God, not a physical common ancestor).

The reason Darwinists have all these phylogenetic conflicts is that the ancestors which would resolve all the conflicts are the very ones they will not admit a priori because those ancestors are conceptual, not physical, and conceptual ancestors are anathema to Darwinsits because conceptual ancestors imply ID.
Like I said, you have to read the whole thing ... if you can stomach it.

I wonder why we call them IDiots?


52 comments :

  1. Cordova's post on Uncommon Descent is a dangerous thing to read. It made me want to bang my head against the wall.

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  2. Or you could argue with a creationist, which amounts to the same thing.

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  3. It is not even strictly true, by the way, that phylogenetic analyses don't contain ancestors, although they only do in a very indirect way. The internal nodes of any phylogeny can be interpreted as hypothetical ancestors and one can infer ancestral character states at those nodes, and of course that is regularly done in evolutionary biology. (E.g. on the lines of "the common ancestor of this group of plants most likely had dry fruits, a woody habit, and occurred in South East Asia.")

    What is more, you can have zero length branches in molecular phylograms. If a terminal is sitting on such a zero length branch it means that the phylogenetics software has reconstructed the sequence at an interior node of the tree as identical to that of the terminal. In other words, you can have ancestral sequences that are still extant, which is a commonplace occurrence in phylogeographic studies.

    It gets more complicated for morphology-based phylogenetics and species trees analyses. At least in the former case, the same may happen but depending on your species concept an ancestral species would by definition not be identical to an extant species even if they are completely indistinguishable. But that is fairly academic stuff.

    More to the point, one could also enter morphological data from a fossil into the analysis and find that it sits on an internal node with a zero length branch. You can never be sure whether it is the actual ancestral species or merely a very very close relative of it but it would be as close as one can ever possibly get.

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    1. Yes, phylogenetics can be used both to reconstruct gene-sets and indeed actual genome sequences using ancestral sequence reconstruction. This has been known for some time.

      In fact many phylogenetic studies done trying to reconstruct the last universal common ancestor, curiously seems to converge on a chemoautotrophic thermophile.

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    2. That is interesting, hadn't heard of that. A chemoautotroph would make sense, although it has to be admitted that these inferences get less reliable the more extinction has happened along a deep branch, and I have no idea how much of the really ancient diversity has been lost. The oxygen catastrophe would have wiped out a lot.

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    3. Yes it's extremely interesting. Here's some recent experimental work on the subject:
      Experimental evidence for the thermophilicity of ancestral life
      http://www.pnas.org/content/early/2013/06/12/1308215110.abstract

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  4. These family trees are not made using biological evidence.
    They still just connect things by morphology and now by DNA concepts.
    Yet from a common blueprint from a creator would also explain these things but with no need for descent relationships.
    Like need would lead to like reply.
    So there is no such thing as mammals or reptiles but rather they simply have some like traits for like needs as a original blueprint would account for.
    Drawing descent ideas between and from different kinds of " mammals" is just speculation.
    Its not biological evidence as evolutionists think it is.

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    1. That's odd, I thought I had clicked on the reply button. See next comment.

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    2. RB:"Yet from a common blueprint from a creator would also explain these things but with no need for descent relationships."
      You're saying there's no need for 'descent', but there's no need for a common bluprint or a designer here, so.....



      RB:
      'They don't use biological evidence, they only use morphology and genetics'

      That really says it all, doesn't it?

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    3. Byers opines: "So there is no such thing as mammals or reptiles"

      At the Scopes trial, when WJ Bryan said humans were not mammals, everyone thought it was a joke. It wasn't and it still isn't.

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    4. Robert Schenck
      Morphology comparisons and DNA are not biological investigation of the relationships between creatures. They are themselves just speculations of how creatures are related.
      Yet there is no actual biological research going on.
      Just connecting dots.
      Just lines of reasoning.
      So finding OTHER lines of reasoning for relationships by morpholoy and DNA nullify's the first lines.
      So a common blueprint EQUALLY would predict these relationships by DNA/morphology.
      Therefore these things are not independently standing on the merits of biological investigation.
      No biology is going on here and so error can have a option of having entered through a crack in the wall.

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  5. I assume you would only count it as "biological evidence" if we could observe all billions of years of evolution while they happened. See, there is this thing called plausibility, and it allows us to weigh different options against each other even while we don't have a complete picture of every tiny detail that is going on.

    We can observe evolution happening in every living population around us, even within the human species, and we arrive at some fairly plausible looking scenarios if we extrapolate from there (and that is before mentioning stratified fossils and all that).

