Sunday, February 13, 2011

This Just In: Plants Have Leaves—Evolution Must Be True

As if evolution was not silly enough already evolutionists are now claiming that the fact that different plants all have leaves is a compelling evidence for their belief that all of nature just happened to spontaneously arise, all by itself. I occasionally enjoy a good spoof, but this is no joke. You can see this evolutionary logic for yourself right here. Some may find this unbelievable but this example, while stupefying, is actually representative of evolutionary thinking.

Evolutionary cannot explain how a single protein first arose, much less molecular machines, cells, multicellular organisms, nervous systems, cellular transduction, and a thousand other designs. In fact biology is full of fantastic, unique solutions no one would have ever guessed. Consider all the different kinds of plants biology has to offer.

Cactus plant leaves, for instance, are like spines whereas poinsettia leaves are like flower petals. On the other hand the venus flytrap leaves are like jaws that close to catch insects, and the pitcher plant leaves form a pitcher to catch insects. Of course beyond unfounded speculation about blind mutations just happening to construct such marvels, evolutionists have no scientific explanation for how these arose. Yet amazingly, in biology’s unlikely designs such as these evolutionists are certain their idea is proven. They write:

In the following photos of plants, the leaves are quite different from the “normal” leaves we envision. Each leaf has a very different shape and function, yet all are homologous structures, derived from a common ancestral form. The pitcher plant and Venus’ flytrap use leaves to trap and digest insects. The bright red leaves of the poinsettia look like flower petals. The cactus leaves are modified into small spines which reduce water loss and can protect the cactus from herbivory.

Derived from a common ancestral form? And how do evolutionists know these radically different designs evolved from a common ancestor? Well, because they are homologous, that’s how. And after all, homologous structures share a common ancestor. Amazing.

The next example, the tetrapod forelimb, is equally silly. Take a look at the eusthenopteron forelimb and the rabbit forelimb, for instance, in the figure. Like the plant leaves, these designs are radically different.

Yet we are told this “demonstrates their common ancestry.” Demonstrates their common ancestry? How are these demonstrations of common ancestry? In fact there is no demonstration of common ancestry here. Evolutionists show some nice illustrations of radically different plants and animals, and simply assert that this is a demonstration of common ancestry. This is the height of absurdity.

The evolutionary argument is that evolution is restricted to certain designs. And while such designs evolve a bit, the underlying design framework is unchangeable. Evolution is stuck with it. Hence these similarities, even such remote similarities, are compelling demonstrations of evolution.

There are two problems here. First, the claim affirms the consequent. If a hypothesis successfully makes a prediction, that does not mean the hypothesis is correct. Second, the claim is false. Evolutionists routinely ascribe complete redesigns to evolution. Evolution is supposedly capable of complete makeovers. But then when a pattern is observed, we are told evolution is stuck with it. Evolutionists just make up whatever suits the moment. In fact if evolution is so stuck with designs, then it would clearly be falsified, as it wouldn’t be able to come up with all those new designs it is always devising.

But if all this seems unlikely, is it not better than separate ancestry? Using this reasoning, evolution, it turns out, is impervious to low likelihoods. It doesn’t matter if the evidence is astronomically unlikely. In fact, the more unlikely the better because the alternative is even worse. Evolutionary philosopher Elliott Sober has analyzed how common descent advances via this contrastive thinking. The powerful arguments and evidence do not actually bolster the theory but rather they rebuke the alternative. He explains it this way:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Evidence and Evolution, p. 314]

In other words, it doesn’t matter that common descent is not a good theory. It must be true because the alternative is even worse. Sober refers to this mode of reasoning as Darwin’s Principle. It seems evolutionists can talk themselves into anything, including the claim that leaves prove their unlikely idea. Religion drives science and it matters.

Addendum:

An evolutionist commented that my Sober quote above is misleading, and my summary that it doesn’t matter that common descent is not a good theory is erroneous. He reasoning was that I took the Sober quote out of context and used an ellipses to manipulate the meaning of the quote.

This is yet another example of how evolutionists are unable to face the reality of their theory and its implications. No matter how much evidence they are presented with, evolutionists will never agree with the obvious. First the idea that the ellipses hides some crucial message from Sober that is the key to the passage, and without it I have manipulated the meaning, is pathetic. In fact, what I omitted were three sentences that further reinforce the point. I omitted them simply because they are redundant and full of jargon. Here they are:

An easy way to see this point is to imagine that Pr(1 --> 1) = 1, Pr(0 --> 1) = 0, and let Pr(Z = 1) = p, where Z, recall, is an ancestor of the observed species X and Y. Then the likelihood of CA is p and the likelihood of SA is p^2, so the likelihood ratio of CA to SA is 1/p. Now it is obvious how the evidence for CA gets stronger as p gets smaller.

