Home » Intelligent Design » The Evolutionary Tree Continues to Fall: Falsified Predictions, Backpedaling, HGTs and Serendipity Squared

The Evolutionary Tree Continues to Fall: Falsified Predictions, Backpedaling, HGTs and Serendipity Squared

Charles Darwin’s theory of evolution states that the species arose from earlier species. Slight changes accumulating over long time periods resulted in one species giving rise to a new species, over and over.  Read more

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118 Responses to The Evolutionary Tree Continues to Fall: Falsified Predictions, Backpedaling, HGTs and Serendipity Squared

  1. Does the evolutionary tree falling make the same sound as one hand clapping?

  2. The problem is that most people can’t see the forest for the trees. And if the tree falls in the forest and no-one is there, can we be sure it made a sound?

  3. As time pants on to the end, discovery reveals that rather than another human fabricated iconic image from Idolatry of a singular tree, it appears there are many orchards with thousands of trees(and quite possibly twice or three times as many shrubs and ruderals).

    Interestingly, the ancient Germanic tribes once worshiped a tree as an image of their god(or at least one of them). That’s why the definite article has the masculine ‘Der’ Baum.

  4. Slight changes accumulating over long time periods resulted in one species giving rise to a new species, over and over.

    Yet, according to at least some of the DarwinDefenders here at UD — and with no dissent from the others — to say that “one species changed into another” is to commit the mortal sin of Not Understanding Science.

  5. Here’s a good piece by author Kevin Kelly from his book, “Out of Control”
    =======

    “Around the world, a few naturalists are conducting long-term observations of evolving populations of organisms in the wild: snails in Tahiti, fruitflies in Hawaii, finches in the Galapagos, and lake fish in Africa. Every year that these studies go on, there is a better chance that scientists can unequivocally demonstrate long-term evolution in action in the field. Shorter-term studies using bacteria, and recently flour beetles, show short-term evolution of organisms in the lab. So far, these experiments with populations of living creatures have matched the results expected from neodarwinian theory. The beaks of finches in the Galapagos really do thicken over time in response to drought-induced changes in their food supply, just as Darwin predicted.

    These careful measurements prove that self-governing adaptation does spontaneously occur in nature. They also unequivocally demonstrate that noticeable change can emerge on its own by summing up the steady unnoticeable work of incremental deletions of the unfit. But the results do not show new levels of diversity, new kinds of creatures, or even new complexity emerging.

    Despite a close watch, we have witnessed no new species emerge in the wild in recorded history. Also, most remarkably, we have seen no new animal species emerge in domestic breeding. That includes no new species of fruitflies in hundreds of millions of generations in fruitfly studies, where both soft and harsh pressures have been deliberately applied to the fly populations to induce speciation. And in computer life, where the term “species” does not yet have meaning, we see no cascading emergence of entirely new kinds of variety beyond an initial burst. In the wild, in breeding, and in artificial life, we see the emergence of variation. But by the absence of greater change, we also clearly see that the limits of variation appear to be narrowly bounded, and often bounded within species.”

  6. Eocene, nice find, to further back up your quote:

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.”
    R. Milner, Encyclopedia of Evolution (1990)

    New Research on Epistatic Interactions Shows “Overwhelmingly Negative” Fitness Costs and Limits to Evolution – Casey Luskin June 8, 2011
    Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn’t run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
    http://www.evolutionnews.org/2.....47151.html

    At one of her many public talks, she [Lynn Margulis] asks the molecular biologists in the audience to name a single unambiguous example of the formation of a new species by the accumulation of mutations. Her challenge goes unmet.
    Michael Behe – Darwin’s Black Box – Page 26

    Natural Selection and Evolution’s Smoking Gun, – American Scientist – 1997
    “A matter of unfinished business for biologists is the identification of evolution’s smoking gun,”… “the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.”
    Keith Stewart Thomson – evolutionary biologist

    “The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the position of some people at the meeting, the answer can be given as a clear, No.”
    Roger Lewin – Historic Chicago ‘Macroevolution’ conference of 1980

    “The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared.”
    from page 32 “Acquiring Genomes” Lynn Margulis.

    Selection and Speciation: Why Darwinism Is False – Jonathan Wells:
    Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another.”
    http://www.evolutionnews.org/2.....why_d.html

    Wired Science: One Long Bluff – Refuting a recent finch speciation claim – Jonathan Wells – Nov. 2009
    Excerpt: “Does the report in Wired Science mean that “biologists have witnessed that elusive moment when a single species (of Galapagos finch) splits in two?” Absolutely not.”
    http://www.evolutionnews.org/2.....bluff.html

    As well, materialists never mention the fact that the variations found in nature (such as peppered moth color and finch beak size) which are often touted as solid proof of evolution are always found to be cyclical in nature. i.e. The variations are found to vary around a median position with never a continual deviation from the norm. This blatant distortion/omission of evidence led Phillip Johnson to comment in the Wall Street Journal:

    “When our leading scientists have to resort to the sort of distortion that would land a stock promoter in jail, you know they are in trouble.”

  7. 7
    Elizabeth Liddle

    Cornelius Hunter:

    A small but important point:

    You talk about “one species giving rise to a new species, over and over” – better to talk about “one species splitting into two, over and over”.

    “Species” is an essentially horizontal concept, that describes non-interbreeding extant populations, like dogs and cats. Dogs will never “give rise to” cats. But dogs may subdivide into two independently adapting populations, so that after many generations, we can talk about two “species” of dog.

    Neither of those species are the species we now have, although one may be much more like it than the other, and when our descendents find fossils of our dogs, they may well be tempted to say they are the same species as one of their two extant species.

    But it would be misleading – not least because clearly a long-dead population cannot interbreed with its remote descendents!

    As for your article (which I enjoyed btw!), I have a couple of comments:

    The tree of life, as derived from phenotypic traits, still stands as a tree. What is more, genetic trees are indeed substantially congruent. However, as you rightly note, there are incongruences that cannot merely be put down to “noise”. Something else is going on.

    And that something else appears to be HGT – in other words that something, other than heredity, is determining where various genes end up.

    That doesn’t, as your linked article, points out, mean that the phenotypic trees don’t imply heredity, it just means that there is a second system spreading genetic material through the tree by a different mechanism. In eukaryotes one of those mechanisms is viruses.

    To give a model example:

    Imagine a simple heredity model where you start off with a single string, keep reproducing from it, from its descendents, and so on, while also occasionally mutating the string.

    You will of course end up with a tree structure where your final population has quite a lot of variance, and you can trace each variant back up the tree, and find out where the mutation first appeared in that lineage.

    Now add an additional system: take a second smaller, string, and have it do the same, so that it also has a tree structure. However, instead of running the second tree independently of the first, instantiate each of these strings as an new insert into an individual in one of the original strings, and allow it to propagate by jumping between lineages on the original (just as a virus does).

    That will really mess up the phylogenies of the first tree, because unless you know who was the parent of each individual, you will be tempted to assume inheritance relationships where none exist; A may not have inherited xyz from is parent, but acquired it from a virus that it caught from B, making it look as though A is more closely related to B than it actually is.

    If the virus has no phenotypic effects, we will find ourselves with molecular trees that are incongruent with the phenotype-derived trees.

    And I suggest that even if the virus does have phenotypic effects it almost as likely, I suggest, that the same will be true, as any phenotypic effects of a viral insertion in one individual are unlikely to resemble the phenotypic effects in another, and the trait resulting from the insertion in the original individual will simply behave like any other heritable trait thereafter.

    But it is important to note that while the incongruences are extremely interesting, and HGT is a fascinating addition to our knowledge, broadly, genetic phylogenies do confirm phenotypic ones, and occasionally, when they do not, make predictions about new phenotypic data that are later confirmed.

    I think it is really important to distinguish between the falsification of a specific prediction, and the falsification of a whole theory.

    In a trivial sense, Darwin’s model has been falsified countless times; we know that heredity and population change is much more complicated than he envisioned. Indeed, Darwin had very little idea about how heredity even worked, and even less how variance was generated. So when you talk about “falsified predictions” it’s extremely important to be precise about exactly what hypothesis generated the falsified prediction.

    In this case, the falsified hypothesis is that all genetic material is inherited. We now not it is not. Here are a few other falsfied evolutionary hypotheses:

    That all heritable phenotypic variance is genetic (Lamarck wasn’t so wrong, not that Darwin thought so either).

    That all characteristic traits of populations are adaptive (we know they are not – drift is a very important factor).

    That all adaptation must arise from incremental beneficial mutations (we now not that even deleterious mutations can propagate through the population and serve as precursors for later beneficial mutations).

    That all adaptation arises from novel genetic changes (much adaptation is simply changes in the frequency of existing alleles).

    So there are a few more for your next article :)

    But none of this rattles the foundations of biology – it merely adds to the richness and complexity.

    What really would rattle the foundation of biology would be something like the discovery that the earth is only 6,000 years old, and that the geologic column has no correlation with age.

    Or, perhaps more plausibly, that large parts of the genome are “latent” genetic material that can be activated by environmental triggers in order to generate a better adapted phenotype.

    That would stab at the heart of Darwin’s theory. In fact, I’d go so far as to say it would falsify it :) A lot better than that pre-Cambrian rabbit, anyway, which almost certainly just fell down some old mine working.

  8. Ilion @4:

    Yet, according to at least some of the DarwinDefenders here at UD — and with no dissent from the others — to say that “one species changed into another” is to commit the mortal sin of Not Understanding Science.

    Elizabeth Liddle @7:

    You talk about “one species giving rise to a new species, over and over” – better to talk about “one species splitting into two, over and over”.

    LOL.

    Elizabeth Liddle was introduced to the concept of anagenesis right here at UD (apparently she’d never heard of it before.)

    Then promptly ignored it.

    Apart from the logical absurdity inherent in the very idea of one species splitting into two.

  9. In a trivial sense, Darwin’s model has been falsified countless times…

    Trivial because falsification isn’t important to the theory.

    So when you talk about “falsified predictions” it’s extremely important to be precise about exactly what hypothesis generated the falsified prediction.

    Yeah Dr. Hunter. Next time make it clear you’re talking about the tree of life please.

  10. But it is important to note that while the incongruences are extremely interesting, and HGT is a fascinating addition to our knowledge, broadly, genetic phylogenies do confirm phenotypic ones, and occasionally, when they do not, make predictions about new phenotypic data that are later confirmed.

    And now, if the trees don’t agree, we can blame it on HGT!

    ad hoc squared!

  11. Elizabeth @7:

    “You talk about “one species giving rise to a new species, over and over” – better to talk about “one species splitting into two, over and over”.”

    Yet, of course, evolutionary theory has no valid way to distinguish between the two, right? Under evolutionary theory it is just as likely that a tiger could turn into an elephant (over time) as it is that an amoeba could turn into an elephant. There is no reason to prefer one over the other.

  12. Eric Anderson,

    Lizzie:“You talk about “one species giving rise to a new species, over and over” – better to talk about “one species splitting into two, over and over”.”

    Yet, of course, evolutionary theory has no valid way to distinguish between the two, right?

    Not sure what you mean here – it seems that evolutionary theory does a fine job of distinguishing related species.

    Under evolutionary theory it is just as likely that a tiger could turn into an elephant (over time) as it is that an amoeba could turn into an elephant. There is no reason to prefer one over the other.

    This would not be accurate under evolutionary theory. Never mind that fairly simple analysis dismisses the notion that either tigers or amoebas can give rise to elephants, for evolutionary theory to be accurate, neither tigers nor amoebas can “turn into” anything other than tigers or amoebas respectively. Tigers might eventually split into two (or more) separate groups of independent breeding tiger groups, both with slightly different phenotype characteristics from one another. This is why Lizzie suggested using the concept of “splitting” as opposed to “begetting”.

    That aside, there are a number of reasons given evolutionary theory to predict some speciation characteristics. For example, we can quickly eliminate elephants splitting off from tigers because of the lack of immediate phenotype relationships. In other words, the differences between elephants and tigers require intermediate phenotypical fixations.

    Think of it this way – a cousin, an offspring of one of your parents’ siblings, is very closely related to you. What are chances that you and your spouse could have a child that is identical to one of your cousins? The answer, of course, is zero, even if, I might add, you were to have a child with your sibling’s spouse. The fact is, neither you nor your wife carry the genetic material to create an offspring that is identical to your sibling and his or her spouse’s genetic makeup, even with genetic drift and mutation.

    Tigers and elephants are even more distant cousins, so there is no direct route (genetically speaking) between the two. This is what Lizzie tried to get across by noting splits occurring over and over. Once you have several branches between to species, there’s no way to biologically create a direct branch between the two and evolutionary theory predicts this.

    In fact, if someone were to find an example of two disparate groups gaining a direct bridge biologically, evolutionary theory would be in serious trouble.

  13. @Doveton

    RE: Post #12

    Tigers might eventually split into two (or more) separate groups of independent breeding tiger groups, both with slightly different phenotype characteristics from one another. This is why Lizzie suggested using the concept of “splitting” as opposed to “begetting”.

    So the independently breeding tiger groups are still of the same species. How would the branch divergence lead to different species of tiger? Would those species not be successful in an interbreeding program?

    So let me ask a question in the form of an illustration. Let’s say that there is a species of Tiger called Red Tiger.
    I take several breeding pairs of Red Tigers and put them on an isolated island (Red Island). I take several other breeding pairs of Red Tigers and put them on another isolated island (Blue Island). Such that I had the Red Island Red Tigers (RIRT) and Blue Island Red Tigers (BIRT). Is the theory that over time the RIRT and BIRT offspring will become different species, such that it is no longer suitable to call them both “Red Tigers”?

  14. Ciphertext,

    So the independently breeding tiger groups are still of the same species. How would the branch divergence lead to different species of tiger? Would those species not be successful in an interbreeding program?

    The moment the disparate tiger groups no longer interbred, they would, for all practical purposes, be separate species. And this is what occurs in nature. The Galapagos marine iguanas are only slightly phenotypically different from their land iguana cousins and their Equador mainland ancestors. Marine iguanas and land iguanas do sometimes interbreed, producing hybrid pink iguanas, but this now happens rarely and the two groups are phenotypically become more diverse.