    Similar evidence for a creator is nonexistent. In fact the entire argument is circular: complex life is taken to be evidence for its creator, but that only works if life is assumed to be created in the first place, for which one has to assume the existence of a creator in the first place, and round and round we go. And that is before we ask who created the creator.

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    1. Yes we observe evolution happening. However what we observe cannot be extrapolated into universal common descent. There isn't any instance of microevolution that can be extrapolated into new body parts and new body plans.

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    2. Yes there is, it can all be extrapolated into common descent and macroevolutionary bodyplan transitions, since it's simply "more of the same". There is no magical barrier that mysteriously comes down from nowhere and "stop" the accumulation of microevolutionary change. It's a creationist fantasy, and you people have never been able to detail an actual mechanism that would achieve this sudden "only within-kind" evolution-blocking effect.

      Furthermore, since "mere" microevolutionary evolution has been directly observed to impact both bodyplan morphology and behavior, foremost of which are selective breeding experiments with many large animals like dogs, cows etc.(and that selective breeding was utilised long before we knew anything about evolution) - we have therefore direct evidence that genetic changes influence bodyplans and that natural selection over longer timescales can result macroevolutionary change. To deny this is, again, to insist that there's some mysterious magical barrier that sets in and stops it. It is to deny a perfectly logical and reasonable inference (and to deny many of the other independent evidence that supports this inference).

      There simply is no good reason to think that natural selective pressures operating over long time scales can't achieve extensions of what human beings have done in a few thousand years, and sometimes as little as centuries. Add drift, recombination and changing environments on continental scales over geological time, and the whole thing becomes all the more plausible.

      Furthermore, since we have hundreds of millions of years of fossil transitions (in correct chronological order) implying long-term macroevolutionary change, and since common descent is also implied by phylogenetics (and that phylogenetic reconstruction to the most overwhelming degree is congruent with the relationships inferred from morpholgy), the case is beyond reasonable doubt.

      You're living in a state of irrational denial.

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    3. " 'mere' microevolutionary evolution has been directly observed to impact both bodyplan morphology and behavior, foremost of which are selective breeding experiments with many large animals like dogs, cows etc.

      "selective breeding" is merely selecting extant morphological variants from with a particular genus or species.

      … and that selective breeding was utilised long before we knew anything about evolution. We have therefore direct evidence that genetic changes influence bodyplans and that natural selection over longer timescales can result macroevolutionary change.

      A flagrantly false assumption. There are absolutely NO mutationally induced genetic changes that are operatives within the selective breeding process.

      And finally, your extrapolation:

      There simply is no good reason to think that natural selective pressures operating over long time scales can't achieve extensions of what human beings have done in a few thousand years, and sometimes as little as centuries. Add drift, recombination and changing environments on continental scales over geological time, and the whole thing becomes all the more plausible.

      Equating manual selection (or for that matter, natural selection) with effectuating a genetic change that has not mutationally occurred, is extrapolation on steroids.

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    4. For clarity, change "with effectuating a genetic change" to "employing an effectuated genetic change".

      Selection is not causative, just selective, but w/o something adaptive or novel to select from, there would be nothing new to 'fixate' within a population.

      And again, selective breeding does nothing to initiate genetic change short of removing some genetic information in most cases.

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    5. "And again, selective breeding does nothing to initiate genetic change short of removing some genetic information in most cases."

      Nor does it need to. It has been found that, for example, the natural rate of mutation of Amazonian guppies in the wild is more that an order of magnitude greater than that which is mathematically necessary to account for the observed macro-evolution vs. time in the fossil record. (Source: Ken Miller's "Finding Darwin's God".) This is of course very old news among biologists, but perhaps not among the general public.

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    6. Should be "more than an order of magnitude" not "more that" - sorry for the typo.

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    7. "selective breeding" is merely selecting extant morphological variants from with a particular genus or species.
      Yes, and morphological variation is generated by mutation and genetic recombination. Mutation happens at every generation, and in sexually reproducing species, new combinations are generated at meiosis. I never even tried to imply that selection is the source of variation, it is merely the retainer of adaptively beneficial alleles. But new variation is nonetheless generated at every single variation.

      "… and that selective breeding was utilised long before we knew anything about evolution. We have therefore direct evidence that genetic changes influence bodyplans and that natural selection over longer timescales can result macroevolutionary change."
      A flagrantly false assumption. There are absolutely NO mutationally induced genetic changes that are operatives within the selective breeding process.

      Directly observationally false and a single documented case is enough to annihilate your objection.
      I submit to you the case of <a href="http://www.oeb.harvard.edu/faculty/hoekstra/PDFs/Linnen2013Sci.pdf>Deer Mice</a> camouflage evolution. Direct documented case of natural selection retaining mutation-induced (in this several different single-nucleotide polymorphisms) variation that is adaptively beneficial depending on environment.