So in this example, Sober argues that the common ancestry hypothesis (CA) improves as its likelihood decreases. It is no different than the surrounding passage. His reasoning is that as the likelihood of CA decreases, the likelihood of the separate ancestry hypothesis (SA) decreases even more. So when compared to SA, CA looks better when the evidence says it is even more unlikely. It is an example of how evolutionists use pretzel logic to try to make their idea attain that status of a fact.

But the evolutionist complained that "It's a pretty big stretch (to put it mildly) to take this specific argument about probabilities of character states and represent it as referring to the entire theory of common descent."

But of course I did not represent it as referring to the entire theory of common descent. As I explained above, the Sober analysis applies to the evolutionist's silly arguments that plants having leaves demonstrates common descent. In fact, I was quite clear about this: I wrote:

But if all this seems unlikely, is it not better than separate ancestry?

In other words, I first explained that the evolutionist argument appears silly, and I then provided a particular evolutionary interpretation of the evidence to which the Sober analysis directly applies.

This is a good example of how debates and discussions go with evolutionists. They begin with a religiously motivated, unscientific idea, and from there is it absurdities, fallacies and canards, one after the other.

340 comments:

  1. Hunter:

    First, the claim affirms the consequent. If a hypothesis successfully makes a prediction, that does not mean the hypothesis is correct.

    Failure to understand inductive reasoning is a fatal handicap in critiquing science. As Zachriel pointed out in the previous thread, affirming the consequent is a logical fallacy of the conditional, in which:

    IF P, THEN Q.
    Q, THEREFORE P

    The fallacy lies in asserting that the hypothesis follows NECESSARILY from the evidence. But in inductive tests of hypotheses¸ evidence does not affirm the hypothesis incontrovertibly. Instead, evidence may increase or decrease the LIKELIHOOD of the hypothesis.

    Inductive reasoning is not special to science. It is used in our courts of law. And we all use it in everyday problem-solving: “She looks unhappy. Is she mad at me?” The hypothesis that she is mad is supported by the evidence of her facial appearance, but is subject to further inquiry. It may turn out that she has a gas bubble.

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  2. Hunter:

    Evolutionists show some nice illustrations of radically different plants and animals, and simply assert that this is a demonstration of common ancestry. This is the height of absurdity.

    Such assertions might be absurd if they were as arbitrary as the word “simply” in “simply assert” implies. But there is more to it than that. Apparently Hunter has momentarily forgotten that common ancestry is supported by a consilience of evidence from geology, paleontology, ecology, comparative anatomy, developmental biology, molecular biology, genomics, etc.

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  3. geology?

    Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. - Paul G. Falkowski - Professor Geological Sciences - Rutgers

    paleontology?

    Punctuated Equilibrium and Patterns from the Fossil Record - Casey Luskin
    Excerpt: “The Cambrian Explosion is by no means the only “explosion” in the fossil record. One evolutionist concedes that for the origin of fishes, “this is one count in the creationists’ charge that can only evoke in unison from paleontologists a plea of nolo contendere [no contest].” Plant biologists have called the origin of plants an “explosion,” saying, “the … radiation of land (plant) biotas is the terrestrial equivalent of the much-debated Cambrian ‘explosion’ of marine faunas.” Vertebrate paleontologists believe there was a mammal explosion because of the few transitional forms between major mammal groups: “There are all sorts of gaps: absence of gradationally intermediate ‘transitional’ forms between species, but also between larger groups — between, say, families of carnivores, or the orders of mammals.” Another study, “Evolutionary Explosions and the Phylogenetic Fuse,” found a bird (as well as a mammal) “Early Tertiary ‘explosion’” because many bird and mammal groups appear in a short time period lacking immediately recognizable ancestral forms. Finally, others have called the origin of our own genus Homo, “a genetic revolution” where “no australopithecine (ape) species is obviously transitional” leading one commentator to call it, like others called the Cambrian Explosion, a “big bang theory” of human evolution."

    ecology?

    Earth's Capacity To Absorb CO2 Much Greater Than Expected: Nov. 2009
    Excerpt: New data show that the balance between the airborne and the absorbed fraction of carbon dioxide has stayed approximately constant since 1850, despite emissions of carbon dioxide having risen from about 2 billion tons a year in 1850 to 35 billion tons a year now. This suggests that terrestrial ecosystems and the oceans have a much greater capacity to absorb CO2 than had been previously expected.
    http://www.sciencedaily.com/releases/2009/11/091110141842.htm

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  4. comparative anatomy?

    Investigating Evolution: Homology - video
    http://www.youtube.com/watch?v=XgXT9sU6y18

    If you want to make evolutionist Henry Gee mad at you remind him that he once wrote this following 'true' statement:

    “To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story, amusing, perhaps even instructive, but not scientific.”
    Evolutionist - Henry Gee, editor of Nature, on the feasibility of reconstructing phylogenetic trees from fossils

    developmental biology?