    So let me ask a question in the form of an illustration. Let’s say that there is a species of Tiger called Red Tiger.
    I take several breeding pairs of Red Tigers and put them on an isolated island (Red Island). I take several other breeding pairs of Red Tigers and put them on another isolated island (Blue Island). Such that I had the Red Island Red Tigers (RIRT) and Blue Island Red Tigers (BIRT). Is the theory that over time the RIRT and BIRT offspring will become different species, such that it is no longer suitable to call them both “Red Tigers”?

    Yep…that sums it up quite nicely. Now one condition that does need to be added to your illustration is that the environments Red Island and Blue Island should be different; if they both have the same environments, the selective pressure for any differentiations becoming fixed would be low all other factors being equal.

  15. The moment the disparate tiger groups no longer interbred, they would, for all practical purposes, be separate species.

    Are they both assigned new nomenclature?

  16. The moment the disparate tiger groups no longer interbred, they would, for all practical purposes, be separate species.

    Oddly enough, disparate groups which were long thought to be separate species, but are now known to be interfertile, never get “lumped”; witness lions and tigers, or domestic cattle and any number of wild species … including the American bison. At the same time, groups that were never thought to be disparate, and are known to be interfertile, get “split”; witness chimpanzees and bonobos, or African ‘savannah’ elephants and African ‘forest’ elephants.

  17. … my point being that “evolutionary biologists” are well on their way to making the term ‘species’ vacuous and useless.

  18. This is quite trivial and undisputed – things change, offspring are not identical. All ‘types’ or ‘species’ are headed downward toward genetic oblivion, not upward towards more complexity. Red Island Red Tigers will lose some of the information that BIRT’s keep and vice versa. And both have less than the parent population.

    The tree is very apparent within ‘branches’ , but when you think “Tigers and elephants are even more distant cousins” (LOL) it falls.

  19. 19
    Elizabeth Liddle

    Doveton:

    In fact, if someone were to find an example of two disparate groups gaining a direct bridge biologically, evolutionary theory would be in serious trouble.

    Indeed, which is why the finding of a few direct bridges is, initially, problematic, and presents the question: how are molecular sequences jumping from lineage to lineage? Either our notion of heredity is wrong, or something else is going on in addition.

    Now, there is plenty of reason to believe that our notion of heridity is right – we inherit phenotypic features from our parents, not from mosquitoes, and we know that genotypes map to phenotypes fairly well.

    So why might we have odd bits of DNA that seem to have come from somewhere else entirely?

    Well, there is a known mechanism: viruses.

    The tree of life based on parentage remains intact, and accounts for phenotypic features, and a great proportion of genotypic features too, not surprisingly as we know that the genome is the main carrier of inheritance.

    However, it appears that that tree is also host to another DNA propagation vector that uis orthogonal lineage, and pr0pagates from individual to individual across lineages (“horizontally).

    And we sneeze them out of our noses regularly.

  20. 20
    Elizabeth Liddle

    A general point: “species” is a pretty useful term, when used to categorise extant population, even though species divisions are fuzzier in places than others.

    “Ring species” are a good example, where populations at the extreme ends of a distribution cannot or do not interbreed, even if brought together artificially, but each population in the distribution interbreeds with neighbouring populations.

    Another example is of course populations that do not readily interbreed and produce fertile, viable offspring in the wild, but may to do so in captivity.

    What this means, of course, is that any extant biota (the one around now, for instance) is a horizontal slice through the branching process, and closely related populations may still be able to interbreed, while populations that branched far less recently will not, leaving clear discrete populations.

  21. 21
    Elizabeth Liddle

    I have to say, the arguments against the tree of life seem pretty thin!

    It seems to me the ID hypothesis is orthogonal to it anyway. Darwin provided an explanation for what he considered the data showed – a tree.

    The data still show a tree, if far richer than we once thought, and more complicated than we once thought.

    Darwinian evolution remains a good explanation IMO, but not the only possible one.

    However, trying to claim that the tree itself isn’t there seems a bit daft to me. Not ID’s strongest (or necessary) suit, IMO :)

  22. 22

    “The data still show a tree, if far richer than we once thought, and more complicated than we once thought.”

    Well spun ;-) But you forgot, the data – particularly from the Cambrian Explosion – turns the tree upside down too, Lizzie. Here’s another nice quote:

    “We can tell tales of improvement for some groups, but in the honest moments we must admit that the history of complex life is more a story of multifarious variation about a set of basic designs than a saga of accumulating evidence”.

  23. 23
    Elizabeth Liddle

    Chris, it’s not “spin” at all, it’s the way science works!

    This is a fundamental problem in these discussions, I think.

    On the one side, I’d argue, scientists are saying (including evolutionary scientists): here is a theory that may explain the observed patterns in our data; let’s derive testable hypotheses that will allow us to parameterise the model and refine it so that it accounts for as much of the data as we can.

    On the other hand, you guys are saying: hey, look – the scientists got it wrong again! Yet another ad hoc tweak to save their theory! They are so blinded by their commitment to their theory that they cannot see that it is irredeemably holed, but just keep patching it in the hope of postponing the data of its inevitable demise!

    This is a huge cultural divide!

    How do we bridge it?

    I do recommend, if you have not read it, the essay, The Relativity of Wrong by Isaac Asimov.

    If you have read, it, I’d be interested to know your response. If you haven’t, please do :) It isn’t long.

    IMO it beautifully articulates the scientific paradigm, and I’d argue, if you disagree with that paradigm, fair enough, but in that case your disagreement is with the entire scientific edifice, not just evolutionary theory :)

  24. 24
    Elizabeth Liddle

    Re the Cambrian explosion, I found an interesting graphic here:

    http://winteryknight.files.wor.....losion.gif

    drawn by someone who wanted to make your point, I think.

    But as I read it, it inadvertently makes the opposite point! The Cambrian explosion doesn’t “turn the tree upside down”, but merely marks a horizon. The circles do indeed show hypothesed lineages for which data is scant.

    The “Darwinian” answer is simply that absence of evidence is not evidence of absence, especially, when we have reasons to account for the absence (the Cambrian marks the emergence of biota that fossilise readily), and when already some of those missing lineages are being filled in, partly by genetic evidence.

    http://www.spaceref.com/news/viewpr.html?pid=32333

    But of course this inference only works under the Asimov paradigm!

  25. 25

    Hi Lizzie,

    I’ve not read the essay, but I will. In the meantime, I don’t think you have identified the fundamental problem at all.

    First of all, it is not a case of Lizzie (and scientists) versus Chris (and non-scientists). If anything, it is a case of evolutionists on the one hand moving the goalposts and “us guys” using science to cry foul play!

    Remember: although there maybe “scientific consensus” on your side, Lizzie, we have true science on our side. Which is more important?

    Quite simply the fossil record does not look the way it should look if evolution was true. The Cambrian Explosion – with its sudden appearance of virtually all major body plans – particularly undermines neo-darwinism. And then there’s all the stasis: fossils of things that are still around today have not evolved at all. And then there’s all the discontinunity: the same discontinuinty that we see in all extant species today.

    And if there really was a Tree of Life, we should never, ever find “a peculiar chunk of DNA in the genomes of eight animals – the mouse, rat, bushbaby, little brown bat, tenrec, opossum, anole lizard and African clawed frog – but not in 25 others, including humans, elephants, chickens and fish.” Dismissing that as HGT is simply not good enough.

    Okay, I’ll go and read Asimov now. I hope he says that science should go wherever the evidence leads and theories should be abandoned if they are undermined by the evidence, not preserved because of an a priori commitment to naturalism.

  26. 26

    I just read the essay, Lizzie. Are you’re telling me that believing that life made itself by accident and then evolved through random mutations and natural selection is JUST LIKE believing in a flat Earth, whereas belief in ID is just like believing in a perfectly spherical Earth? If so, then, yes, I see your point. You might have some issues with the details of ID but, at worst, those minor quibbles do not change the fact that ID is mostly right.

    It would be incredibly disappointing if you were trying to claim the opposite: that believing in evolution is just like believing in a spherical Earth. That would merely be advancing a typical low-level evolutionist article of faith: one that is without any empirical or rational basis whatsoever.

  27. 27
    Elizabeth Liddle

    No, Chris. Ouch.

    No, I’m not saying that either ID or evolutionary theory is “like believing in a flat earth!

    Strange how two people can read the same essay and draw such different lessons from it!

    What Asimov is saying is that scientific models become incrementally less wrong as we come to refine them in the light of new data!

    In other words, both ID or evolutionary theory could occupy the “flat earth” model at the beginning of Asimov’s essay, because, as he points out – it’s not a bad model. It’s pretty nearly right.

    However, the curvature of the earth’s surface turns out not to be zero, as was first thought, but very very very slightly positive.

    Now, let us take a slightly more specific theory than “ID” which isn’t actually an explanatory theory at all – it’s a default inference. Let’s propose that the theory is that an Intelligent Designer placed the first unicellular life-form on earth, and frontloaded its genome with inactivated genetic information that would be activated by environmental triggers – genes for flagella, genes for flippers, genes for intelligence, whatever.

    And evolutionary theory was more or less as it is today.

    And that both of them, like flat-earth theory account for the data as we observe them. However, like flat-earth theory, they are very slightly wrong – perhaps ID, while accounting for a lot of the genetic data, seems to hit a snag – brand new sequences seem to appear suddenly in the genetic phylogeny, rather than triggered into action by the environment.

    Ditto, evolutionary theory finds that the genetic phylogenies are not entirely congruent with the phenotypic phylogenies – DNA sequences jump lineage boundaries!

    The theories are falsified! But – not so fast.

    The original theories still account for most of the data, but they can’t be completely true. They need modification, just as flat-earth theory required a slightly positive addition to the postulated curvature parameter of zero.

    So ID adds a tweak – front-loading accounts for most of the data, but we need to hypothesises that new informational sequences are inserted by the Designer into the genome over time. ID-MkII is “slightly less wrong” than ID-MkI.

    It’s not that there has been an “ad hoc patch” to the theory. Rather, it has been elaborated to account for more of the data.

    Ditto with evolutionary theory and viruses. Yes, evolutionary theory as it stood has been “falsified” just as ID-MkI was falsified, but we now have a more complex theory that accounts for the data better. Just as, with ID-MkII, we now know more about the way the Designer implement His Design.

    However, in both cases the original model remains a decent approximation for many purposes. Flat maps work pretty well for limited regions. ID frontloading is still a good-enough description for most purposes; ditto Darwin’s theory.

    The point being that all models are wrong, but some are less wrong than others (hence “the relativity of wrong”); moreover, all models are provisional and subject to constant falsification. That does not mean (or very rarely means) that when a model is falsified, we have to go back to the proverbial drawing board.

    In fact like any “design process” (heh) we keep what works, jettison what doesn’t, and modify what’s left to try to work better (hey, what does that remind you of….?)

    cheers

    Lizzie

  28. Lizzie,

    Indeed, which is why the finding of a few direct bridges is, initially, problematic, and presents the question: how are molecular sequences jumping from lineage to lineage? Either our notion of heredity is wrong, or something else is going on in addition.

    Now, there is plenty of reason to believe that our notion of heridity is right – we inherit phenotypic features from our parents, not from mosquitoes, and we know that genotypes map to phenotypes fairly well.

    So why might we have odd bits of DNA that seem to have come from somewhere else entirely?

    Well, there is a known mechanism: viruses.

    The tree of life based on parentage remains intact, and accounts for phenotypic features, and a great proportion of genotypic features too, not surprisingly as we know that the genome is the main carrier of inheritance.

    However, it appears that that tree is also host to another DNA propagation vector that uis orthogonal lineage, and pr0pagates from individual to individual across lineages (“horizontally).

    And we sneeze them out of our noses regularly.

    Good point, and this gets back to the utility aspect of a scientific explanation and your comment regarding data points and probability accuracy.

    Initial models – such as taxonomy relationships – are not going to have the same level of accuracy and utility (predictability for further finds for instance) that latter models – ones based on more fossil finds, more understanding of geological and ecological shifts, more understanding of hybridization and genetic drift – have.

    Of course, recognizing other opportunities for genetic variation – such as viruses – can only come about if one already has a cognitive model that suggests such relationships and variation in the first place. That’s utility.

  29. Ok…clearly I need to read ahead. My last comment is pretty much covered by your reference to the Asimov essay. Oh well…a little redundancy never hurt anyone. :)

  30. Lizzie,

    However, in both cases the original model remains a decent approximation for many purposes. Flat maps work pretty well for limited regions. ID frontloading is still a good-enough description for most purposes; ditto Darwin’s theory.

    The point being that all models are wrong, but some are less wrong than others (hence “the relativity of wrong”); moreover, all models are provisional and subject to constant falsification. That does not mean (or very rarely means) that when a model is falsified, we have to go back to the proverbial drawing board.

    One of the ways I like to illustrate this is by comparing Classical Mechanics and Relativity. Relativity is definitely a more accurate model of how the physics of the universe work, but from a utility perspective, the vast majority of activities humans engage in on and around Earth can be more easily described and calculated using Classical Mechanics. Classical mechanics works just fine for putting satellites in in orbit for example.

    So has the Classical model been “falsified”? By many standards, yes, but it still has utility at the scales we still operate at.

  31. 31

    Hi Lizzie,

    I’m now with you, thanks for the clarification. And yes, I agree that’s how science works and it is stronger for it: as we make more observations and perform more experiments, we learn more and we revise our theories accordingly.

    Only one problem remains and it is a big one. Evolution: it’s just not science, is it? 19th century science, maybe. But certainly not 21st century science. Darwin himself was completely and utterly wrong (think flat earth wrong) about most of his subject matter, so why are we hanging onto the ambiguous scraps that remain?

    Let me do a Pip and answer that for you: if the theory of evolution was concerned with profound worldview-neutral subject matter it would have been consigned to the scrapheap of bad science long ago: along with Flat Earth theory! But it isn’t, and furthermore, far too many influential people have staked their professional reputation on the theory of evolution being true. Indeed, far too many people NEED the theory of evolution to be true because they absolutely must refuse to allow a Divine foot in the door.

    So, pertinent as Asimov’s essay might be to science or knowledge in general: unless you equate evolutionary theory to flat Earth theory, it is irrelevant to the Tree of Life.