      That is single-nucleotide polymorphisms. A single change in a nucleotide that induces considerable phenotypical change with selective effect. Pay special attention to this part for example "There was oneexception: a serine deletion (DSer) in exon 2 was associated with both ventral color (P= 8.5 ×10−5) and tail stripe (P= 5.4 × 10−6)."

      QED.

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    8. Equating manual selection (or for that matter, natural selection) with effectuating a genetic change that has not mutationally occurred, is extrapolation on steroids.
      You're apparently very confused. I'm still not saying selection is the source of variation, I'm saying selection is that which retains adaptive variation.

      Sexual recombination and mutation is what generates change. Mutations observationally happen and affect morphology and behavior, and sexual recombination even more so.
      In fact, the primary source of variation within sexually reproducing species is genetic recombination. Huge amounts of variation that doesn't even exist as part of the standing variation in populations, can be generated through recombinatorial events alone. In this respect we don't even need to wait for mutations. This is why sex is so important for the evolution of large multicellular species like plants and animals.
      That's why we could make dogs smaller than any wolf ever was. By selecting new recombinations not seen before in nature, because we kept retaining smaller and smaller variants generated at successive generations. At every new generation, new recombinations happened and occasionally the result was an even smaller dog. We then breeded from that dog and kept going. There was never a wolf in existence the size of a chihuahua, it has never been part of the "standing variation" in any wolf population to get that small. It is a new recombinatorial result. Of course, during the evolution of the domesticated dog, mutation has contributed to dog evolution too. Dogs don't just have unmodified "wolf-genes" shuffled into new patterns. Dogs differ more genetically from their wolf common ancestor (up to 15%) than humans do to chimps (~6%).

      Now, for another case in point of significant morphological, recombination-generated change, the Betta double-tail "mutation" in the Betta splendens aquarium fish. That is a fish possessing two separate, distinct tail fins, arranged vertically like the barrels of an 'over-under' shotgun, each with its own distinct set of caudal plates in the caudal peduncle, is governed by a single gene exhibiting classic Mendelian single-factor recessive inheritance.
      See here.

      As that page also explains, the double-tail variant is further subject to change once it arises, and selective breeders (or just sexual selection within the aquarium populatipon) can futher facilitate ever more intricate and elaborate tails (they're apparently "impressive" to females).

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    9. And again, selective breeding does nothing to initiate genetic change short of removing some genetic information in most cases.
      As I just both explained and documented, that is simply false. Gene-shuffling is by definition genetic change, and mere shuffling does not consitute deletions, removal or loss.

      It could be said that stringent selection when employed in selective breeding discards a lot of unwanted change and that would certainly be true, but in this respect selective breeding is actually less forgiving than natural selection which is rarely as stringent and effective as human selective breeders. Consequently in nature, we would expect more genetic variation to be retained over longer timescales that that allowed by selective breeders.

      This is of course an irrelevancy for the this discussion, selective breeding was erected entirely for the purpose of demonstrating that succesive rounds of selection can result in the accumulation of morphological change, even if selction itself is not the source of that change(mutatation and recombination is).

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    10. @Jim V
      "And again, selective breeding does nothing to initiate genetic change short of removing some genetic information in most cases."


      "Nor does it need to. It has been found that, for example, the natural rate of mutation of Amazonian guppies in the wild is more [than] an order of magnitude greater than that which is mathematically necessary to account for the observed macro-evolution vs. time in the fossil record."


      Stated as 'Darwins', a quantitative assessment, yes, there is evidence of an ample number of mutations to fulfill the mathematical requirement, or as Miller stated, "The mechanism(s) of evolution is real, is observable, and is more than adequate to the task(s) at hand." [pg 111, 'Darwin's God']

      But qualitative, not just quantitative is more the definitive requirement of novelty building evolution. There is a continuum of adaptive mutations, possibly a designed-in function to aid in survival.

      The assumption that these kinds, er correction, types of genetic variation can account for revised body plans, and extreme revisions of organ and systemic functionality are highly questionable.

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    11. "selective breeding" is merely selecting extant morphological variants from with a particular genus or species."

      "Yes, and morphological variation is generated by mutation and genetic recombination. Mutation happens at every generation, and in sexually reproducing species, new combinations are generated at meiosis. I never even tried to imply that selection is the source of variation, it is merely the retainer of adaptively beneficial alleles."


      Correct. My 'causative' to 'selective' correction was to correct my own prior statement, not of anything you stated or implied.

      "… and that selective breeding was utilised long before we knew anything about evolution. We have therefore direct evidence that genetic changes influence bodyplans and that natural selection over longer timescales can result macroevolutionary change."