    Response to John Wise - October 2010
    Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html

    Marsupial Embryos Challenge Common Ancestry – Casey Luskin - audio podcast
    http://intelligentdesign.podomatic.com/entry/2011-02-09T16_33_21-08_00

    molecular biology?

    ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
    Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
    *Professor Emeritus of Biochemistry, Colorado State University, USA

    Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
    http://www.metacafe.com/watch/5302950/

    genomics?

    Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009
    Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?"
    http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html

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  5. Hunter:

    In other words, it doesn’t matter that common descent is not a good theory. It must be true because the alternative is even worse.

    On the contrary, common descent is a good enough theory for now in the absence of a plausible alternative.

    If the available evidence supported special creation, it might be considered a plausible option. If anyone should observe the spontaneous appearance of a new life form without any relationship to pre-existing life forms, that would be a strong datum in support of special creation. (Since Pasteur, such reports have been greeted with universal skepticism.)

    It would also be supportive if there were a proposed mechanism for special creation other than miracle. As I recall, Charles Lyell, who believed in the immutability of species, reasoned that there must be such a natural mechanism, but he never proposed one.

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  6. Pendant, that is ludicrous, Darwinists cannot even get close to explaining the origin of life. As you rightly admit no one has ever seen life spontaneously arise from non-life, yet since God does not create life right in front of You this is suppose to count in favor of Darwinism??? That view is totally twisted pendant, the FACT that non-life has not ever generated life, nor has anyone any real clue as to how life might come from non-life, is a point of evidence that counts very strongly against the materialistic theory of Darwinism. Since you will certainly disagree with this clear point, perhaps you would like to write Stephen Meyer and tell him why this supports Darwinism so that he may retract all that he has put forth in his book 'Signature In The Cell'.

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  7. BA77, don't forget to take your meds (the legally prescribed ones, that is) - you're even less coherent than usual.

    "the FACT that non-life has not ever generated life..."

    FACT you say? Careful now, Cornelius doesn't take kindly to such factual claims. You wouldn't be making any unwarranted metaphysical assumptions would you?


    "perhaps you would like to write Stephen Meyer and tell him why this supports Darwinism so that he may retract all that he has put forth in his book 'Signature In The Cell'."

    I suspect Stephen Meyer already knows that his book is rubbish, but as long as the deluded keep spending, why kill the golden goose?

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  8. troy, and yet if you can't support your theory with any evidence, then the next best thing to do is to attack anyone who dares questions it?!? Does Dr. Hunter pay you to be such a shining example of how shallow Darwinists are?

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  9. CH, I'm afraid you're misusing SOber again. you hgighlight this sentence "it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable"

    and then say "In other words, it doesn’t matter that common descent is not a good theory. "

    but, reading the rest of the argument in context, we see that Sober was not referring to the theory of common descent in that sentence. the "very improbable evidence" he is referring to is the probability that the ancestor(s) postulated by the separate and common ancestry argument had the same character state (let's say, leaves) as their descendents. it is part of a larger argument about why neutral traits provide better evidence of common descent than adaptive traits. It's a pretty big stretch (to put it mildly) to take this specific argument about probabilities of character states and represent it as referring to the entire theory of common descent. those interested can find the relevant page on google books.

    another illustration of something my granddad told me: "beware anti-evolutionists bearing quotation marks and ellipses!"

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  10. Dr. Hunter, seeing as you deal with so many vitriolic atheists, this short video may interest you:

    Keith Ward: From Atheism to Christianity
    http://www.youtube.com/watch?v=Md5OFdpHhT4

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  11. Cornelius Hunter: Derived from a common ancestral form? And how do evolutionists know these radically different designs evolved from a common ancestor?

    A consilience of the evidence. Oh, and it's not just similarity, but the nested hierarchy.

    bornagain77: Punctuated Equilibrium and Patterns from the Fossil Record -

    "It is probable that the periods, during which each underwent modification, though many and long as measured by years, have been short in comparison with the periods during which each remained in an unchanged condition."

    bornagain77: Earth's Capacity To Absorb CO2 Much Greater Than Expected:

    You do understand that the CO2 of the atmosphere has increased, as well as the CO2 of the ocean? The former is leading to global warming, while the latter is leading to increased acidification of the oceans.

    bornagain77: If you want to make evolutionist Henry Gee mad at you remind him that he once wrote this following 'true' statement:

    “To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story, amusing, perhaps even instructive, but not scientific.”


    Why would he be mad? It's a nested hierarchyl. It's very difficult to find exact intermediates. However, we can get close to points of divergence in order to fill in historical details.

    kairosfocus: Mosaics such as the platypus point strongly to common design and use of a library of key, adaptable components. This creature is an egg-laying, milk producing, duck-billed, venomous, beaver-tailed and web-footed mammal, whose 18,527 protein-encoding genes “contain alive-and-well representatives from mammals, birds and reptiles.”

    Monotremes are not a mosaic, but share a common ancestor with birds and reptiles about 166 million years ago.