  32. Elizabeth:

    I have to say, the arguments against the tree of life seem pretty thin!

    Not to these scientists:

    Charles Darwin’s tree of life is ‘wrong and misleading’, claim scientists:

    Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: “For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.”

  33. Elizabeth:

    Now, let us take a slightly more specific theory than “ID” which isn’t actually an explanatory theory at all – it’s a default inference.

    That is wrong as the design inference is not a default. Do you understand what “default” means?

    IMy guess is you think archeaology is a default inference too. How about forensics and SETI?

    The design inference is based on our knowledge of cause and effect relationships. It can be tested and falsified.

  34. 34
    Elizabeth Liddle

    Hi Chris: to pick up some of your other points:

    Hi Lizzie,

    I’ve not read the essay, but I will. In the meantime, I don’t think you have identified the fundamental problem at all.

    First of all, it is not a case of Lizzie (and scientists) versus Chris (and non-scientists). If anything, it is a case of evolutionists on the one hand moving the goalposts and “us guys” using science to cry foul play!

    Well let me restate my point by recycling your metaphor above:

    It is a case of scientists constantly moving the goal posts in order to catch as much of the data as possible with as little spare room as possible, versus “you guys” inferring from our moving goal posts that we are not doing what is, in fact intrinsic to scientific methodology :)

    Remember: although there maybe “scientific consensus” on your side, Lizzie, we have true science on our side. Which is more important?

    oo, oo, Chris :) No, I don’t “remember” this :) I hope we both have “true science” on our side, which is the position that our models must be constantly fitted to data, not the other way round. Consensus doesn’t matter terribly, except inasmuch as it is an indicator of consilience which does. And ID will have “true science” on its side just as soon as it makes testable differential hypotheses (like the frontloading hypothesis) and tests them, comparing the model fit to the model fit of an evolutionary model.

    Quite simply the fossil record does not look the way it should look if evolution was true. The Cambrian Explosion – with its sudden appearance of virtually all major body plans – particularly undermines neo-darwinism. And then there’s all the stasis: fossils of things that are still around today have not evolved at all. And then there’s all the discontinunity: the same discontinuinty that we see in all extant species today.

    Actually, Chris, none of those statements are true. There are a very large number of ways the fossil record might look if evolution were true, and the way it does look is one of them. There are also an even larger number of ways the fossil record might look if evolution were false, and the way it looks is not one of them.

    And to illustrate this, let’s say you are in a strange house and it is pitch dark outside. You can hear the wind whistling, and a tapping on the window pane (my son would do a better job of writing this story than I am, but I’ll go on…). At the window is a Venetian blind. Suddenly there is a flash of lightning. Thrown on to the wall opposite the window is the shadow of the slats of the Venetian blind, and in that split second you see the image of what looks like a tree – but is it? There are twigs, but are they really connected to branches? There are branches, but no shadow of the trunk – the window cill is too high to reveal it.

    Does this shadow look like it should if there was a tree out there?

    I think it does :)

    Now, about stasis – this is an easy one, and comes directly from Darwin’s theory with hardly any adjustment. Darwin’s theory, is, essentially, a theory of how populations adapt to an environment. Once they reach an optimum, there is no reason to change further. In fact, no mechanism, under Darwinism, for them to do so (although there is under drift theory, and indeed, apparent stasis sometimes shows evidence of drift – changes over time that appear to serve no adaptive function).

    And about “discontinuity” – again, two easy answers. One is the Venetian blind slats – fossilisation is rare, and the conditions for fossilisation non-random. We do not therefore have a random sampling of all biota – instead some environments, and some kinds of biota give a much higher probability of fossilisation than others.

    The other is also easy, and again, can be derived directly from Darwin’s principle of adaptation. If the environment changes (which it does sometimes, relatively quickly) or if a population, or a subdivision of it, moves into a new enviroment, or is cut off from the old one, then that population may no longer be at an optimum for that environment. And so adaptation begins and we see relatively rapid evolution towards a new optimum for that environment (as can be observed, in real time, in what you would call “micro-evolution”).

    I don’t know if you’ve ever played around with sand on a drum head. You put sand on a drum head and play a sound at a particular frequency (or combination of frequencies. The drum starts to resonate with the sound, and the sand jumps around on the antinodes (which are moving) at random until they settle into a node (on a drum head the nodes are linear, and form a kind of network on the drum head). So you end up with the sand marking the nodal lines. That is stasis. Now, change the sound – immediately the sand starts jumping around again, because what was a node is now an antinode until stasis again sets in and the sand settles into the new nodal lines. Hey presto – punk eek!

    In fact having typed the above, I just googled up this:

    http://vimeo.com/10689468

    :) (Warning – turn the sound down to low!)

    And if there really was a Tree of Life, we should never, ever find “a peculiar chunk of DNA in the genomes of eight animals – the mouse, rat, bushbaby, little brown bat, tenrec, opossum, anole lizard and African clawed frog – but not in 25 others, including humans, elephants, chickens and fish.” Dismissing that as HGT is simply not good enough.

    Why is it not good enough? And what is your quote from? It may not be “good enough” I don’t know.

    Okay, I’ll go and read Asimov now. I hope he says that science should go wherever the evidence leads and theories should be abandoned if they are undermined by the evidence, not preserved because of an a priori commitment to naturalism.

    He does indeed. Indeed, he treats it as a given. However, the point of his essay is that “abandon” can, and does, include minor tweaks to the abandoned theory and adoption of the modified theory.

    And the chief test of every theory is: “how well does it fit the data”?

    (Given two equally well-fitting models, parsimony is often used to choose between them but parsimony isn’t necessarily reliable – better to derive differential hypotheses from each model and test those hypotheses against new data).

  35. 35
    Elizabeth Liddle

    Incidentally, atlhough off topic, if you google “Chladni patterns” you’ll find lots more, including this video:

    http://www.youtube.com/watch?v=Qf0t4qIVWF4

    Which, quite apart from its function in my metaphor is a lovely example of how complex patterns can emerge from Chance and Necessity :)

  36. 36

    Okay Lizzie, my problem here is that, when it comes to evolution, we can talk all day about venetian blinds and sand on drums. And there’s always an excuse when things don’t turn out the way evolutionists predicted they should turn out.

    Do you really not see that stasis is exactly what we’d expect to see if evolution was not true?

    If we did actually find a fossil of a rabbit in the Cambrian, it would just be explained away as an extraordinary example of convergent evolution. If evolutionists can cope with that on the one hand and stasis on the other, they can certainly cope with an upside-down Tree of Life!

    So, I don’t think we’re occupying very productive ground in this discussion. If you are willing and able to test your evolutionist beliefs, then give us an important and specific piece of evidence from the real world that supports these beliefs. I say “real world” because GAs (to cite an example you often return to) deal only in intelligently-designed, goal-driven simulations and so do not shed any light whatsoever on how it is that a single-celled common ancestor evolved (neo-darwinistically) into human beings.

  37. 37

    PS. Very cool video (post 34) by the way, Lizzie! It reminds me of snowflakes. Obviously you don’t think that the salt patterns or snowflakes shed any life whatsoever on the cell though right?

  38. The tree of life based on parentage remains intact…

    As long as you beg the question of whether there is in fact a tree and ignore all contrary evidence.

    …it’s the way science works!

    In your world perhaps, not in ours.

  39. 39
    Elizabeth Liddle

    Chris:

    Obviously you don’t think that the salt patterns or snowflakes shed any life whatsoever on the cell though right?

    I do, actually, Chris, though by a remote connection :)

    Okay Lizzie, my problem here is that, when it comes to evolution, we can talk all day about venetian blinds and sand on drums. And there’s always an excuse when things don’t turn out the way evolutionists predicted they should turn out.

    Do you really not see that stasis is exactly what we’d expect to see if evolution was not true?

    But not relative stasis (slow evolutionary change) punctuated by periods of much more rapid change, nor placeable on an inheritance tree.

    But you raise an important point: some predictions made by a hypothesis are common to the predictions made by other hypotheses, in which case, no matter how true they turn out to be, they aren’t very informative, because they don’t distinguish between alternative hypotheses. Stasis alone would tell us nothing, and stasis only (exactly the same organisms alive in the Cambrian as are alive here, less a few extinctions) would be completely inconsistent with the Darwinian hypothesis.

    But that isn’t what we see at all.

    If we did actually find a fossil of a rabbit in the Cambrian, it would just be explained away as an extraordinary example of convergent evolution. If evolutionists can cope with that on the one hand and stasis on the other, they can certainly cope with an upside-down Tree of Life!

    I find this an odd argument (although it’s not the first time I’ve seen it). The biggest problem with it is: we have no fossil rabbit from the pre-Cambrian!

    And how, or whether, it would be “explained away” would depend entirely on what this hypothetical fossil looked like.

    If it were identical to a modern rabbit, and clearly Cambrian in origins, then it would certainly require a huge revision of our phylogenies, and render most of them totally unsupported by actual data. We’d find ourselves with a new tree in which most of the required links did not simply have gaps but were completely missing. We’d have to postulate, for example, that mammals had a completely different phylogeny to all other vertebrates.

    For which there would be no support from any other fossil apart from that one rabbit.

    So Darwinian evolution would in fact be in dire straits, and, to save it, the hunt would be on for pre-Cambrian precursors of that rabbit. Now, they should be there, because rabbits, unlike wormy things, fossilise pretty well (after all, we just found one…). We would also start looking for post-Cambrian rabbits, indeed evidence of rabbit-stasis from Cambrian to the present day, and we would have to abandon the existing rabbit phylogenies completely.

    Or, as you suggest suggest that rabbits evolved twice, independently, in which case we’d be hunting for post Cambrian descendents of the Cambrian rabbit.

    But my more serious point is – I don’t think it’s valid to argue from what you think Darwinist would do in the circs. I am sure you are right that the first response would be something like: “it’s a fake” and the second, if it were verified, would be to try to fit it into the Darwinian schema.

    But that’s not, as you might think, because of cussed Darwinian presuppositions, but because we have an extremely well-supported model, and the pre-Cambrian rabbit would throw the most colossal spanner into it, and that spanner could only be assimilated by such a radical retweaking of the parameters, and that retweaking make such radical new predictions, so far completely unfulfilled, that Darwinian evolution would, in fact, be in serious trouble, trouble that would only increase as subsequents efforts to find precursors and descendents of said rabbit failed to yield results.

    And, of course, this is entirely hypothetical because right now There Is No Such Rabbit!

    Much more interesting as a potential falsification, as I have suggested, would be actual evidence for an alternative evolutionary pathway – evidence for latent genetic material, for instance, activated by environmental triggers. So epigenetics should be a fertile area of enquiry for ID I think – although again, because Darwinian selection can operate above the level of the phenotype (at the level of the population) epigenetics is not inconsistent in principle with Darwinian evolution, but I’d expect Darwinian theory to make quite different specific predictions than ID.

  40. Do you really not see that stasis is exactly what we’d expect to see if evolution was not true?

    no no no.

    Evolutionary theory clearly predicts both change and not change, even though to evolve is to change.

    Darwin’s theory was clearly a theory of perpetual change.

  41. 41

    Elizabeth,

    Now, about stasis – this is an easy one, and comes directly from Darwin’s theory with hardly any adjustment. Darwin’s theory, is, essentially, a theory of how populations adapt to an environment. Once they reach an optimum, there is no reason to change further. In fact, no mechanism, under Darwinism, for them to do so (although there is under drift theory, and indeed, apparent stasis sometimes shows evidence of drift – changes over time that appear to serve no adaptive function).

    This is not an explanation, but rather a reflection of what it would explain. Change occurs when there is a need to adapt, and stasis when there is no need to adapt.
    But historically, how do we determine whether there was a need to adapt? According to the change. If it changed, adaptation was required. If it didn’t, it wasn’t.

  42. 42

    Lizzie, you say:

    But my more serious point is – I don’t think it’s valid to argue from what you think Darwinist would do in the circs.

    But the whole point I’m making is that evolutionists have got a substantial track record when it comes to explaining away uncomfortable evidence. Never mind 2 Princes or Alastair Campbell, evolutionists are the true Spin Doctors!
    Based on their past behaviour, it is perfectly valid to argue what evolutionists would do when yet more uncomfortable evidence came along to undermine their beliefs.

    Again, it is simply unproductive for you to assert (without proof) that evolutionists have “an extremely well-supported model”… unless you’re talking about funding, not evidence! If you’re talking about specific evidence, then now is the time to produce it. I’ll be disappointed if you mention peppered moths, finches beaks or embryology :-(

  43. 43
    Elizabeth Liddle

    ScottAndrews:

    This is not an explanation, but rather a reflection of what it would explain.

    Not quite getting your distinction here, but perhaps my wording could have been better: Darwin’s principle predicts that populations will moved to an optimum within a given environment (he didn’t express it quite like that, but if you plug in his algorithm, that’s what you get). So, if we observe punk eek in the fossil record, we would hypothesise that the eeks were associated with environmental stability and the punks by environmental change – that’s a prediction for which confirmatory or disconfirmatory evidence can be sought.

    Change occurs when there is a need to adapt, and stasis when there is no need to adapt.

    Right. Or, to put it less teleologically (although it amounts to the same thing) populations will move to an optimum within any given environment, and tend to stay there, so environmental change will tend to be followed by adaptation, and environmental stability will be associated with evolutionary stasis.

    But historically, how do we determine whether there was a need to adapt? According to the change. If it changed, adaptation was required. If it didn’t, it wasn’t.

    Well, scientific progress is iterative, but most obvious examples are the big extinctions, and subsequent rapid evolution, and there has been a lot of research into trying to find evidence for big environmental changes at around the same time.

    More intersting, though, are smaller scale changes, and changes not to the environment itself but to the location of the population.

    Plus the evolving population itself is part of the environment, leading to feed-back loops in which bigger horns in the population increase the advantage of even bigger horns.

    But the short answer is: if you see a “punk” fossil series then you need to be looking for some environmental change that might have rendered the original population no longer at an optimum.

    That evidence can be independent of the evidence of punk.

    Of course the other possible trigger for a punk series might be a novel feature, but I suspect that is rare. For example rudimentary vision might have triggered a huge punk sequence in which a new optimum appears on the horizon.