      "A … false assumption [IMO]. There are absolutely NO mutationally induced genetic changes that are operatives within the selective breeding process."

      "Directly observationally false and a single documented case is enough to annihilate your objection."

      "I submit to you the case 'Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene' Direct documented case of natural selection retaining mutation-induced (in this several different single-nucleotide polymorphisms) variation that is adaptively beneficial depending on environment.


      I downloaded the .pdf, and will read it and comment shortly.

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    12. "Equating manual selection (or for that matter, natural selection) with effectuating a genetic change that has not mutationally occurred, is extrapolation on steroids."

      "You're apparently very confused. I'm still not saying selection is the source of variation, I'm saying selection is that which retains adaptive variation.
      "

      Correct, and I had corrected that misstatement as follows:

      "For clarity, change "with effectuating a genetic change" to "employing an effectuated genetic change"."

      What I had meant was that equating long term evolutionary change to what we do by selective breeding in the short term is to my mind, an unfounded extrapolation (forget the steroids). ;~)

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    13. "Sexual recombination and mutation is what generates change. Mutations observationally happen and affect morphology and behavior, and sexual recombination even more so."

      Both plus genetic drift are valid operatives

      "In fact, the primary source of variation within sexually reproducing species is genetic recombination. Huge amounts of variation that doesn't even exist as part of the standing variation in populations, can be generated through recombinatorial events alone."

      Yes, but with no 'look ahead' function for building incrementally non-functional, but functional at a later time constructs, the amount of change, however generated, does not explain certain complexities and novelties.

      "In this respect we don't even need to wait for mutations. This is why sex is so important for the evolution of large multicellular species like plants and animals."


      True, and yes, sexual bimorphism is essential for evolutionary progressions (sorry unicellulars), but (1) is that all that is/was required to build novelty and complexity, and (2)how did diploid bisexual phyla originate?

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    14. @Mikkel: "Now, for another case in point of significant morphological, recombination-generated change, the Betta double-tail "mutation" in the Betta splendens aquarium fish.

      That is a fish possessing two separate, distinct tail fins, arranged vertically like the barrels of an 'over-under' shotgun, each with its own distinct set of caudal plates in the caudal peduncle, is governed by a single gene exhibiting classic Mendelian single-factor recessive inheritance.


      From the linked page: "Doubletail bettas are expected to differ in several ways from the singletail:"

      1. Possess two distinct 'tails' or caudal lobes instead of one, with complete separation to the base of the caudal peduncle.

      2. Possess a wider caudal peduncle to support the double lobes.


      Split or double morphologies sometime occur, and when they do, selective breeding might beget more of them.

      Mikkel: As that page also explains, the double-tail variant is further subject to change once it arises, and selective breeders (or just sexual selection within the aquarium populatipon) can futher facilitate ever more intricate and elaborate tails (they're apparently "impressive" to females)."

      Me: "Selective to females" might well confer a selective advantage. But again, what is available to manually select and breed does not necessarily equate with other traits that may develop long term.

      And of course, another possibility is intervention, a form of genetic engineering to produce a radical re-design. And not in one 'poof', but incrementally as the timeline plays out.

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    15. @Mikkel:

      Me: "And again, selective breeding does nothing to initiate genetic change short of removing some genetic information in most cases."

      Mikkel: "As I just both explained and documented, that is simply false. Gene-shuffling is by definition genetic change, and mere shuffling does not consitute deletions, removal or loss."

      Some losses in some cases, but using what is there, rather than by a mutational process.

      "This is of course an irrelevancy for the this discussion. Selective breeding was erected entirely for the purpose of demonstrating that succesive rounds of selection can result in the accumulation of morphological change ... "

      I still take umbrage with your statement, however:

      "There simply is no good reason to think that natural selective pressures operating over long time scales can't achieve extensions of what human beings have done in a few thousand years, and sometimes as little as centuries. Add drift, recombination and changing environments on continental scales over geological time, and the whole thing becomes all the more plausible."

      Selective breeding responds to the personal 'wants' of the breeder rather than environmental pressures, is limited to available existing genes rather than chance mutations, nor are either equatable in any way to the formation of observed novelty and complexity within the observed domains.

      Anyway, regarding the liklihood/possibility of a form of genetic engineering at historic points in time, we ourselves are on the cutting edge IMO. Check this out:
      http://www.scs.illinois.edu/~zhaogrp/publications/HZ45.pdf

      And of course this:
      http://en.wikipedia.org/wiki/Genetic_engineering

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    16. We could play some sort of Bingo with this. So far I can tick the fields marked circular reasoning, god of the gaps, argument from personal incredulity and Omphalos/Last Thurdsayism.