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  12. Zach, excuses for why Darwinism continually does not fit the evidence are not scientific explanations, but merely rationalizations to protect an anti-Theistic worldview. A materialistic anti-Theistic worldview that is devoid of any foundation in science in the first place! (Aspect; falsification of local realism)

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  13. bornagain77: excuses for why Darwinism continually does not fit the evidence are not scientific explanations, but merely rationalizations to protect an anti-Theistic worldview.

    You raised what you thought were objections. We showed they were without merit. If you have an argument to make, you will need to be more specific.

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  14. bornagain77: A materialistic anti-Theistic worldview that is devoid of any foundation in science in the first place!

    We don't subscribe to a "materialistic anti-Theistic worldview".

    bornagain77: (Aspect; falsification of local realism)

    If you're referring to tests of Bell's Inequality, it may mean either locality or counterfactual definiteness are violated. This would be largely irrelevant to biology.

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  15. Zach you state this;

    This would be largely irrelevant to biology.,,,

    actually since it has to do with the foundation of reality itself, it has every thing to do with biology and everything else in the universe. Yet since you state a distortion of the truth so readily, and think you are 'smart' about it. I will leave you in your delusions.

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  16. Cornelius:

    Derived from a common ancestral form? And how do evolutionists know these radically different designs evolved from a common ancestor? Well, because they are homologous, that’s how. And after all, homologous structures share a common ancestor. Amazing.

    They are thought to have common ancestry because of the similarities they share. Since these similarities are thought to exist because of common ancestry, the structures are homologous.


    If a hypothesis successfully makes a prediction, that does not mean the hypothesis is correct.

    And a less than correct prediction does not mean that the hypothesis is incorrect. I.e. the likelihood of the hypothesis (Pr(observation|hypothesis)) does not tell very much about the probability of the hypothesis (Pr(hypothesis|observation)). So why do you think that your Sober quote is so important?

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  17. I'm not a scientist nor do I attempt to play one on my blog. I have merely a 50,000 foot view of these topics so my following question may be ill-conceived, but I'll ask:

    Since evolution relies on genetic mutation as the first step in its progression, is genetic mutation understood as a two-step process? First, the re-ordering of the DNA to produce a new string of amino acids, as well as a compatible change in the folding of those amino acids to produce a different functioning protein.

    If both steps are required to produce a change in species, it seems the probability of an mutated gene marrying up with a compatible change in amino acid folding is extremely astonomical given the number of potential other variances (given the possibility of many folding options for the same amino acid string).

    If the question is valid, how does evolution account for the improbability? If the premises that underly the question are invalid, please correct them (if they are so far off base that correcting them here is unlikely then just tell me to start over).

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  18. bornagain77: actually since it has to do with the foundation of reality itself, it has every thing to do with biology and everything else in the universe.

    As science is structured to answer limited questions, it's not clear you have shown any scientific relevance. For instance, even if the universe was designed for some cosmic purpose, the Theory of Gravity still works at describing the planets in their courses, and Germ Theory still works at describing diseases and their courses.

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  19. rpvicars: ... it seems the probability of an mutated gene marrying up with a compatible change in amino acid folding is extremely astonomical given the number of potential other variances (given the possibility of many folding options for the same amino acid string).

    As the typical human has a couple of hundred mutations, your concern doesn't seem well-placed.

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  20. nano:

    ===
    but, reading the rest of the argument in context, we see that Sober was not referring to the theory of common descent in that sentence. the "very improbable evidence" he is referring to is the probability that the ancestor(s) postulated by the separate and common ancestry argument had the same character state (let's say, leaves) as their descendents. it is part of a larger argument about why neutral traits provide better evidence of common descent than adaptive traits. It's a pretty big stretch (to put it mildly) to take this specific argument about probabilities of character states and represent it as referring to the entire theory of common descent. those interested can find the relevant page on google books.

    another illustration of something my granddad told me: "beware anti-evolutionists bearing quotation marks and ellipses!"
    ===

    I addressed this with an addendum to the OP.

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  21. Zachriel, "As the typical human has a couple of hundred mutations, your concern doesn't seem well-placed."

    If the premises are valid, which is the question, then even once is improbable, so a "only" couple hundred doesn't make it more likely. I'm just trying to make sure I have an accurate understanding...

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  22. Hawks:

    ===
    They are thought to have common ancestry because of the similarities they share. Since these similarities are thought to exist because of common ancestry, the structures are homologous.
    ===

    No, go back and read the website, or the OP. The website is presenting evidence for evolution (not interpreting the evidence according to evolution).


    ===
    And a less than correct prediction does not mean that the hypothesis is incorrect.
    ===

    Isn't science wonderful. We can't explain how even a protein first evolved, but no problem. Bad predictions don't matter anymore.