    Which is why “fitness landscape” is a better generalisation than “the environment” – populations move to fitness peaks within a high-and- growing-dimensioned landscape.

    But my short answer still holds in general, I think :)

  44. ScottAndrews,

    This is not an explanation, but rather a reflection of what it would explain. Change occurs when there is a need to adapt, and stasis when there is no need to adapt.
    But historically, how do we determine whether there was a need to adapt? According to the change. If it changed, adaptation was required. If it didn’t, it wasn’t.

    The way you’ve phrased the above sets up an inaccurate depiction of evolution, Scott. Evolutionary Theory does not suggest that any organism needs to adapt. Evolution as a process doesn’t include need as a driving mechanic. There’s no organism population out there in nature (this includes us humans) that is aware of what biological changes would best suite given environmental changes and then chooses those changes it feels it needs.

    So no, change does not occur when there is a need to adapt from an evolutionary theory perspective. Rather, changes occur – all the time. IF those changes are useful for adapting to environmental changes, they will have a better chance of being passed on to the next generation and so on. Need does not come into the picture.

    When Lizzie notes above, “there is no reason to change further”, what she means is that there is no selective pressure or rather nothing advantageous to select when a population reaches an optimum balance with its environment. She’s not saying there is no need to change – changes will take place anyway – but rather that any changes that might take place are not very likely to be selected for when a group of organisms are already optimized in a given environment.

  45. Lizzie,

    My apologies. I really shouldn’t try to explain what you mean when you know better than I what you were getting at and do a much better job of doing that anyway. I’ll stop doing that now. :)

  46. 46

    Elizabeth,

    But my short answer still holds in general, I think

    That was, in fact, an elaboration on your short answer, and the objection also still holds.

    Why do birds and bats fly while dogs and snails don’t? The answer boils down to, ‘Birds and bats needed to but dogs and snails were fine without it.’ It fits anything that has been observed and predicts anything that will be observed. It explains everything and nothing.

  47. 47

    Doveton,

    You’re missing the point: evolution is a theory designed to explain the origin of species as a direct result of continuous but massive changes that have occurred throughout the history of life, changes that should form a tree-like pattern.

    Does the fossil record show us any of these changes? No. Does it even show us a tree-like pattern? Of course not. It only provides evidence of sudden explosive appearances, long-term stasis, and sudden extinctions, often cataclysmic ones.

    All of that is the very last thing evolutionists expected to see, but rather than admitting that fatal problem, they’ve spent decades trying to explain it away instead. Unsuccessfully.

  48. 48

    Doveton,

    So no, change does not occur when there is a need to adapt from an evolutionary theory perspective. Rather, changes occur – all the time. IF those changes are useful for adapting to environmental changes, they will have a better chance of being passed on to the next generation and so on. Need does not come into the picture.

    Allow me to rephrase. Why do birds and bats fly while dogs and snails don’t? Flying is useful for birds and bats not not for dogs and snails. How do we know that flying is useful for birds and bats but not for dogs and snails? Because birds and bats fly but dogs and snails don’t.
    Having made that correction, it’s much less circular. :)

  49. 49

    Scott Andrews said:

    Why do birds and bats fly while dogs and snails don’t? The answer boils down to, ‘Birds and bats needed to but dogs and snails were fine without it.’ It fits anything that has been observed and predicts anything that will be observed. It explains everything and nothing.

    Exactly. Well-funded, very large and detailed collections of just-so-stories do not amount to the theory of evolution being “well-supported” where it really matters: evidence.

  50. ScottAndrews,

    Why do birds and bats fly while dogs and snails don’t? The answer boils down to, ‘Birds and bats needed to but dogs and snails were fine without it.’ It fits anything that has been observed and predicts anything that will be observed. It explains everything and nothing.

    Except that evolutionary theory doesn’t explain birds and bats flying and dogs and snails not flying the way you just described it. Birds and bats never needed to fly (and still don’t – see the Galapagos Cormorants, emus, ostriches, penguins), but rather gained changes that allowed flight, which under the circumstances and environments at the time were an advantage. Dogs and snails have never had any changes that allowed flight to take place, so flight was never a characteristic that could have been selected for. Of course, there’s nothing to suggest that flight would have been selected in either dogs or snails since both compete in their respective environments quite nicely without that trait.

  51. 51
    Elizabeth Liddle

    But the whole point I’m making is that evolutionists have got a substantial track record when it comes to explaining away uncomfortable evidence. Never mind 2 Princes or Alastair Campbell, evolutionists are the true Spin Doctors!
    Based on their past behaviour, it is perfectly valid to argue what evolutionists would do when yet more uncomfortable evidence came along to undermine their beliefs.

    But this is exactly what I’m disputing, Chris. I do realise that this is the perception here, but I consider it unfounded, or at least, if founded, self-correcting (by which I mean sure, all scientists have a tendency to argue positively for their claims, but the system is largely self-correcting).

    So can you give me some actual examples?

    Again, it is simply unproductive for you to assert (without proof) that evolutionists have “an extremely well-supported model”… unless you’re talking about funding, not evidence! If you’re talking about specific evidence, then now is the time to produce it. I’ll be disappointed if you mention peppered moths, finches beaks or embryology :-(

    No, I’m talking about evidence. Not only that, I am talking about consilient evidence. And I will group it into two categories: evidence for common descent and adaptive change through bifurcating lineages (which could conceivably also be explained by design), and evidence that Darwin’s mechanism actually works, can be observed to work, and that its prerequisites are present.

    The items you mention come into the second category.

    The first category includes:

    The fact that both extant and fossil biota can be readily placed into nested hierarchies (as noted by Linnaeus) using phenotypic “characters” ie. that these “characters” are non-randomly distributed, and form a tree.

    The fact that with some interesting exceptions, genetically derived phylogenies map on to phenotypically derived phylogenies, and that the interesting exceptions are susceptible to viable alternative mechanisms (e.g. viruses.

    The fact that these phylogenies predicted the finding of actual fossil animals, in a particular place (the finding of Tiktaalik). A case of intelligent design if ever I saw one – what was the probability of Shubin stumbling on Tiktaalik by chance!)

    The fact that there are a large number of transitional series in the fossil record (which is not to say we have actual lines of descent, but evidence of populations at least closely related to populations on actual direct lineages).

    The fact that we also see the transitional stages of evolving features (e.g. limbs).

    In the second category, which is of course trickier because we cannot observe much evolutionary distance in real time, I would include:

    All the examples you mention, which includes both actual lab experiments with manipulated variables as well as field work, and to which I would add Lenski’s e-coli experiments and vast amounts of work on fruitflies.

    The fact that GAs work (novel solutions are found to problems presented as a fitness function).

    The fact that the prerequisites for Darwinian mechanisms are present in life – replication with variance in the ability to replicate in a given environment. Note that with those prerequisites in place, adaptation by natural selection is bound to occur.

    The fact that many mechanisms have already been found that generate (randomly) the kind of variance required for Darwinian evolution to occur.

    The fact that “irreducible complexity” simply does not work as an argument, because the fact that a feature cannot function if one part is removed does not infirm the possibility that the feature itself could have evolved via pathways that involved subtraction rather than addition; nor is it true that all precursors for a feature have to be advantageous to be propagated through a population (drift) and can even in fact be slightly deleterious.

    The fact that novel functions have been shown to be traceable to specific mutations (citrate metabolism in e-coli; antifreeze in arctic fish; nylon metabolism in bacteria in Japanese nylon-factory waste pools).

    I could go on, but I hope that’s a start :)

  52. Chris Doyle,

    You’re missing the point: evolution is a theory designed to explain the origin of species as a direct result of continuous but massive changes that have occurred throughout the history of life, changes that should form a tree-like pattern.

    Yes, that’s an accurate description.

    Does the fossil record show us any of these changes? No. Does it even show us a tree-like pattern? Of course not. It only provides evidence of sudden explosive appearances, long-term stasis, and sudden extinctions, often cataclysmic ones.

    I disagree. While the fossil record may not show changes taking place – it is after all a series of snapshots – it does show distinct morphological incremental changes across closely related species. The fossil evidence we have for cetaceans is one of the better examples.

    I’m not even sure what you mean by “sudden explosive appearance” considering the timeline records and “not tree-like” given the same. How is this not tree-like:

    http://en.wikipedia.org/wiki/F.....morpha.jpg

    How is 65 million years “explosive”?

    http://www.dickrussell.org/gra....._page.html

    I suppose we in science see a bit more nuance in the fossil record that you do not.

    All of that is the very last thing evolutionists expected to see, but rather than admitting that fatal problem, they’ve spent decades trying to explain it away instead. Unsuccessfully.

    I would argue that we just haven’t seen the fossil record as you have.

  53. ScottAndrews,

    Allow me to rephrase. Why do birds and bats fly while dogs and snails don’t? Flying is useful for birds and bats not not for dogs and snails. How do we know that flying is useful for birds and bats but not for dogs and snails? Because birds and bats fly but dogs and snails don’t.
    Having made that correction, it’s much less circular. :)

    While that’s true it is less circular, it still doesn’t reflect what I noted evolutionary theory actually states.

  54. Doveton,

    There isn’t any genetic evidence to support the claim that non-flying animals can gain flight via an accumulation of genetic accidents.

    There isn’t even a way to test it.

    As for the fossil record, well the vast majority is of marine inverts (>95%) and we do not see any evidnce of a tree nor universal common descent in that vast majority.

  55. 55
    Elizabeth Liddle

    Scott Andrews:

    That was, in fact, an elaboration on your short answer, and the objection also still holds.

    Why do birds and bats fly while dogs and snails don’t? The answer boils down to, ‘Birds and bats needed to but dogs and snails were fine without it.’ It fits anything that has been observed and predicts anything that will be observed. It explains everything and nothing.

    Sheesh, preserve me from flying snails!

    :D

    No, it doesn’t “boil down to” what you said. I mean I’d love to fly, and I could argue that I need to, but I can’t. I’d also love to be able to apparate but I can’t.

    And I’d say that the argument you hint at there, is actually a very good example of why evolution is a good explanatory model. If wings are cool, why didn’t the ID give every species wings? If flow-through lungs are cool, why didn’t the ID give every species flow-through lungs?

    If bird-wings are cool, why bother to make a bat with a quite different type of wing, nonetheless reusing the same basic body plan? If sidewinding works, why give lizards legs?

    Well, you can answer: “because the ID felt like it” or you can answer: because morphology is constrained by inheritance. As it must be, if evolution is true.

    And I think the second is a much more satisfying answer. Not only that, but you can keep your ID, and give him/her credit for having initiated such an elegant system :)

  56. Joseph,

    There isn’t any genetic evidence to support the claim that non-flying animals can gain flight via an accumulation of genetic accidents.

    While that may well be true, could you explain why you think that’s relevant in light of this discussion thus far?

    The reason I ask it, as it stands your statement is similar to stating that there isn’t any genetic evidence for why chloroplasts are green. My response to such an observation would be, “Ok. And…?”

    There isn’t even a way to test it.

    Ok. And…?

    As for the fossil record, well the vast majority is of marine inverts (>95%) and we do not see any evidnce of a tree nor universal common descent in that vast majority.

    I certainly see evidence of a tree and common descent. Here’s a good example:

    http://biology-web.nmsu.edu/ni.....heLab.html

    and here:

    http://mollus.oxfordjournals.o.....7.abstract

    And here:

    http://paleobiol.geosciencewor.....ct/26/1/19

    And so on.

  57. Doveton:

    I certainly see evidence of a tree and common descent.

    Good for you. Unfortunately that point of view is still untestable.

    Also evolutionary biologists have said there isn’t any evidence for a tree of life. Strange…

  58. 58

    Doveton,

    Birds and bats never needed to fly (and still don’t – see the Galapagos Cormorants, emus, ostriches, penguins), but rather gained changes that allowed flight, which under the circumstances and environments at the time were an advantage. Dogs and snails have never had any changes that allowed flight to take place

    According to your explanation, your second statement is an assumption. Perhaps some specimens of dogs and snails did make small changes in the direction of flight, but they weren’t advantageous.

    I’m going to get this right if I keep trying:

    Why do birds and bats fly while dogs and snails don’t? Birds and bats gained changes that allowed flight, which under the circumstances and environments at the time were an advantage.
    And how do we know that birds and bats gained changes that allowed flight, which under the circumstances and environments at the time were an advantage, but dogs and snails did not?
    Because birds and bats fly while dogs and snails do not.
    Is that better? :)

  59. I certainly see evidence of a tree and common descent.

    Good for you. Unfortunately that point of view is still untestable.

    You could test it by following the links and either acknowledging the relationships that the studies (and tests) show or you could follow the links and report on what you see as errors in the testing methods used.

    Also evolutionary biologists have said there isn’t any evidence for a tree of life. Strange…

    Would you be so kind as to site a reference for this please? Thanks in advance.

  60. Doveton,

    There isn’t any way to test the claim that a prokaryote can “evolve” into anything but a prokaryote.

    Relationships? Based on common design or common descent?

    As for the link supporting my claim see comment # 31

  61. When Lizzie notes above, “there is no reason to change further”, what she means is that there is no selective pressure or rather nothing advantageous to select when a population reaches an optimum balance with its environment.

    And yet, according to Darwin, there is always selective pressure.

    It’s core to his theory.

  62. ScottAndrews,

    According to your explanation, your second statement is an assumption. Perhaps some specimens of dogs and snails did make small changes in the direction of flight, but they weren’t advantageous.

    Fair enough. I sit corrected. For snails and dogs, at the very least flight was not a selected trait.

    I’m going to get this right if I keep trying:

    Well, from my point of view the catch above is good indicator you are on the right track. :)

    Why do birds and bats fly while dogs and snails don’t? Birds and bats gained changes that allowed flight, which under the circumstances and environments at the time were an advantage.
    And how do we know that birds and bats gained changes that allowed flight, which under the circumstances and environments at the time were an advantage, but dogs and snails did not?
    Because birds and bats fly while dogs and snails do not.
    Is that better? :)

    Hmmm…well, you are closer, however the evolutionary explanation you provided answers a different question than the one you are asking. Try this instead:

    I’m going to get this right if I keep trying:

    From an evolutionary perspective, why do birds and bats fly while dogs and snails don’t?