      The personal incredulity one is particularly obvious in the thread above. Anybody who argues that gradual changes in allele frequencies are incapable of producing new body plans simply fails to grasp the magnitude of what "hundreds of millions of years" actually means. That is of course understandable to a degree; we are simply ill equipped to intuit about anything more than a human lifetime, which is why intuition is such a poor guide in these matters.

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    17. "So far I can tick the fields marked circular reasoning, god of the gaps, argument from personal incredulity and Omphalos/Last Thurdsayism."

      • If my premise is true (IC/NEC), then my conclusion is true (design). Circular only if a false premise is presented.

      • I have never posited a monotheistic God, an a priori assumption, and without scientific evidence.

      • Personal incredulity? No, statistical improbability. And I will side with the data, when and if reductive exclusivity is confirmed.

      • And regarding Omphalos theology, no, what is observable is not a 'charade', just another mind-game fallacy.

      It's just a little hard to digest, if one is a committed reductionist.

      And regarding the question of umbilical cord connection points (omphalos, yes or no?), they will always form in placental mammals.

      Sorry to disappoint ... :)

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    18. Mikkel, I have a question for you-- and I'm going to ignore the troll who among other things appears ignorant of the Luria Delbruck experiment, mutation accumulation experiments, Perfeito et al., nylonase bug etc. etc.

      Let's talk about sex. I read somewhere, I forget where (Sean Carroll?) about sex producing gains in complexity in one generation-- e.g. a butterfly with let's say a smile pattern on its wings mates with a butterfly with let's say an eye pattern, and the offspring has a smiley face on its wings. That would be a gain in complexity by sex alone. Does that ring any bells?

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    19. Lee Bowman,

      No idea what IC/NEC is but above I pointed out where the circularity lies. You cannot conclude that there is a creator merely by assuming that things must have been created, nor vice versa. To break the circularity, you need some outside information that makes it appear plausible that there is a creator.

      And of course there is no scientific evidence whatsoever for a creator, nor has anybody suggested a mechanism for how the process of creation would have proceeded. It's magic! In contrast, evolutionary biology has proposed numerous processes generating biological diversity and structure, and those processes are observable and have been tested.

      I find creationist claims on this thread insufficiently coherent and elaborated to address them adequately, and that includes you cryptic remark on statistical improbability. Not only does the vast majority of theoretical and experimental evolutionary biologists disagree with you, there is also all the other evidence to be considered. Phylogenetic structure in con-coding DNA, fossils, biogeography, etc, it all fits into one nice image that looks precisely as one would expect things to look if evolution were true and quite differently from what we expect special creation to look like (unless under a trickster god/Last Thursdayism scenario).

      I will assume you do know what the Omphalos hypothesis is and are merely deliberately obtuse.

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    20. "No idea what IC/NEC is but above I pointed out where the circularity lies. You cannot conclude that there is a creator merely by assuming that things must have been created, nor vice versa. To break the circularity, you need some outside information that makes it appear plausible that there is a creator."

      ID does not propose a singular creator per se, a religious concept; just verification of design inferences, where evident. The design source could be an intelligent mechanism, multiple alien entities, surrogates acting under a higher authority, or other unknown inteligencia. If natural causation fails as causative (unguided), then guided (interventionary) is a logical alternative. If not, feel free to propose another.

      Incremental evolution is a known operative, largely if not totally adaptive, but unknown regarding its mechanisms in toto. Embryogenesis is the creative process, but more likely than not, 'itself' a designed process. Billions of years of algae and prokaryotes may seem odd, but vast time is only a factor to limited time entities like 'us'. Design inteligencia may have varied throughout time, and may or may not be operative at this juncture. ID makes no predictions regarding.

      "And of course there is no scientific evidence whatsoever for a creator, nor has anybody suggested a mechanism for how the process of creation would have proceeded. It's magic! In contrast, evolutionary biology has proposed numerous processes generating biological diversity and structure, and those processes are observable and have been tested."

      Sorry, but they have not been empirically verified to form complex structures, just minor adaptations. Extrapolation is the current 'key' to observability.

      "I find creationist claims on this thread insufficiently coherent and elaborated to address them adequately, and that includes you cryptic remark on statistical improbability."

      A design theorist is not necessarily a creationist, nor am I. I will go with the evidence wherever it leads.

      "Not only does the vast majority of theoretical and experimental evolutionary biologists disagree with you, there is also all the other evidence to be considered."

      And I am open to any and all evidence that presents. But that would refer to efficacious and of course cohesively related evidence only. Bacterial adaptations do not count as either genotypic or phenotypic confirmatory data regarding evolutionary progressions.