    ===
    I.e. the likelihood of the hypothesis (Pr(observation|hypothesis)) does not tell very much about the probability of the hypothesis (Pr(hypothesis|observation)). So why do you think that your Sober quote is so important?
    ===

    The Sober analysis is important because it reveals the bankrupt thinking evolutionists employ.

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  23. CH: "It must be true because the alternative is even worse. "

    What are those alternatives CH? You never speak of them (you are too busy dismantling evolution). Sure, we know what some of them are - ID, various forms of creationism, OEC, YEC etc, etc. But you personally never speak to any of these. In the end, it isn't the criticism of evolution that is going to persuade people, but the presentation of a proper and viable scientific alternative. I don't know if you get this or not.

    I think it's sad that you seem to want to expend your energies only on dismantling evolution, rather than focusing on a viable alternative. Your choice of course, but frankly it seems a completely dead-end endeavor (certainly as measured by the fact that what you are posting on this web site is materially no different from what it was 1 and 2 years ago). Maybe you think it's a successful strategy, I don't know, but certainly there do not seem to be any evolution supporters here who have been persuaded of your approach.

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  24. Cornelius:

    No, go back and read the website, or the OP.

    From the website:

    Evolutionary theory predicts that related organisms will share similarities that are derived from common ancestors. Similar characteristics due to relatedness are known as homologies. Homologies can be revealed by comparing the anatomies of different living things, looking at cellular similarities and differences, studying embryological development, and studying vestigial structures within individual organisms.

    Are you simply moaning because this website gives a simple overview of evidence?

    More from Cornelius:

    ...evolutionists are now claiming that the fact that different plants all have leaves is a compelling evidence for their belief that all of nature just happened to spontaneously arise, all by itself.

    I didn't see where the website made that claim. Can you copy the quote and a link?

    Bad predictions don't matter anymore.

    Evolution given common ancestry can't be expected to predict very much. Neither can evolution given separate ancestry. Predictions get better when more assumptions are added. The point of Sober's example is that CA will most likely fare better than SA.

    The Sober analysis is important because it reveals the bankrupt thinking evolutionists employ.

    I might be important because it reveals how you like missing the point.

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  25. Cornelius:

    "The Sober analysis is important because it reveals the bankrupt thinking evolutionists employ."

    No, in my opinion it reveals either that (1) you don't understand the analysis, or (2) you deliberately misrepresent it, secure in the knowledge that your target audience of scientific illiterati will swallow it hook-line-and-sinker.

    If you have any experience (and I know you do) with statistical modeling, then you know that the likelihood of a specific outcome of a (partially) stochastic process is typically very low. One of the reasons to work with log-likelihoods.

    If there are two competing hypotheses, one where the likelihood of a specific realization is p, and another hypothesis that specifies that the same outcome is achieved in two independent realizations, each with likelihood p (hence the p^2), then the relative likelihood of the first is 1/p. Which increases as p becomes smaller.

    A small p does not mean that common descent is unlikely. It simply means that a specific outcome, under the assumption that common descent is true, is unlikely. It is even more unlikely that the same specific outcome was obtained by two independent evolutionary histories. That's why two independent histories is the least plausible hypothesis.

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  26. CH (and troy),
    you need to go back and read the entire section of Sober's book again.

    you write,
    "So in this example, Sober argues that the common ancestry hypothesis improves as its likelihood decreases"

    This is absolutely false. let's look at what SOber wrote:
    "Then the likelihood ratio of CA is p and the likelihood ratio of SA is p^2, so the likelihood ratio of CA to SA is 1/p." what is p? you seem to interpret it as "the common ancestry hypothesis", leading you to think that the less likely the CA hypothesis is, the more likely it is to be true. this is indeed "up is down." However, reading the preceding paragraph clarifies things.
    SOber writes there "However, the key to answering the 2nd question is that the observation that x=1 and y=1 produces stronger evidence favoring CA over SA the lower the probability is that the ancestors postulated by the two hypotheses were in state 1."

    thus, p is the probability that the ancestors of species x and y had the same trait as x and y.
    (cont.)

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  27. (cont.)
    troy has pretty much stolen my thunder, but i'll continue. so a smaller p makes separate ancestry less likely, because both ancestors of x and y would have to have this low-probability trait. by contrast, under common ancestry, only one ancestor would have to have this low probability trait.

    neutral traits are low probability traits, while adaptive traits are high probability traits. this is because a lack of selection on the neutral trait makes convergence towards a neutral trait much less likely than towards an adaptive trait. SOber's point here is that neutral traits (with low p values) provide better evidence for CA than adaptive traits. CH's interpretation of this paragraph is completely wrong. maybe he wasn't being devious, but rather just plain old confused.

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  28. I think Troy has effectively answered that point. It is even clearer, if Cornelius has bothered to include the preceding sentences, which setups the argument. Google book search "Then the likelihood of CA is p and the likelihood of SA" and read the paragraph spanning 313-314 and tell Troy he is wrong.