    Birds and bats fly while dogs and snails do not because the flight traits gained in the former two groups of organisms was selected while the flight trait was either not available or not selected in the latter two groups of organisms.

    Pretty straight forward explanation.

    Now, if you want to know how the two groups gained the flight trait, that’s a different question. Still further different is the question of how the two other groups did not gain said trait, a question I might add that I certainly have no way to answer since there are many possible explanations (as you pointed out above) how an organism might not come up with a given trait.

    I’m reminded here of a joke I heard some time ago – why don’t snakes have legs?

    They are against wearing leather shoes.

    Not a very good joke imo, but it does illustrate a point – why questions can be answered in a variety of ways and many times the answers are informative, but not very useful. How questions, otoh, tend to be both informative and useful.

  63. Elizabeth Liddle:

    No, I’m talking about evidence… evidence that Darwin’s mechanism actually works, can be observed to work, and that its prerequisites are present.

    Great! That’s what you’ve been asserting and we’ve been asking for since you first showed up here, and what we are still waiting for.

    Time to put up or shut up, as they say.

  64. 64

    Doveton,

    Birds and bats fly while dogs and snails do not because the flight traits gained in the former two groups of organisms were selected while the flight trait was either not available or not selected in the latter two groups of organisms.

    I’m being a bit facetious, obviously, but I must add the final piece:

    We know the above because the flight traits gained by the former two groups of organisms was selected while the flight trait was either not available or not selected in the latter two groups of organisms because the former group flies while the latter group does not.

    What I’m demonstrating is the circular nature of the explanation. We don’t actually know which selective pressures applied to birds or bats but not to dogs or snails. We infer that those pressures were part of the cause from the existence of the traits we credit them with helping to produce.
    We can make occasional wild guesses at what those selective pressures might have been, but are at a loss to explain why other organism were not affected. This shows that we know little or nothing of the proposed cause, only of the effects.

    The result? The variations are held as evidence of the selective pressure, while the selective pressure in turn is used to explain the variations.

  65. 65
    Elizabeth Liddle

    ScottAndrews – another factor, of course is just – luck.

    Good old stochastic processes. Critters that acquired wings were those for whom some slight mutation started to push them in that direction. Now, before you say, “what use is half a wing”, consider tree-dwelling critters. Tree dwellers live with one heck of a hazard – falling out of trees. And what kills you when you fall out of a tree is the deceleration as you hit the ground hit the ground times your mass. And what affects the deceleration is your terminal velocity, also if you are lucky, any shock absorbers you happen to have.

    So baby animals in trees that are light, and fluffy will have a better chance of reaching maturity and having offspring than baby animals that are heavy and bald. And baby animals that can spread something out, however small, as they fall, are more likely to survive than baby animals that don’t.

    So potentially we have flying snakes, flying squirrels, sugar gliders, and fruit bats. But whether we get them or not, and what we get, depends no only on the environment (being born up a tree) but on what marginally advantageous traits happen to show up, because there is more than one way of not falling out of a tree, including being able to hang on.

    And once a population starts down a particular “solution path” then other “solutions” may become irrelevant, or even conflict with other things. For example if hanging on stops baby monkeys dying, being strong, and therefore dense may be advantageous (hang on better) but not much use for saving you if you do let go. So the monkeys that survive to breed are the strong clingers, and they won’t evolve to fly.

    Of course fruitbats both cling and fly – clever things! There is more than one way to skin a cat.

  66. Joseph,

    There isn’t any way to test the claim that a prokaryote can “evolve” into anything but a prokaryote.

    Sure there is:

    http://www.ncbi.nlm.nih.gov/pubmed/12446813

    and

    http://www.bacterialphylogeny.info/eukaryotes.html

    as examples.

    Relationships? Based on common design or common descent?

    The relationships illustrated in the links I provided.

    As for the link supporting my claim see comment # 31

    Oh…the New Scientist quotes. Here:

    http://www.texscience.org/repo.....09feb7.htm

    http://sandwalk.blogspot.com/2.....wrong.html

    http://scienceblogs.com/evolut....._journ.php

    http://scienceblogs.com/pharyn.....in_was.php

    http://scienceblogs.com/evolvi.....ongish.php

    And so on and so forth…

    In the immortal words of several evolutionary biologists who wrote back to the New Scientist about the cover story:

    “First, it’s false, and second, it’s inflammatory.”

    So no, “evolutionary biologists” (plural) have not said that there is no evidence for the tree of life even according to New Scientist article (which the Telegraph repeated). Graham Lawton, the writer, merely took a bunch of quotes out of context, exaggerating and misrepresenting them.

    In any event, if this is the reference you are relying upon then I feel quite secure that I and my colleagues can continue to rely the evidence for the Tree of Life.

  67. 67

    Elizabeth,

    Allow me to revise again (borrowing some text from Doveton):

    Birds and bats fly while dogs and snails do not because the flight traits gained in the former two groups of organisms by luck were selected while the flight trait was either not available or not selected in the latter two groups of organisms.

    We know the above because the flight traits gained by the former two groups of organisms by luck were selected while the flight trait was either not available or not selected in the latter two groups of organisms because the former group flies while the latter group does not.

    For example if hanging on stops baby monkeys dying, being strong, and therefore dense may be advantageous (hang on better) but not much use for saving you if you do let go. So the monkeys that survive to breed are the strong clingers, and they won’t evolve to fly.

    The trouble is, you’re inventing this selective pressure to fit the evidence. You can’t do that and follow the evidence to a cause at the same time.

    What evidence do we have that there was ever a time when monkeys or their predecessors were dropping off trees left and right and that this caused them to cling rather than fly or gallop? The only evidence is that monkeys cling instead of flying or galloping.

  68. ScottAndrews,

    I’m being a bit facetious, obviously, but I must add the final piece:

    Oh I know. And perfectly good facetiousness imo. :)

    We know the above because the flight traits gained by the former two groups of organisms was selected while the flight trait was either not available or not selected in the latter two groups of organisms because the former group flies while the latter group does not.

    Mmm…not quite. We know that specific incremental characteristic changes that ultimately could support flight were selected in the former two groups because we have the fossil evidence that indicates such.

    We also suspect that no specific incremental characteristic changes for flight came up for the latter to organisms because thus far none of the closely related fossilized ancestors show any such traits.

    What I’m demonstrating is the circular nature of the explanation.

    Well no…you’re demonstrating the circular nature of your particular phraseology by presuming that evolution relies upon the understanding of variations show selection. However, we only think in terms of variations show selection because we understand evolution (or at least genetics).

    Your explanation relies upon a post-hoc conclusions based upon an understanding of the principles of evolutionary relationships rather than focusing upon the principles that evolutionary theory actually studies and describes.

    In other words, your confusing the conclusions drawn from evolutionary theory with the phenomenon of evolution being studied.

    For example, you’ve presented the ability to fly as post-hoc evidence for the selection of said trait, which is fine, but that’s just oversimplification of what genetics and breeding demonstrate.

    Evolutionary evolutionary presents the explanation for how that relationship works, and that explanation provides the evidence for the selection of given traits that leads to a given ability, hence the focus on hereditary mechanisms, competition for resources and breeding, relative offspring success (against those offspring without a given trait), fossil records of trait development through related organisms, and so on.

    In other words

    We don’t actually know which selective pressures applied to birds or bats but not to dogs or snails. We infer that those pressures were part of the cause from the existence of the traits we credit them with helping to produce.
    We can make occasional wild guesses at what those selective pressures might have been, but are at a loss to explain why other organism were not affected. This shows that we know little or nothing of the proposed cause, only of the effects.

    Sort of – we know some of the selective pressures for trait adoption in some cases – hence the reason we can surmise others with a certain degree of accuracy – hence the reason we can breed dogs and horses and other organisms with certain traits. But that’s neither here nor there.

    The real point is that we don’t need to know the specific selective pressures to answer your question. Here’s the answer again reworded to take selection out:

    Birds and bats fly while dogs and snails do not because the flight traits gained in the former two groups of organisms were selected neutral or advantageous to the overall survival of bird’s and bat’s offspring while the flight trait was either not available or not selected a non-hereditary neutral anomaly in the latter two groups of organisms.

    I won’t argue that it would be interesting to know them and that they would certainly fill in a good deal of understanding on the mechanics of the process, but one can still know enough about the mechanics of the process to answer the question you’ve posed without knowing the selective pressures.

    The result? The variations are held as evidence of the selective pressure, while the selective pressure in turn is used to explain the variations.

    No. The variations are held as evidence of selective pressure as a result of understanding that the mechanisms of heredity, competition, reproductive success, offspring relative success and mortality rates, etc. lead to variation. The two understandings are not, however, used to explain each other.

  69. ScottAndrews,

    Birds and bats fly while dogs and snails do not because the flight traits gained in the former two groups of organisms by luck were selected while the flight trait was either not available or not selected in the latter two groups of organisms.

    Just going off on a tangent here based on what you wrote Lizzie. Why are you substituting “by luck” in the above? Such implies that you think that those organisms that gained flight were in some way more fortunate than those who did not gain flight. I really don’t think that most (if any) organisms that get flight are more lucky than those who didn’t. Looking strictly at the lineage of cormorants and turkeys, for example, those two groups seem to show that at least some organisms are perfectly successful giving up the trait.

  70. 70

    Doveton,

    We know that specific incremental characteristic changes that ultimately could support flight were selected in the former two groups because we have the fossil evidence that indicates such.

    We hold that selection is the cause of the variation in fossils, and the evidence is that the fossils are varied.

    What’s mind-straining is that each case of circular reasoning is used to bolster the other case of circular reasoning in a similarly circular manner. It’s employed with regard to living things and to fossils, and either case can and is used to support the other.

    The variations are held as evidence of selective pressure as a result of understanding that the mechanisms of heredity, competition, reproductive success, offspring relative success and mortality rates, etc. lead to variation.

    That’s exactly what I’ve been saying. The variations are the evidence of the selective pressure, which in turn is used to explain the variations.

    You can use “X” – anything at all – to explain variations if the variations, which clearly exist, are accepted as evidence of X.

  71. 71

    Doveton,

    Just going off on a tangent here based on what you wrote Lizzie. Why are you substituting “by luck” in the above?

    I was quoting her. But she was referring to element of chance, not good fortune.

  72. 72

    Doveton,

    For example, you’ve presented the ability to fly as post-hoc evidence for the selection of said trait, which is fine, but that’s just oversimplification of what genetics and breeding demonstrate.

    Evolutionary evolutionary presents the explanation for how that relationship works

    There is no basis in breeding to show how a change such as gaining flight would occur. Genetics offers nothing in this respect either. Countless research papers describe the difference in genes and proteins between two organisms but leave the pathway between them hanging as something assumed and yet omitted.

    In the historical sense no evidence is provided for selection besides the variation it explains.

  73. Morning Doveton,

    While the fossil record may not show changes taking place – it is after all a series of snapshots – it does show distinct morphological incremental changes across closely related species.

    This just isn’t true and this is plainly obvious from the fact that you claim that:

    The fossil evidence we have for cetaceans is one of the better examples.

    If that’s the best you can do (and given that it was the first example you gave, it probably is) then your beliefs are literally in a whale of trouble. If you require any further confirmation of that fact, just re-read what you wrote here:

    I suppose we in science see a bit more nuance in the fossil record that you do not.

    Are you serious, Doveton? Do you know how ridiculous that statement makes you sound? You can’t substantiate your disagreement with me so you have to make an appeal to authority instead: always a bad sign. But then lumping yourself in with that authority, well, you can’t expect to be taken seriously after a move like that.

  74. Lizzie, post 50, that’s much more like it (from a proper scientist, too)! I will respond to that fully sometime this weekend, hopefully.

    Have a good one!

  75. 75
    Elizabeth Liddle

    Doveton and ScottAndrews:

    ScottAndrews,

    Birds and bats fly while dogs and snails do not because the flight traits gained in the former two groups of organisms by luck were selected while the flight trait was either not available or not selected in the latter two groups of organisms.

    Just going off on a tangent here based on what you wrote Lizzie. Why are you substituting “by luck” in the above? Such implies that you think that those organisms that gained flight were in some way more fortunate than those who did not gain flight. I really don’t think that most (if any) organisms that get flight are more lucky than those who didn’t. Looking strictly at the lineage of cormorants and turkeys, for example, those two groups seem to show that at least some organisms are perfectly successful giving up the trait.

    Scott is correct – I wasn’t using “luck” in the sense of “good luck” – I should have said “chance” I guess.

    My point really is that which path a population starts going down at the beginning may be mostly chance (even drift), but if that direction turns to be pushing on an open door, the population will keep going in that direction,which may in turn close other doors. In my hypothetical example, a tree-dwelling population might find itself getting lighter and fluffier because smaller and fluffier means better survival from a fall; another might find itself getting stronger at clinging, because being good at clinging stops you falling, but can no longer move in the direction of ligher and fluffier because of the muscles it has found effective for clinging with.

    But the door a population starts pushing on may be largely a matter of chance.

  76. 76
    Elizabeth Liddle

    Chris, I’m sort of intrigued by your skepticism vis a vis whale evolution.

    I mean skepticism is healthy and all that, but I think Doveton’s point – though somewhat tactlessly expressed! – references this gulf that I know I’ve talked about here as well (possibly just as tactlessly) between the kind of assumptions we take for granted so much in science that they are rarely made explicit, namely, that all conclusions are provisional, and that science is about fitting models to data, not proof, and the way science is perceived by those outside the field – Finding Out Stuff. That’s why I posted the link to Asimov’s essay – but, curiously, your interpretation of it was itself an illustration of the gulf!

    There’s a paper here about whale phylogeny that you might find interesting:

    http://webh01.ua.ac.be/funmorp.....en2007.pdf

    On the other mind you might dismiss it as more Just So stories.

    I’d be interested to know whether you do!

    This is not meant to be patronising at all – I think there really is a huge gulf, and scientists bear primary responsibility for it IMO (and science journalists a little of it as well). I’ve had interesting arguments with lawyers about science, and lawyers are pretty smart people. But a lawyer’s take on evidence is so different from a scientist’s, it is hard to bridge the gulf.