      "Phylogenetic structure in non-coding DNA, fossils, biogeography, etc, it all fits into one nice image that looks precisely as one would expect things to look if evolution were true and quite differently from what we expect special creation to look like (unless under a trickster god/Last Thursdayism scenario)."

      Correct. According to the data, there was no "special creation", and of course, no "trickster" god. Evolutionary lineages are real.

      "I will assume you do know what the Omphalos hypothesis is and are merely deliberately obtuse."

      That would be under philosophy, not science.

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    21. Regarding IC/NEC, Behe's irreducible complexity and my non-evolvable complexity. Both have some commonality; one looking backward, the other bottom up (simple to complex).

      NEC is discerned where

      • multiple or co-dependent systems would have no reproductive advantage (or function for that matter) if evolved separately

      • where intermediates would similarly have no usable function, sans the infrequent exaptation examples, and thus have to reproductive or survival advantage, and

      • where certain intermediates would be disruptive to extant functions.

      These premises are subject to further confirmation or falsification, but are clearly on the table as investigative science. Maybe it's high time to table the 'religion' canard.

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    22. Bowman hypothesizes "non-evolvable complexity", but that only proves that IDers use strictly negative argumentation. Besides the obvious fact that in living organisms there ISN'T any non-evolvable complexity-- the defining feature of life, as opposed to human designed technology, is that life is complex WITHOUT non-evolvable complexity-- it's also ridiculous to have an alleged "theory" based on what scientists allegedly can't explain. It's like when vitalists said "Chemistry can't explain this or that action of an organism, that's positive evidence that the Vital Force did it." Creationists used to be vitalists. Get a real theory-- the kind that makes testable predictions.

      Bowman's examples of non-evolvable complexity are the same creationist arguments we've seen for 120 years. "Transitions are impossible." Every concrete example cited by creationists for 120 years has been OBSERVATIONALLY refuted by finding transitional fossils, living intermediates, or living juvenile forms with the EXACT properties creationists called "impossible"!

      Creationists were adamant, ADAMANT that the half-whale, the half-bat, the half-flatfish, the half-amphibian, the half-eye, the half-warm blooded mammal, the half-turtle, the half-giraffe, the half-bird and even the half-feather were all IMPOSSIBLE and could NEVER exist and if they ever did they would KILL the animal DEAD. But we found every one of them and more.

      The creationists have a demonstrated track record, more than a century long, of saying they can prove an intermediate is IMPOSSIBLE and then looking like total assholes when it appears in the fossil record, in living species or juvenile forms.

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    23. Alex SL
      I don't think observing evolution counts as biological investigation. A space alien showing us a video of evolution of anything would just be a video. Even though a true account.
      Biological investigation must be based on biological processes being demonstrated as actual and actually working .
      Repeatable one might say.
      There is no complaint in medicine or flying planes about methodology in drawing results. It works repeatedly.

      Extrapolation is not biological research. its just a line of reasoning standing on the merits of the reasoning. Conclusions not standing on observation, repeatable details, and raw evidence that such and such did happen.

      I say extrapolation is not science. Evolution is based on extrapolation almost entirely.
      Process and and true results are not being demonstrated by investigation methods.
      Evolution is not using the scientific method and because this is not noticed therefore evolution has not been corrected for its errors by scientific methodology.
      One can't correct extrapolation. True or not its an abstract and has nothing to do with scientific investigation.

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    24. Astonishing how many people feel qualified to tell a phylogeneticist how evolutionary research works. Maybe in turn I should start explaining to my dentist how they should do their job...

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    25. @Lee Bowman
      What I had meant was that equating long term evolutionary change to what we do by selective breeding in the short term is to my mind, an unfounded extrapolation (forget the steroids). ;~)
      But why is it an unfounded extrapolation? It's not like we're doing this in a vacuum. The relationships are already implied by phylogenetics and morphology, and it is so unbelievably simple an extrapolation. We observe small amounts of change within human lifetimes, why can't this change simply multiply proportionally over longer timescales? Why? What prevents the accumulation here?

      We have all he observations we could hope for within human lifetimes, if it really was the case that small-scale changes could accumulate over longer timescales. We have fossil transitions and their chronologies that support it. We have the phylogenetic relationships that are congruent with the morphologically inferred ones. We see mutations accumulate slowly in human lifetimes. We observe that mutations and genetic recombination affect morphology. We observe that natural(and artificial) selection retains adaptive variants.

      Why, then, is the extrapolation that this happens over longer timescales, an unreasonable extrapolation to you? What can you offer here other than stubborn incredulity or blanket denial?