    Cornelius seems to thrive on scouring the internet and books, and finding snippets to critique. Is it really intellectually satisfying to take one paragraph of a 300+ page book, and say gotcha!, without properly introducing the argument being made. When Troy describes it, or we take the time to read the preceding paragraph it makes so much more sense!

    Or is it better to critique one slide of a website that appears designed for middle-school students (indeed, the science advisors are from middle and high schools):

    "The next example, the tetrapod forelimb, is equally silly. Take a look at the eusthenopteron forelimb and the rabbit forelimb, for instance, in the figure. Like the plant leaves, these designs are radically different."

    Are they? Humerus, radius and ulna, carpal bones. Might be harder to interpret without other species: Ancanthostega, Tiktaalik, Ichtyostega, Limnoscelis-but it seems like there is a pretty nice record of modification with descent of these homologous structures. No?

    http://www.devoniantimes.org/opportunity/tetrapodsAnswer.html

    We're supposed to scoff at the plants, too. Venus flytraps have the same origins (leaf buds) and structures (vasculature) as leaves. They close by alteration of turgor pressure-an osmotic effect in most leaves. Cactus needles start from leaf primordia, elongate, and lay down fiber, then die. They can be induced to form with hormones of leaf signaling pathways. I'm not sure of the molecular details (might be tough to find that research!), but is there any counter-evidence these are non-homologous structures other than Cornelius' incredulity?

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  29. RobertC:

    ===
    Cornelius seems to thrive on scouring the internet and books, and finding snippets to critique.
    ===

    Scouring the internet? Janfeld supplied the link, and I checked it out. That's hardly scouring the internet.

    ReplyDelete
  30. what's particularly funny about CH's confusion over p is that SOber defines it right there in the sentence he quotes:
    "An easy way to see this point is to imagine that Pr(1->1)=1, Pr(0->1)=0 and let Pr(Z=1) = p, where Z, recall, is an ancestor of the observed species x and y." so p is the probability that a trait of the ancestor z is the same as that in x and y. so by ellipsing this sentence in the original post (and numerous others), he eliminated the definition of p, and thus thought it was "the common ancestry hypothesis". the fact that he went apoplectic over being called out on this deletion makes it even richer..

    ReplyDelete
  31. RobertC: Cornelius seems to thrive on scouring the internet and books, and finding snippets to critique.
    ===

    CGH: Scouring the internet? Janfeld supplied the link, and I checked it out. That's hardly scouring the internet.
    ++++++++++

    Apologies, I stand corrected. I gave you too much credit, in thinking you had put in some effort to find these snippets to critique. I 'm sure you did some background research, in say, forearm evolution, or the structure of Venus flytrap traps before posting, and have some evidence to counter the evidence-supported consensus presented by the website? Or did you just click and scoff?

    ReplyDelete
  32. troy:


    ===
    If there are two competing hypotheses, one where the likelihood of a specific realization is p, and another hypothesis that specifies that the same outcome is achieved in two independent realizations, each with likelihood p (hence the p^2), then the relative likelihood of the first is 1/p. Which increases as p becomes smaller.
    ===

    Right ...


    ===
    A small p does not mean that common descent is unlikely.
    ===

    You're confusing the terminology. From Sober:

    ###
    Fisher dubbed Pr(O|H) the likelihood of H. Because Fisher's terminology has become standard in statistics, I will use it here. However, this terminology is confusing, since in ordinary English, "likely" and "probably" are synonymous. So beware! You need to remember that "likelihood" is a technical term. [9]
    ###

    A small p indeed means that common descent has low likelihood.


    ===
    It simply means that a specific outcome, under the assumption that common descent is true, is unlikely.
    ===

    Right.

    ReplyDelete
  33. nano:

    ===
    you write,
    "So in this example, Sober argues that the common ancestry hypothesis improves as its likelihood decreases"

    This is absolutely false.
    ===

    No, it is absolutely true.


    ===
    let's look at what SOber wrote:
    "Then the likelihood ratio of CA is p and the likelihood ratio of SA is p^2, so the likelihood ratio of CA to SA is 1/p." what is p? you seem to interpret it as "the common ancestry hypothesis",
    ===

    No, it is the probability of the evidence, given the hypothesis.

    ===
    leading you to think that the less likely the CA hypothesis is, the more likely it is to be true.
    ===

    No, the less likely the evidence is, given CA, the higher the likelihood ratio (favoring CA) becomes.

    ReplyDelete
  34. nano:

    ===
    SOber's point here is that neutral traits (with low p values) provide better evidence for CA than adaptive traits. CH's interpretation of this paragraph is completely wrong. maybe he wasn't being devious, but rather just plain old confused.
    ===

    No, Sober's point is that deleterious traits provide the best evidence. Then neutral and then adaptive.

    My interpretation of the passage is according to the intent of the author and standard terminology.