    And then there are engineers….

  77. 77

    Hiya Lizzie,

    Everybody here would grant the assumptions that you’ve listed precisely because we’re all interested in “Finding Out Stuff.” Furthermore, those assumptions allow us to keep an open mind and prevent dogma arising. However, there’s another assumption that evolutionists take for granted and that is: evolution is true. And the problem with this assumption is that it is detrimental to “Finding Out Stuff”. It closes minds and swamps us with dogma. If you removed that evolutionist assumption, I think you would see the huge gulf close very quickly.

    I don’t know if you checked out either of the links I mentioned to Doveton in relation to whale evolution: but, in direct response to the PDF you referenced, here is another one.

    Incidentally, browsing the many articles in the http://www.scienceagainstevolution.org website will give you an insight into the roots of my skepticism.

  78. 78
    Elizabeth Liddle

    Chris:

    I’m not sure whether you perhaps missed my point, or making a more subtle one. You wrote:

    Everybody here would grant the assumptions that you’ve listed precisely because we’re all interested in “Finding Out Stuff.”

    My point is that science is not, primarily (or at least methodologically) about “Finding Out Stuff”. It’s about fitting models to data. Now, finding a well-fitting model may be a kind of “Finding out” of a kind of “Stuff” but not, I suggest, in the way it’s commonly understood. So we get headlines like “scientists find the ancestor of the whale”. What the scientists have actually found is a model of whale evolution that is a good fit to the data (and that data may be fairly sparse). And while some “findings” may be such overwhelmingly well-fitting models that we regard them as “facts”, actually there are no “facts” in science. Everything is always up for grabs. It’s just that if we regarded everything as equally up for grabs, we’d never make any progress. Hence Asimov’s point about “the relativity of wrong”. We know that the curvature of the earth is near zero. We have always known that. We have always know that we do not live on a tiny spherical asteroid like The Little Prince. But we can probe that value to find it more and more precisely. Nonetheless, the dimensions of the earth, and its shape, will never be an an challengeable “fact”. It will always be subject to refinement (ditto for the age of the earth, of course).

    However, there’s another assumption that evolutionists take for granted and that is: evolution is true. And the problem with this assumption is that it is detrimental to “Finding Out Stuff”.

    Two questions: what do you understand by the phrase:”Evolution is true”?

    Second: can you give me an example of where this assumption has been detrimental to “Finding Out Stuff”?

    Thanks!

    It closes minds and swamps us with dogma. If you removed that evolutionist assumption, I think you would see the huge gulf close very quickly.

    It’s a gulf I’d gladly see closed, Chris! But I suggest that what really needs removing is the assumption that evolutionists make the assumption you assume they make!

    That’s why I’d like you to unpack the assumption you think they make!

  79. 79

    Hi Lizzie,

    You asked:

    So can you give me some actual examples (of evolutionists as the true Spin Doctors)?

    The Cambrian Explosion, for starters. Asking for 75 minutes of your time is unreasonable, I know, but please try and watch the Darwin’s Dilemma documentary if you want to discuss this further. And then every instance of “convergent evolution” (ie. between placental and marsupial mammals) and “divergent evolution” (ie. between the Y chromosome in humans and chimps). Convergent evolution is a term evolutionists use to simply explain away the problem of supposedly distantly related species being uncomfortably similar. Divergent evolution glosses over the opposing problem of supposedly closely related species being uncomfortably dissimilar.

    Now then, onto your evidence:

    Your first piece, biological classification/common descent has been dealt with here.

    Your second piece is actually another example of evolutionists as true Spin Doctors: using HGT to magic away exceptions to the tree of life where none are permitted.

    You then mention Tiktaalik which is the only specific reference you make to substantiate your third, fourth and fifth piece of evidence. But, we now know that Tiktaalik is irrelevant to evolution.

    So much for the first category. Next we have the second category.

    You first of all cite “all the examples” I mentioned. I honestly don’t know what you’re referring to there.

    You add Lenski’s e-coli experiments which have been dealt with here (in a comment addressed to Ellazimm originally, but one that I’ve referred you to before today).

    You mention fruitflies: mere sub-specific variety (within a pre-existing, unevolved gene pool), at best. A failure to recognise the fact that fruitflies also demonstrate genetic homeostasis, at worst.

    GAs: intelligent designers using intelligently designed systems to achieve intelligently designed goals. IOW, irrelevant.

    Replication with variance has been dealt with here.

    Then yet more spinning when you mention “irreducible complexity”. Evolutionists have this notion that the IC argument (like Paley’s watch argument) has been dealt with when it hasn’t. All we see are gross misunderstandings of the argument or lack of awareness of the obstacles to overcoming IC. Behe himself answers most of your objections here.

    What you call “novel functions” in bacteria, I call missing the point. If you read the post I referenced earlier , you will see why.

    Finally, antifreeze in arctic fish: the Edge of Evolution, at best. Sub-specific variety (within a pre-existing, unevolved gene pool) at worst.

    So, by moving onto actual specific evidence for evolution, we are definitely moving in the right direction and I applaud and encourage that, Lizzie. However, as I’ve demonstrated above, the one-liner scattergun approach to evidence for evolution is weak and ineffective (although it did allow me to highlight some unanswered posts!) Can I please request a more practical and focused approach instead? Pick one piece of evidence, preferably one that is particularly important and significant to you personally, and use the entire post to detail why that piece of evidence supports evolution. I will then respond in full (avoiding reliance on links which are frankly no substitute for debate). I think that is the most productive way forward in this discussion.

  80. 80
    Elizabeth Liddle

    Chris, thanks, and I will watch that video.

    Also respond in more detail to your post, and try to check the links as well.

    However, I will say that the “pick one piece of evidence” approach is problematic.

    What matters, so often, in huge domains of science like evolutionary theory, or the age of the earth, is the consilience of multiple pieces of often independent evidence.

    Any one piece may have multiple possible explanations. But a good theory will cover lots of pieces of evidence. It may not be the neatest, or even the most intuitive, explanation for any one piece, but the model we want is one in which all the explanations for all the pieces hang together.

    But I’ll try to explain what I mean in more detail with respect to your post above later, hopefully having had time to watch the video!

    Thanks.

    Lizzie

  81. 81
    Elizabeth Liddle

    BTW, Chris:

    You then mention Tiktaalik which is the only specific reference you make to substantiate your third, fourth and fifth piece of evidence. But, we now know that Tiktaalik is irrelevant to evolution.

    No, we certainly do not!

    More on that later, but the short answer is that the footprint finding AND Tiktaalik are both hugely relevant to evolution, specifically fish-tetrapod transition!

    There’s an old creationist canard, much mocked in evolutionary circles, that goes “then why are there still monkeys?”

    Casey Luskin is making the exact same error – “then why were there still Tiktaaliks?”

    I actually know Per Ahlberg, who has worked on both, and I’ll try to dig out what he wrote about them. It’s fascinating work!

  82. 82

    the footprint finding AND Tiktaalik are both hugely relevant to evolution

    Every living thing and every fossil are relevant to evolution, because their very existence is evidence of the various evolutionary processes (some blanks to be filled in later) which must have produced them.


  83. There isn’t any way to test the claim that a prokaryote can “evolve” into anything but a prokaryote.

    Doveton:

    Sure there is:

    http://www.ncbi.nlm.nih.gov/pubmed/12446813

    and

    http://www.bacterialphylogeny.info/eukaryotes.html

    as examples.

    Except there isn’t any evidence that endosymbiosis took place other than “it looks like it did”. Your first link doesn’t help.

  84. The theory of evolution does not expect nor predict a tree of life because the theory of evolution is silent on the origin of living organisms and it is the origin that determines how many trees there will be.

    (it is a given that basic fact will be lost on evos)

  85. 85
    Elizabeth Liddle

    ScottAndrews:

    Every living thing and every fossil are relevant to evolution, because their very existence is evidence of the various evolutionary processes (some blanks to be filled in later) which must have produced them.

    Exactly. In fact even that is an understatement – every living thing and every record of every living thing is the explanadum – that to be explained.

    To say that tiktaaliks are irrelevant to evolution is like saying that calcium is irrelevant to chemistry!

    And evolutionary theory, inter alia, posits that all living things can be placed on a hierarchical tree diagram by means of phenotypic characters and that this tree that will tend to be deeply nested.

    Tiktaaliks can be placed on the tree, together with the Zachelmie footprints, as below:

    http://talkrational.org/showth.....post755320

    Also, a good cautionary paper here:

    http://rspb.royalsocietypublis......2010.1321

    (Not open access, but the abstract is good).

    Casey Luskin writes:

    New scientific discoveries are exciting because they force us to revise, rethink, and improve our scientific explanations. In fact, neo-Darwinian evolution is certainly not refuted by these newly discovered tetrapod tracks. However, it’s clear that evolutionary thinking led some researchers to make a prediction here. They claimed this prediction was a great confirmation of evolutionary theory. But this prediction is now known to be false. Neo-Darwinism lost an important argument.

    This is an equivocation wrt the word “prediction”. The extraordinary prediction referred to by Shubin was that tetrapod fossils, showing transitional features between extant fossil tetrapods, would be found in a particular stratum, that was known to be exposed in a particular place on the earth’s surface, namely, late Devonian river sediments on Ellesmere Island,Canada. Far from their prediction being “now known to be false” – they found them!

    The prediction Luskin is claiming is “now known to be false” is not clear, but it clearly isn’t Shubin’s because Shubin’s was successful.

    In fact, what Luskin is complaining about is that tiktaalik isn’t “transitional”, although he tries to rebut claims that this is what he is doing, extremely unsuccessfully. The prediction was absolutely correct – they predicted where the Tiktaaliks would be, and there they were.

    The did not predict that they would find the earliest tetrapods at that location in the geologic column, but that they would find tetrapods with transitional features at that location.

    As Luskin correctly notes, this hoohah is all about rhetoric, not about science. There is a perfectly good phylogeny on which both Tiktaalik and the other early tetrapods, including the Zachelmie footprint-makers, can be placed, and the features of Tiktaalik remain as transition as ever.

    Just as modern tarsiers have transitional features between modern lemurs and new world monkeys, yet all are extant species.

  86. Elizabeth,

    Have you read Shubin’s book “Your Inner Fish”?

    Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythungs” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10

    But anyway, the point is had the new data been available to Shubin- the data that puts the transition back to before 390 million years ago- that whole set up would be meaningless and wrong. Meaning he would not have been looking where he did.

  87. Even Shubin understood the place to look for evidence of the transition is between two periods- the period in which there weren’t any tetrapods and the period in which there are tetrapods.

    Tiktaalik was found after tetrapods existed.

  88. 88

    Exactly. In fact even that is an understatement – every living thing and every record of every living thing is the explanadum – that to be explained.

    I realize I’m being repetitious, which is a bit lame. But I’m pointing out that each living this is evidence of [non-specific ever changing] evolutionary causes because only those causes could have produced them.

    Take away the assumption that the [non-specific ever-changing] evolutionary causes are responsible, and living things are no longer evidence of them.

    It’s circular.

  89. 89

    each living this thing

  90. 90

    I think it’s only a matter of time before intelligent design is incorporated as another evolutionary mechanism. Not in the sense of intelligently guided evolution, but in the sense that designing and making something is an evolutionary mechanism.

    That way the theory of evolution will encompass every known and unknown cause imaginable. Then all evidence will always support it and no evidence will ever undermine it.

    It sounds silly, but it’s not much of a stretch. Right now ‘evolutionary mechanisms’ include a broad range of causes, usually with no specifics, along with absolutely any non-intelligent cause that might be observed or imagined later. There’s only one step left to take.

  91. Shapiro is already proposing natural genetic engineering.

  92. ScottAndrews,

    Doveton,

    We know that specific incremental characteristic changes that ultimately could support flight were selected in the former two groups because we have the fossil evidence that indicates such.

    We hold that selection is the cause of the variation in fossils, and the evidence is that the fossils are varied.

    Again, no, this is incorrect. First, in Evolutionary Theory, selection is not the cause of variation; selection is the term that describes the relative breeding fitness of offspring based on environment and traits. Mutation and genetic drift and genetic shift are what cause variation; selection is the term used to describe the disproportion of those organisms with a favorable trait change over those without said trait.

    What’s mind-straining is that each case of circular reasoning is used to bolster the other case of circular reasoning in a similarly circular manner. It’s employed with regard to living things and to fossils, and either case can and is used to support the other.

    There is no circularity as I’ve shown. I think you are just confused about the terms as used in Evolutionary Theory.

    The variations are held as evidence of selective pressure as a result of understanding that the mechanisms of heredity, competition, reproductive success, offspring relative success and mortality rates, etc. lead to variation.

    That’s exactly what I’ve been saying. The variations are the evidence of the selective pressure, which in turn is used to explain the variations.

    That is not what I noted above. Selective pressure is not used to explain variation; mutation, drift, and shift (among other things) along with hereditary mechanism, competition, mortality, etc. are.

    You can use “X” – anything at all – to explain variations if the variations, which clearly exist, are accepted as evidence of X.

    Except that there’s a “Y” you keep leaving out.

  93. ScottAndrews,

    Doveton,

    For example, you’ve presented the ability to fly as post-hoc evidence for the selection of said trait, which is fine, but that’s just oversimplification of what genetics and breeding demonstrate.

    Evolutionary evolutionary presents the explanation for how that relationship works.

    There is no basis in breeding to show how a change such as gaining flight would occur. Genetics offers nothing in this respect either. Countless research papers describe the difference in genes and proteins between two organisms but leave the pathway between them hanging as something assumed and yet omitted.

    I didn’t phrase that well – my point had nothing to do with breeding demonstrating the genetics of flight; my point was the perspective on post-hoc explanations for traits. People who do breeding (I had neighbors who bred show dogs and my wife is now into horses wherein there are a number of folks breeding show and racing horses) evaluate breeding success in terms of post-hoc evidence in a number of situations. You’ve merely taken that explanation as being evolutionary theory’s explanation in toto. My point is the post-hoc explanation is now what evolutionary theory states.

    In the historical sense no evidence is provided for selection besides the variation it explains.

    As I explained above, evolutionary theory does not suggestion that selection causes variation. Selection is the term for those characteristics of the environment that promote favorable variances and demote unfavorable variances.