      Can you offer a mechanism that blocks the accumulations of change? One that isn't just an ad-hoc rationalization? What is it that compels you to object to the inference? Any observations of this mysterious evolution-preventing barrier that your rejection entails?

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    26. Really, your denial here has the same quality of failure as the idea that adding steps can't ever lead to a staircase, or that adding pennies never leads to a million dollars(or whatever arbitrary large amount). What mechanism prevents the accumulation of change?

      Why should we not take all the evidence from our observations together and find it reasonable that evolution did and does happens to greater extends than we have observed within our lifetimes, simply given even more time?

      I'm sorry, but no matter how I try to view at this, all we're being offered by the creationist side is stubborn denial.

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    27. "In fact, the primary source of variation within sexually reproducing species is genetic recombination. Huge amounts of variation that doesn't even exist as part of the standing variation in populations, can be generated through recombinatorial events alone."
      Yes, but with no 'look ahead' function for building incrementally non-functional, but functional at a later time constructs

      There is no requirement for "look ahead function" in order for genetic recombination to result in neutral-but-later-adaptive change. It seems you've invented a problem it isn't even clear exists.
      It is often the case that environment determines functionality, so what might in one environment prove detrimental to the host organism, can in another turn out to be selectively beneficial. The Betta double-tail variant is a good example of such recombination-generated variation that has selective effects that depends on environment.

      the amount of change, however generated, does not explain certain complexities and novelties.
      This is news to the worlds evolutionary biologists. Also an unsupported blind assertion.

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    28. "In this respect we don't even need to wait for mutations. This is why sex is so important for the evolution of large multicellular species like plants and animals."
      True, and yes, sexual bimorphism is essential for evolutionary progressions (sorry unicellulars), but (1) is that all that is/was required to build novelty and complexity, and (2)how did diploid bisexual phyla originate?

      At the earliest stage, probably through some form of single-celled eukaryotic conjugation or similar type of sharing of genetic material. That's of course a very interesting subject in it's own right and has a pretty substantial litterature devoted to it. I'm sure you can find something recent on the origin and evolution of sexual reproduction online.
      I recommend starting here for a short primer:
      https://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction
      But nothing beats the specialist litterature of course, and I'm not a specialist in the field.

      Me: "Selective to females" might well confer a selective advantage. But again, what is available to manually select and breed does not necessarily equate with other traits that may develop long term.
      Of course not, there are no guarantees in evolution. Over 99.9% of all species that ever lived have gone extinct. But life overs pretty much the entire surface of our planet and in many places goes up to a few kilometers into the ground. All environments on the planet are constantly sampled by variation generated by mutation and recombination.
      Evolution simply retains "something, anything that works". That one species in one environment (say, in a north-american forest or river) evolved in the wrong direction and is heading for extinction just means that another one will eventually take it's place and adapt for the niche it failed to, given time. Of course, sometimes environmental changes are too fast and happen on a global scale, and that's where we get mass-extinctions. Nonetheless, global-scale environmental sampling of generated variants goes on and when conditions settle down again, diversification explodes. This makes intuitive sense and is confirmed in the fossil record.

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    29. And of course, another possibility is intervention, a form of genetic engineering to produce a radical re-design. And not in one 'poof', but incrementally as the timeline plays out.
      But why believe in an unobserved entity. And not just an unobserved entity(like, another collection of matter), but some mysterious and unfathomably intelligent being that has apparently existed for billions of years, can reach in through physical matter and structures and manipulate the genomes of living organisms creating entire genes and new structures, on oganisms everywhere on the planet (truly on a global scale), over geological eons, with planning and foresight and so on? Isn't that the motherloadly most grotesque of all extrapolations?

      Especially when compared with evolution, which simply takes the observed and multiplies it over longer timescales. Mutations and genetic recombination happens, they're observed facts. The phenotypical variation which results from mutations and recombination samples environmental niches(has adaptive impact), it's an observed fact. Environmens change over time due to geological and atmospheric processes, it's an observed fact. And so on and so forth, evolutionary theory, macroevolutionary change and transitions and common descent simply take observed facts and multiply them over the available time on our planet.

      In every concievable way, evolution wins hands down as the most plausible and simplest hypothesis, and consequently the only one we're justified believing. It works only with the observed, doesn't postulate unobserved mechanisms that possibly violate the laws of physics. In fact, many of the properties of evolution (like some selective pressures) are logically entailed by our extant knowledge of physics. Take water, all objects submerged in a body of water are subject to hydrodynamic drag. This is, has always been, and will always be a fact. In this respect, natural selection for reduction of hydrodynamic drag for purely physical and energetic reasons will have been in operation on all aquatic forms of life for the entire history of life. It is no surprise that aquatic life finds itself having largely all found similar adaptive solutions to reduce drag. Most fish look roughly alike in body shape: Long and slim.