    ReplyDelete
  35. rpvicars: ... : rpvicars: ... it seems the probability of an mutated gene marrying up with a compatible change in amino acid folding is extremely astonomical given the number of potential other variances (given the possibility of many folding options for the same amino acid string).

    rpvicars: ... : If the premises are valid, which is the question, then even once is improbable, so a "only" couple hundred doesn't make it more likely.

    Xue Y et al., Human Y chromosome base substitution mutation rate measured by direct sequencing in a deep-rooting pedigree, Current Biology 2009.

    Mutations occur all the time, and the offspring are still usually healthy. Your original statement applies just as much to bacteria, and we can directly experiment on bacteria. Of bacterial mutations, the majority have little or no effect, some are deleterious, and a very few are beneficial.

    ReplyDelete
  36. nano:

    ===
    what's particularly funny about CH's confusion over p is that SOber defines it right there in the sentence he quotes:
    ===

    No, what is particularly telling here is how evolutionists respond to problems with their theory and their reasoning. They consistently project all kinds of misreads to avoid criticism of their ideas.


    ===
    "An easy way to see this point is to imagine that Pr(1->1)=1, Pr(0->1)=0 and let Pr(Z=1) = p, where Z, recall, is an ancestor of the observed species x and y." so p is the probability that a trait of the ancestor z is the same as that in x and y. so by ellipsing this sentence in the original post (and numerous others), he eliminated the definition of p, and thus thought it was "the common ancestry hypothesis". the fact that he went apoplectic over being called out on this deletion makes it even richer..
    ===

    Pathetic.

    ReplyDelete
  37. CH,
    "My interpretation of the passage is according to the intent of the author and standard terminology. "

    but your interpretation is wrong. Sober defines p right there in the sentence as Pr(z=1). how is this in any way consistent with your statement "So in this example, Sober argues that the common ancestry hypothesis (CA) improves as its likelihood decreases"? this is a completely false statement.

    ReplyDelete
  38. Cornelius:

    "A small p indeed means that common descent has low likelihood."

    No, it doesn't. It means that a specific outcome of an evolutionary process with common descent has a low likelihood. It doesn't mean that common descent has low likelihood.

    You know this. You're just trying to fool the suckers.

    ReplyDelete
  39. This comment has been removed by the author.

    ReplyDelete
  40. This comment has been removed by the author.

    ReplyDelete
  41. RObertC,

    your summary is not quite right. "It is more likely for a feature to have emerged as a result of two species being related than unrelated." it doesn't have to do with the emergence of the feature, but the probability of the ancestor having the feature to begin with. ancestors are likely to have adaptive traits, less likely to have deleterious or neutral traits

    ReplyDelete
  42. nano:

    ===
    but your interpretation is wrong. Sober defines p right there in the sentence as Pr(z=1). how is this in any way consistent with your statement "So in this example, Sober argues that the common ancestry hypothesis (CA) improves as its likelihood decreases"? this is a completely false statement.
    ===

    No, it is not false. When I say "Sober argues that the common ancestry hypothesis (CA) improves" I mean that the likelihood ratio increases. The likelihood ratio is the probability of the evidence given CA, divided by probability of the evidence given SA. Is it not fair to say that CA "improves" if the likelihood ratio increases?

    And second, when I say "as its likelihood decreases" I mean just that. The likelihood of CA is the numerator of the likelihood ratio. That is, the probability of the evidence given CA.

    You seem to be confused again, but I'm not quite sure how to explain it beyond what I've said here. Perhaps you can formulate a more specific reason why you think my statement is completely false.

    ReplyDelete
  43. troy:

    ===
    "A small p indeed means that common descent has low likelihood."

    No, it doesn't.
    ===

    Yes, it does.

    ===
    It means that a specific outcome of an evolutionary process with common descent has a low likelihood.
    ===

    Same thing. You seem to be laboring to avoid the problem.

    ReplyDelete
  44. "And second, when I say "as its likelihood decreases" I mean just that. The likelihood of CA is the numerator of the likelihood ratio. That is, the probability of the evidence given CA."

    Just for clarification, what is 'it' in "its likelyhood decreases"?

    ReplyDelete
  45. RobertC:

    " Just for clarification, what is 'it' in "its likelyhood decreases"? "


    The common ancestry hypothesis

    ReplyDelete
  46. troy:

    $$$$$$$$$$$$$$

    ===
    It means that a specific outcome of an evolutionary process with common descent has a low likelihood.
    ===

    Same thing. You seem to be laboring to avoid the problem.

    $$$$$$$$$$$$$

    Well, let me amend that. It is not quite the same thing. To correct your wording, you need to replace "likelihood" with "probability." So it should read:

    "It means that a specific outcome of an evolutionary process with common descent has a low probability."