  94. Chris Doyle,

    While the fossil record may not show changes taking place – it is after all a series of snapshots – it does show distinct morphological incremental changes across closely related species.

    This just isn’t true and this is plainly obvious from the fact that you claim that:

    The fossil evidence we have for cetaceans is one of the better examples.

    If that’s the best you can do (and given that it was the first example you gave, it probably is) then your beliefs are literally in a whale of trouble. If you require any further confirmation of that fact, just re-read what you wrote here:

    I suppose we in science see a bit more nuance in the fossil record that you do not.

    Are you serious, Doveton? Do you know how ridiculous that statement makes you sound? You can’t substantiate your disagreement with me so you have to make an appeal to authority instead: always a bad sign. But then lumping yourself in with that authority, well, you can’t expect to be taken seriously after a move like that.

    Chris, just a point to consider: writing an emotionally-laced complaint indicating you’re greatly insulted and frustrated by my post is not a rebuttal. I can’t do anything with general claims of disagreement and insistence that my “beliefs are in trouble” or how ridiculous I sound if you can’t provide a sound rebuttal to the actual points I raised and the reference to the cetacean fossil record I provided. I may well sound arrogant for lumping myself in with scientists, but the fact is I am a researcher in ecology and biology and thus I am part of that group.

    So at this point, your claim that I have not substantiated my disagreement with you is unfounded – I provided a perfectly apt reference to support my point, which at this point you have not rebutted.

    For example, what specifically about the cetacean fossil record does not show distinct morphological incremental changes across closely related species? That would be a reasonable start to actually rebutting my point.

  95. Doveton,

    If highlighting the fact that your argument rested upon an invalid appeal to authority (compounded with your own personal authority) is what you call an “emotionally-laced complaint”, then I’m guilty as charged. But then, so are you. And I’m not going to waste my time with someone who feels the need to appeal to his own personal authority in order to substantiate a point.

    But, if you are more impressed by the truth than you are by yourself, then click on the two hyperlinks in my previous post and you will find substantial rebuttal to your “reference to the cetacean fossil record”.

  96. Hi Lizzie,

    In post 58 you wonder whether or not I missed your point or was making a more subtle one. I think I was making a more subtle one, but perhaps not successfully!

    If “Finding Out Stuff” is how we learn about things and increase our knowledge, then the scientific method is just one way of “Finding Out Stuff”. I appreciate that you are advocating a cautious, non-dogmatic, open-minded approach to scientific knowledge, Lizzie. However, most people don’t think like that. On the contrary, people often try to persuade us that their side of the argument is true because it is backed up by indisputable scientific facts! This is particularly true of evolution and most evolutionists agree with Richard Dawkins when he says “It is absolutely safe to say that, if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).”

    Elsewhere, there are more settled and entirely undisputed areas of science. Sure, they are subject to refinement. But we’re not going to return to a geocentric view of the solar system nor a flat Earth. When it comes to “Finding Out Stuff” that stuff has been well and truly “Found Out”.

    The difference between you and me, Lizzie, is that you put evolution in the category of “Found Out” and I do not. Your perspective here is what I understand by the phrase “Evolution is true”.

    Where has the assumption that “Evolution is true” been detrimental to “Finding Out Stuff”? Well, dismissing the vast majority of our DNA as “Junk”, in terms of the delays and reduced resources in exploring this DNA further, for starters. Or ripping out so-called vestigial organs (every single one of which is now known to serve a function) at the first sign of trouble. Then there’s the vast, countless sums of money that have been wasted on trying to find evidence to support evolutionist beliefs. But, the most detrimental effect of all is the fact that propagating the claim that “Evolution is true” has leant vital support to the atheistic worldview.

    You did ask ;-)

  97. Chris Doyle,

    I don’t know if you checked out either of the links I mentioned to Doveton in relation to whale evolution: but, in direct response to the PDF you referenced, here is another one.

    You know, I apologize. I freely admit I dismissed those references when I first started to read them since they were written by an engineer who freely admits to having done no actual research in biology or paleontology. That’s a rather rude and arrogant stance to take, so here’s my analysis of Mr. Do-while Jone’s assessment.

    Mr. Jones first assesses the famed paleontologist George Gaylord Simpson’s puzzlement over whales (as written about by Niles Eldredge in 1991), a curious problem to raise considering the number of fossils Simpson had to work with back in 1926 (when he first started reviewing whale fossils) through 1938 (when Simpson began trying to reconcile the gaps). As Dr. Fitzgerald and Dr. Thewissen’s work now shows, the amount of time is not only not an issue now, it has now been well-established at 65 million years.

    It seems the Mr. Jone’s material is considerably out-of-date – his most recent reference is from 2001. Cetacean evolution research has grown considerably in the last few years alone, but clearly the largest jump in our understanding came between 2003 and 2007 when Dr. Thewissen provided such abundant and detailed finds that filled in a number of gaps. The validity of Mr. Jone’s assessment comes into question in light of this.

    For example, Mr. Jones posts a criticism of the of “accepted order of the archaeocete species, in terms of both morphological (primitive to advanced) and stratigraphical (lower/older to higher/younger) criteria, is Pakicetus, Ambulocetus, Rodhocetus, Indocetus, Protocetus, and Basilosaurus” from Ashby Camp (1998), stating “There isn’t any proof that one evolved into the other. They could just as easily have been separate species that had some coincidental similarities that evolutionists mistook for evidence of evolution.” Interestingly, I reviewed eleven different books and research papers on the subject and not one indicated that any of the species necessarily evolved directly into any other one, so Mr. Jones’ criticism does not seem accurate. But Mr. Jones does not actually criticize the one element that all of the research papers do note – the chronological order of trait changes each of the above specimens demonstrate for cetacean evolution.

    Mr. Jones also notes the early criticism by Zimmer that there aren’t enough whale fossils. This too is from Eldedge’s book from 1991 and is clearly no longer a valid criticism. Thewissen alone has provided several dozen from a variety of different strata.

    Mr. Jones criticizes the idea that Pakicetus and Basilosaurus could be related (citing Lenny Flank from 1995) because Pakicetus was found in Pakistan and Basilosaurus was found in Louisiana. Aside from the fact that geography clearly doesn’t matter to many whale species as they currently are capable of (and regularly do) swim all over the world, Basilosaurus fossils were discovered in a number of places, including in Pakistan in 1997.

    The long and short of it is that none of Mr. Jones’ criticisms appear valid in light of extensive data today. If you have something more recent I’d be more than happy to consider it.

  98. Sorry Lizzie, that was a response to Post 78, not 58.

  99. Lizzie,

    I mean skepticism is healthy and all that, but I think Doveton’s point – though somewhat tactlessly expressed!

    Mea Culpa, Lizzie. I just get a little tired of the tactlessness of claims and opinions absent actual work in the field being presented as having the same credibility and validity as actual research having been performed. The reference to Mr. Jones’ claims rehashing very old claims about the fossil record comes is a case in point, particularly given that Mr. Jones appears to have been selectively reading from even the work contemporary to his claims.

    My statement that we scientists see a bit more nuance in the data was an attempt at being sarcastic about Chris’ claim that the appearance of whales was “explosive” when all contemporary evidence and analysis implies otherwise. Clearly I should have just explained that in a straight forward manner instead.

  100. Chris Doyle,

    If highlighting the fact that your argument rested upon an invalid appeal to authority (compounded with your own personal authority) is what you call an “emotionally-laced complaint”, then I’m guilty as charged.

    Except that my argument doesn’t rest on or even include an appeal to authority. My comment on scientists seeing more nuance was a poke at your claim of “explosive appearance” given that the links I provided show the opposite. The whole point is, it doesn’t take a lot of nuance to see that the fossil record is anything but explosive, so I’m still waiting for you to explain that claim.

    But then, so are you. And I’m not going to waste my time with someone who feels the need to appeal to his own personal authority in order to substantiate a point.

    Well, having not claimed any personal authority on whale evolution, I’m not sure what your affront is in reference to. Regardless, since I’ve addressed many of the criticisms provided by Mr. Do-while Jones, perhaps you’d care to comment on why you feel they are valid.

    But, if you are more impressed by the truth than you are by yourself, then click on the two hyperlinks in my previous post and you will find substantial rebuttal to your “reference to the cetacean fossil record”.

    See my rebuttal there of.

  101. 101

    I’m sorry Doveton, but your response to Do-While Jones’ articles is weak and inadequate, particularly in light of your (apparently oversold) scientific credentials.

    First of all, the http://www.scienceagainstevolution.org website has been producing monthly newsletters since October 1996. Jones frequently bases his articles on the latest scientific publications. So, the first article, written in August 1999 was based on Faith McNulty’s “How Whales Walked Into The Sea” and cited (at the time) recent issues of ‘Science News’, ‘Nature’, ‘Scientific American’ and ‘Science’. The second article, written in November 2001 was based on (at the time) recent issues of ‘National Geographic’, ‘Nature’ and ‘Science’.

    Now, in response to me, you actually quoted a reference I made to Lizzie on the very subject of so-called whale evolution. Did you honestly not check that? Because if you did, you would’ve quickly learned that since Do-While Jones first two articles on the subject, he has written another three: one in September 2003, one in December 2006 and one in January 2008 (which was a direct response to the source Lizzie made reference to).

    So, you can imagine, and indeed, understand how disappointed and unimpressed I was when you said:

    Cetacean evolution research has grown considerably in the last few years alone, but clearly the largest jump in our understanding came between 2003 and 2007 when Dr. Thewissen provided such abundant and detailed finds that filled in a number of gaps. The validity of Mr. Jone’s assessment comes into question in light of this.

    Things go from bad to worse when you fails to even acknowledge, let alone address, the most serious problems that Jones highlights. For example, Jones points out that:

    All the creatures (Pakicetus, Ambulocetus, Protocetus, Indocetus and Rodhocetus)…appear in the fossil record at the roughly same time.

    He also highlights the fact that “Their argument as to whether or not similar teeth prove evolution is contradictory”.

    Then there is the fact that “Evolutionists have told us that Pakicetus couldn’t even hear under water. But toothed whales (and dolphins, etc.) have ultrasonic sonar” and “Echolocation and high-frequency hearing are crucial for sensory perception in toothed whales… As a part of this functional adaptation, numerous structural specializations are developed in the inner ear and in the petrosal bone containing the inner ear.”

    Jones continues:

    For years, evolutionists have claimed that whales evolved from something like a wolf. But when they analyzed the DNA, whale DNA was closer to hippo DNA than wolf DNA.

    And that’s just the first article. In the second article, Jones highlights the fact that:

    All the postcranial bones indicate that pakicetids were land mammals, and it is likely that they would have been thought of as some primitive terrestrial artiodactyl if they had been found without their skulls.

    And points out that “Thewissen’s new fossil discoveries show that Pakicetus has practically nothing in common with Ambulocetus or Basilosaurus.”

    So, “The only parts of Pakicetus that look like a whale are the teeth and the ears.”

    But then:

    Deep, near-vertical gouges constitute most of the dental wear in pakicetids. Cladistic arguments have been used to link this wear pattern to aquatic predation on fish, but no functional model or modern analogue is known. Moreover, this kind of dental wear also occurs in raoellid artiodactyls. Although this dental wear probably represents a distinctive way of food processing, it does not necessarily imply aquatic life.

    Furthermore:

    Although there is a general resemblance of the teeth of archaeocetes [ancient whales] to those of mesonychids, such resemblance is sometimes overstated and evidently represents evolutionary convergence.

    So much for the teeth. How about the ears?

    Unlike any other cetacean, the pakicetid outer ear was unspecialized and similar to that of land mammals…(and) inconsistent with good underwater hearing.

    Which raises the question, if the only parts of Pakicetus that look like a whale are the teeth and the ears, but in fact, neither teeth nor the ears are remotely whale-like, then how desperate must things be for evolutionists that they have to offer up such pitiful evidence to support their beliefs?

    Finally, we learn that:

    the morphology of the newly adapted animals is generally so greatly modified, because of the high selective pressure, that any resemblance to the original ancestor is quickly obliterated.

    Now, Doveton attempted to justify his bragging on the grounds that I had the temerity to “claim that the appearance of whales was “explosive”.” Yet, we can only describe it as ‘explosive’ when “any resemblance to the original ancestor is quickly obliterated.”

    Doveton lazily dismisses everything I’ve detailed above with the following statement:

    The long and short of it is that none of Mr. Jones’ criticisms appear valid in light of extensive data today.

    I have gone to much more effort for Doveton than he has done for me. As far as I’m concerned this is the last word on the subject. However, if Doveton demonstrates awareness and understanding of the wide range of problems that the just-so-story of whale evolution is riddled with and then produces a response that properly details the evidence for whale evolution (properly taking into account the five articles by Do-While Jones), then this discussion can continue.

  102. Chris Doyle,

    I’m sorry Doveton, but your response to Do-While Jones’ articles is weak and inadequate, particularly in light of your (apparently oversold) scientific credentials.

    Now that’s irony, Chris…very funny statement – you denigrate my scientific credentials while relying upon a self-professed electrical engineer’s opinions regarding paleontology and biology.

    Anyway, I’m sorry Chris, but I can’t take your reference seriously for one main reason: he will not admit that he was wrong. Having made claims that later evidence demonstrated was just plain false, Mr. Jones’ refusal to remove the claims or note corrections demonstrates that he is nothing more than a crank speaking out of his field of expertise with no scientific credibility. I have no interest in such folk’s claims myself and I know of no one in any actual scientific field who does.

    As for your claim,

    Things go from bad to worse when you fails to even acknowledge, let alone address, the most serious problems that Jones highlights.

    Utter nonsense. There’s nothing compelling in any of Jones’ arguments because none of them deal with what evolution actually notes as I already demonstrated. What is interesting is that you have not even attempted to address the issues Lizzie and I have already noted, demonstrating that you have no interest in what science actually states, preferring instead made-up nonsense unrelated to reality. For instance, you insist that this is one of the “more serious problems Mr. Jones’ notes:

    All the creatures (Pakicetus, Ambulocetus, Protocetus, Indocetus and Rodhocetus)…appear in the fossil record at the roughly same time.