      Time and again, evolution is the simplest explanation which doesn't postulate onobserved entitites or hitherto inexplicable mechanisms to explain the observed diversity and quality of life on our planet.

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    30. @Mikkel Rumraket Rasmussen: very well-argued and very convincing, in my opinion.

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  6. Cordova even succeeds in presenting a cladogram that isn't a cladogram. Getting birds and mammals together without mentioning any synapomorphy ..
    How anyone can confuse 'synapomorphies with 'ancestors', even 'conceptual ancestors', beats me. And Cordova says he got that pseudo-cladogram from a website where I can't find it.

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  7. So there is no such thing as mammals or reptiles but rather they simply have some like traits for like needs as a original blueprint would account for.

    Except of course for moles and notoryctids, which do share a common ancestor from the time of Noah's Flood, 'coz they look the same, modulo pouch. In other words, parallel adaptations indicate common origin, and homologies indicate "conceptual ancestry" in God's mind (into which you creationists have a privileged insight). What a pity you'll never be capable of realising just how crazy you are.

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    1. Its not crazy but a re examination of presumptions. This has overturned science conclusions before.
      There has never been a reason to lump "mammals" together or "reptiles" together.
      They did this too quickly based on shared traits.
      Yet missed the option that shared traits was simply from shared needs and unrelated to biological relationship.
      Moles having fur like tigers is just a coincidence.
      There is no reason to think it shows common ancestry. Even if true it would be just extrapolation.
      Yet from a common blueprint from the creator of physics it would also be this way.
      Thats what i would do!

      Joining creatures together in descent trees has all been a grand hunch.
      The DNA stuff is just more hunching it up.
      There is another option that just by existing places the stress on the first options to show they are the product of scientific investigation and not just lack of imagination and first impressions.

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    2. The stupid is acutely painful, but I can bear enough for this point: if the morphology is just a hunch and the DNA is just a hunch, why are they both (for the most part) giving us the same hunch? How weird is that?

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  8. I knew that I was in for a lot of stupid, so it took me a while to gather myself and actually click on and read Sal's post. It did not expect what I got.

    "A jaw as the physical ancestor of perch, salamander, lizards, pigeon, mouse, chimp wouldn’t be a viable physical ancestor, but it is a viable conceptual ancestor!"

    This is so egregiously, unfathomably stupid it boggles the mind. Holy Fucking Shit... "what can men do against such reckless stupidity?".

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  9. From preface of "The First Chimpanzee", (2001):

    I know my molecules had ancestors, the paleontologist can only hope that his fossils had descendants."
    VINCENT SARICH

    Maybe Sal would care to google Vincent Sarich for some enlightenment?

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  10. Completely ridiculous, he's saying that because one type of method in biology doesn't explicitly recover ancestry, but instead recovers sister-groups, that then ALL methods fail to recovery ancestry, and that they fail BECAUSE there is no ancestry.

    I mean, he clearly doesn't understand what matzke means by phylogenetic methods, and he obviosuly doesn't understand what 'sister-groups' mean either, since they imply descent from a common ancestor.

    He's either an idiot who doesn't understand what he's talking about, OR he's an engaged in facile wordplay, which effectively makes him an idiot anyway.

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    1. I don't really understand the confusion. If you have sisters, doesn't that require that you also had parents? Even if your parents are extinct or unknown?

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  11. Cordova:"The reason Darwinists have all these phylogenetic conflicts is that the ancestors which would resolve all the conflicts are the very ones they will not admit a priori because those ancestors are conceptual, not physical, and conceptual ancestors are anathema to Darwinsits because conceptual ancestors imply ID."

    So he's arguing that there's a reason for the conflicts between different phylogenetic reconstructions, it's because there are no real ancestors. If we used 'conceptual' or 'god's blueprints' for phylogenetic reconstruction, we'd have no conflict or errors. But then he produces nothing of the sort, so if creationists can't present independent non-conflicting 'reconstructions', how can Cordova pretend that they're correct, by his own criteria they're 'demonstrably false'. Hell when different creationists are given the same 'holy, innerant, unalterable bible' they still get conflicting and contradictory theologies, sometimes held by the same person!
    If what he was saying were true, phenetics would be a branch of theology.

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  12. Ah, Sal "DNA Steganography" Cordova. Y'know the movie credits where it shows the name of the director? Well one of Sal's theories is that DNA contains hidden messages saying stuff like "Body by God."

    Next to that, this crap sounds almost tame.

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