    How is this suppose to be some big problem for evolution? Paleontologists never suggested that any of these animals evolved directly into one another. They demonstrate a progression of characteristics chronologically, not a direct ancestral relationship. So Jones’ complaint here is moot – he’s not addressing what the science actually notes, preferring instead to knock down a strawman based on his own ignorance. No thanks.

    Oh…and where is Squalodon in Jones list? Where’s Remingtonocetus? Where’s Basilosaurus? Where’s Cetotherium? Oh…Squalodon, Remingtonocetus, and Cetotherium weren’t discovered when Jones was writing and for whatever reason Jones just ignores the inconvenience of Basilosaurus to the point he’s attempting to make.

    Jones’ complaint about teeth shows the same issues as above. He complains that modern whale teeth don’t resemble Basilosaurus’ teeth, but fails to note that no paleontologist or evolutionary biologist ever suggested they should, noting instead the characteristic accumulation toward modern whales. Of course, now that abundant fossils of Squalodon and Cetotherium have been discovered and analyzed demonstrating a direct transition between whale ancestor dentition and modern whale dentition, has Jones noted he was wrong in his assessment? No.

    Bottom line, your reference is not worth consideration. If and when you find a credible reference to rebut the evidence and research of whale evolution, I’ll be more than happy to consider it.

  103. Doveton @12:

    Reread carefully what I wrote: “Under evolutionary theory it is just as likely that a tiger could turn into an elephant (over time) as it is that an amoeba could turn into an elephant. There is no reason to prefer one over the other.”

    Of course I am referring to a change over long periods of time from one species to another, not a single individual waking up one day as a member of another species. Over time, evolutionary theory has absolutely nothing conherent to say about whether creature x would eventually spawn creature z, as opposed to creature y eventually spawning creature z.

    Sure, we can gaze at various anatomies today and see what we think looks most similar and try to construct some hypothetical past pathway, but we need to keep in mind that: (i) it is only hypothetical, and (ii) it didn’t have to turn out that way. This is why prominent evolutionists correctly argue that under evolutionary theory if you run the tape over again you’d get a completely different result.

    Some think the tape is fixed and that certain species lead to other species inevitably, or more generally, that life inevitably leads to humans, for example. That’s a nice idea, but then of course it isn’t driven by traditional evolutionary mechanisms is it? It is either some kind of built in plan, or some kind of inevitable emergent property — neither of which have anything to do with traditional evolutionary theory.

    So that is my point to Elizabeth. She has no reason for evolution to behave the way she imagines it behaves, in terms of how many species arise and from where.

  104. Doveton @102:

    “If and when you find a credible reference to rebut the evidence and research of whale evolution, I’ll be more than happy to consider it.”

    Do you mean “evolution” in the sense of the hypothesized whale family tree, or do you mean “evolution” in the sense of the alleged mechanism of RM+NS? Or both?

  105. Doveton:

    Bottom line, your reference is not worth consideration. If and when you find a credible reference to rebut the evidence and research of whale evolution, I’ll be more than happy to consider it.

    Bottomm line if and when someone presents positive testable evidence that a land ungulate can evolve into a cetacean I will consider it.

    But given the observed birth-rates all you can do is wish for magical mystery mutations or the past being much different, reproduction-wise, than the present. Meaning you have to make up more stuff.

  106. Reread carefully what I wrote: “Under evolutionary theory it is just as likely that a tiger could turn into an elephant (over time) as it is that an amoeba could turn into an elephant. There is no reason to prefer one over the other.”

    Of course I am referring to a change over long periods of time from one species to another, not a single individual waking up one day as a member of another species. Over time, evolutionary theory has absolutely nothing conherent to say about whether creature x would eventually spawn creature z, as opposed to creature y eventually spawning creature z.

    My bad Eric. I misunderstood.

    However, your assessment above isn’t quite accurate. According to Evolutionary Theory, there is a significantly greater chance that an amoeba group would eventually have enough splits to arrive at an elephant group than a tiger group could. The reason is illustrated via phylogenetic systematics. Basically, in order for a tiger group to split and become an elephant group, specific phylogenetic traits would have to be “backed out” of the tiger group. Evolutionary Theory predicts that that sort of event either does not occur or occurs so infrequently as to make it improbable. By the same token, ET predicts that tiger groups can’t ultimately evolve back to amoebas; mutation, genetic drift, and genetic appears incapable of backing traits out of an organism. Traits can be changed, but not entirely removed.

    In other words, evolution can only build on what is there.

    Sure, we can gaze at various anatomies today and see what we think looks most similar and try to construct some hypothetical past pathway, but we need to keep in mind that: (i) it is only hypothetical, and (ii) it didn’t have to turn out that way. This is why prominent evolutionists correctly argue that under evolutionary theory if you run the tape over again you’d get a completely different result.

    True for the most part. I will just not that the evolutionary tree isn’t constructed merely based on “what looks most similar” – there’s a little bit more involved.

    Be that as it may, it is correct to say that specific outcomes of evolution are not predictable. For example, we cannot know what mutations will necessarily pop up in a given species, nor can we necessarily predict what mutations might ultimately become fixed. And since mutation is random, as you note, if we started again back in time, it is highly unlikely we’d get the same outcome we see today.

    Some think the tape is fixed and that certain species lead to other species inevitably, or more generally, that life inevitably leads to humans, for example. That’s a nice idea, but then of course it isn’t driven by traditional evolutionary mechanisms is it? It is either some kind of built in plan, or some kind of inevitable emergent property — neither of which have anything to do with traditional evolutionary theory.

    I agree.

    So that is my point to Elizabeth. She has no reason for evolution to behave the way she imagines it behaves, in terms of how many species arise and from where.

    On this I disagree. Seems to me that Lizzie’s note above about splitting is quite accurate. We do know that species split into subspecies and eventually independent species. Have we seen amoebas splitting and ultimately becoming elephants? No, but the phylogenetic relationships are fairly compelling given what we do know about splitting.

  107. Eric Anderson,

    “If and when you find a credible reference to rebut the evidence and research of whale evolution, I’ll be more than happy to consider it.”

    Do you mean “evolution” in the sense of the hypothesized whale family tree, or do you mean “evolution” in the sense of the alleged mechanism of RM+NS? Or both?

    Either one would be fine since I brought up whale evolution as an example of how research on the latter has led to compelling knowledge.

  108. Doveton, perhaps a PhD in evolutionary biology who has problems with whale evolution???

    Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology
    http://www.metacafe.com/watch/4165203/

    Now Doveton it seems to be a problem with the Darwinists’s very own equations, in population genetics, for predicting change. The numbers simply don’t crunch!,,

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co.....ns-part-5/

    But hey Doveton, if you know what mistake they are making in their math to get such a ‘wrong’ answer, then you can apply for a job at Oxford:

    Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe
    Excerpt: Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. …
    http://biologicinstitute.org/2.....emagician/

  109. From the actual job description:

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

  110. We have never observed amoebas spliting into anything but amoebas. And we have never observed prokaryotes “evolve” into something other than prokaryotes.

    It seems your claims aren’t even wrong…

  111. 111

    “Traits can be changed, but not entirely removed.”

    So the distinction between changing from a bellows lung to a flow-through lung, or changing from a flow-through lung to a bellows lung, is simply the recognition that respiration occurs anyway? In other words, its a trait that is changed but never removed? The same, supposedly, could be said for blood tempurature, reproduction method, or any other observable in nature. What is ‘necessary’ becomes evidence for a particular theory.

    Now thats a powerful arguement.

  112. We have never observed amoebas spliting into anything but amoebas. And we have never observed prokaryotes “evolve” into something other than prokaryotes.

    True, and we haven’t observed the core of the Earth or how the Earth developed, but that doesn’t reduce the validity and credibility of scientific models explaining such based upon extrapolations from observations of seismic measures, ground movement, oceanic movement, volcanic eruptions, and magnetic field studies, gravity measurements, etc.

    So whether anyone has directly observed amoebas/prokaryotes splitting into other organism groups does not reduce the validity and credibility of the extrapolation based model that predicts they have done and can do so.

  113. UB,

    “Traits can be changed, but not entirely removed.”

    So the distinction between changing from a bellows lung to a flow-through lung, or changing from a flow-through lung to a bellows lung, is simply the recognition that respiration occurs anyway? In other words, its a trait that is changed but never removed? The same, supposedly, could be said for blood tempurature, reproduction method, or any other observable in nature. What is ‘necessary’ becomes evidence for a particular theory.

    Now thats a powerful arguement.

    I guess I need to be more clear about the term “trait” as I used it.

    (genetics) Characteristics or attributes of an organism that are expressed by genes and/or influenced by the environment.

    Traits include physical attributes of an organism such as hair color, leaf shape, size, etc., and behavioral characteristics, such as bird nesting.

    http://www.biology-online.org/dictionary/Traits

    “Trait” then does not refer to processes such as respiration, metabolic processes (that confer relative blood temperature), or reproduction, but rather the organs or other attributes organisms use for such processes.

  114. Bornagain77,

    Doveton, perhaps a PhD in evolutionary biology who has problems with whale evolution???

    Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology
    http://www.metacafe.com/watch/4165203/

    Now Doveton it seems to be a problem with the Darwinists’s very own equations, in population genetics, for predicting change. The numbers simply don’t crunch!,,

    Hmmm…it wouldn’t be a bad start if Sternberg actually cited the math used and the computer programs required to do the computation. As it stands, it’s an interesting, if not very compelling argument since it’s nothing more than Sternberg making a claim.

    If Sternberg decides to provide the actual computations demonstrating that population genetics is a problem for whale evolution, I’ll reconsider my response.

    As for your other two references, I don’t see what they have to do with my point.

  115. Well Doveton, I’m sure Sternberg will be more than willing to help you out. Here is his website:

    http://www.richardsternberg.org/publications.php

    Perhaps you failed to notice that the calculation here;

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co.....ns-part-5/

    was done by two Darwinists???

    Doveton, does that help??? I have a few request of my own, can you please find me the literature that falsifies this:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    http://www.scitopics.com/The_L.....iency.html

    The GS (genetic selection) Principle – David L. Abel – 2009
    Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.”
    http://www.bioscience.org/2009.....6/3426.pdf
    http://www.us.net/life/index.htm

  116. Bornagain77,

    Well Doveton, I’m sure Sternberg will be more than willing to help you out. Here is his website:

    http://www.richardsternberg.org/publications.php

    Considering he has not gotten back to Dr. John Wise from SMU on his criticisms from 2009, I’m betting he won’t get back to me.

    Perhaps you failed to notice that the calculation here;

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co…..ns-part-5/

    was done by two Darwinists???

    Again, I don’t see what that has to do with what I noted about whale evolution, but since you insist, here is Dr. Rick Durrett’s criticism:

    http://www.genetics.org/conten.....l.pdf+html

    So it appears both Behe and Sternberg are a bit naive in their use of mathematics.

    Doveton, does that help??? I have a few request of my own, can you please find me the literature that falsifies this:

    Well, I’m still waiting for a credible reference to rebut the evidence and research of whale evolution I presented. And since I already responded to these Dr. Abel references, I see no reason to respond to them again.

  117. Doveton you have not adequately responded to anything that Abel has put forth, An adequate responce would be to actually generate functional coded information by material processes, but since that is impossible from first priciples of science, i’m sure I will be waiting for hell to freeze over before I ever get a straight answer from you,,, as to Durret:

    The final conceptual error that Durrett and Schmidt commit is the gratuitous multiplication of probabilistic resources. In their original paper they calculated that the appearance of a particular double mutation in humans would have an expected time of appearance of 216 million years, if one were considering a one kilobase region of the genome. Since the evolution of humans from other primates took much less time than that, Durrett and Schmidt observed that if the DNA “neighborhood” were a thousand times larger, then lots of correct regulatory sites would already be expected to be there. But, then, exactly what is the model? And if the relevant neighborhood is much larger, why did they model a smaller neighborhood? Is there some biological fact they neglected to cite that justified the thousand-fold expansion of what constitutes a “neighborhood,” or were they just trying to squeeze their results post-hoc into what a priori was thought to be a reasonable time frame?

    When I pointed this out in my letter, Durrett and Schmidt did not address the problem. Rather, they upped the stakes. They write in their reply, “there are at least 20,000 genes in the human genome and for each gene tens if not hundreds of pairs of mutations that can occur in each one.” The implication is that there are very, very many ways to get two mutations. Well, if that were indeed the case, why did they model a situation where two particular mutations — not just any two — were needed? Why didn’t they model the situation where any two mutations in any of 20,000 genes would suffice? In fact, since that would give a very much shorter time span, why did the journal Genetics and the reviewers of the paper let them get away with such a miscalculation?

    The answer of course is that in almost any particular situation, almost all possible double mutations (and single mutations and triple mutations and so on) will be useless. Consider the chloroquine-resistance mutation in malaria. There are about 10^6 possible single amino acid mutations in malarial parasite proteins, and 10^12 possible double amino acid mutations (where the changes could be in any two proteins). Yet only a handful are known to be useful to the parasite in fending off the antibiotic, and only one is very effective — the multiple changes in PfCRT. It would be silly to think that just any two mutations would help. The vast majority are completely ineffective. Nonetheless, it is a common conceptual mistake to naively multiply postulated “helpful mutations” when the numbers initially show too few.

    Here’s a final important point. Genetics is an excellent journal; its editors and reviewers are top notch; and Durrett and Schmidt themselves are fine researchers. Yet, as I show above, when simple mistakes in the application of their model to malaria are corrected, it agrees closely with empirical results reported from the field that I cited. This is very strong support that the central contention of The Edge of Evolution is correct: that it is an extremely difficult evolutionary task for multiple required mutations to occur through Darwinian means, especially if one of the mutations is deleterious. And, as I argue in the book, reasonable application of this point to the protein machinery of the cell makes it very unlikely that life developed through a Darwinian mechanism.
    http://behe.uncommondescent.co.....ns-part-5/

  118. As to Sternberg,,, Doveton give the guy a chance, I mean Darwinists did treat the guy like a leper for crying out loud, as they do with anyone who dares question the almighty power of unguided processes to produce sophisticated machinery that puts anything man has made to shame! All this in spite of the fact that no one can seem to find evidence of unguided processes doing as such today.

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