    ReplyDelete
  47. CH,
    the problem with your reasoning is apparent in your conflation of "common descent has a low likelihood" with "a specific outcome of common descent has a low probability." These are not the same thing. for example, the probability that a common ancestor Z of descendents x and y has a neutral trait (say, a belly button, which both x and y have) is low (say, 0.1), because there is no selection pressure for belly buttons. this specific outcome (presence of belly buttons in x and y) has a low probability given CA. the probability that each of the ancestors Z and Z' in the SA hypothesis has belly buttons is equally low (0.1) to that in the ancestor in the CA hypothesis. However, because there are two ancestors in the SA hypothesis, the overall probability is squared (0.1*0.1 = 0.01). if the probability is less than one, squaring it will result in a lower number for SA then CA, hence increased ratio of CA to SA.

    the important point here is that the probability of belly buttons in the ancestor (what SOber defines as p) is independent of the CA or SA hypothesis. it is a function of whether the trait is deleterious, neutral or adaptive. however, the outcome of the process varies only according to how many ancestors are considered (one for CA, two for SA).

    ReplyDelete
  48. Hmm.

    As the likelyhood of the common ancestry hypothesis decreases, the likelyhood of separate ancestry declines more. Therefore, common ancestry is more favorable in the head-to-head comparison even as its probability declines. Ok.

    Similar scenario: My wife drives 30 miles to work, while I walk 2 blocks. The probability of my reaching work without delay is much greater than hers. A weather condition that decreases my probability of reaching work will even more greatly impact hers. Therefore, as my probability of reaching work decreases, the comparison of the probability of my reaching work and her's improves. This doesn't address what p actually is.

    The author shows why this is in at least one model on the same page, where p is redefined to be the ancestral state. Much confusion ensues (perils of picking 1 page from google book previews, and arguing over it).

    Cornelius ignores the demonstration, invokes that the probability of common ancestry is small (how?), and concludes the only support for evolution is contrastive reasoning that makes separate ancestry look worse. (Wonder what the other 300+ pages argue).

    ReplyDelete
  49. (cont)
    so, the probability of a specific outcome of CA is low only because the probability of the trait in the ancestor is low. and the probability of the ancestor having the trait is low because the trait is deleterious or neutral.
    the probability of a specific outcome of SA is low because the probability of the trait in the ancestors is low. this probability is lower than CA because there are two ancestors that both must possess the trait.
    so "common descent has a low probability" " and " a specific outcome of common descent has a low probability" are two different things bc the latter depends on the probability of the trait in the ancestor.

    ReplyDelete
  50. nano:

    ===
    so "common descent has a low probability" " and " a specific outcome of common descent has a low probability" are two different things
    ===

    Of course, I never said otherwise. You seem to be conflating "probability" with "likelihood."

    ReplyDelete
  51. nano:

    ===
    the problem with your reasoning is apparent in your conflation of "common descent has a low likelihood" with "a specific outcome of common descent has a low probability." These are not the same thing.
    ===

    Of course they're the same thing. That is how likelihood is defined.

    You seem to be taking pains to do everything you can to avoid the point.

    ReplyDelete
  52. RobertC:

    ======
    Hmm.

    As the likelyhood of the common ancestry hypothesis decreases, the likelyhood of separate ancestry declines more. Therefore, common ancestry is more favorable in the head-to-head comparison even as its probability declines. Ok.
    ======

    Well I'm glad that finally has your "OK."


    ======
    Cornelius ignores the demonstration, invokes that the probability of common ancestry is small (how?), and concludes the only support for evolution is contrastive reasoning that makes separate ancestry look worse.
    ======

    More strawmen. I of course said no such thing. On the other hand, it is true that contrastive reasoning is where most of the powerful metaphysics comes from. If only evolutionists understood their own apologetics.

    ReplyDelete
  53. nano:

    ===
    the problem with your reasoning is apparent in your conflation of "common descent has a low likelihood" with "a specific outcome of common descent has a low probability." These are not the same thing.
    ===

    See my 2:18 pm comment.

    ReplyDelete
  54. This comment has been removed by the author.

    ReplyDelete
  55. nano:

    ===
    You seem to be at pains to avoid the fact that Sober explicitly defined p as pr(Z=1). so p, the likelihood of CA, is only low because pr(Z=1) is low. and pr(Z=1) is only low when considering a deleterious/neutral trait. but this has nothing to do with CA, and everything to do with the adaptiveness or non-adaptiveness of the trait.it is not possible to formulate a hypothesis that has high probability when the trait is deleterious or neutral. and CA has high probability when the trait is adaptive. why do you ignore this point? and why do you not point out that CA only has low probability when the trait is deleterious or neutral?
    ===

    No, you're confusing several things at once here. First, CA has never been shown to have high probability. And you're confused about adaptive traits. Sober's point is that CA doesn't hold much advantage over SA when considering adaptive traits (ie, the likelihood ratio isn't very high). It is the neutral and especially deleterious traits that are selected for evolutionary arguments, for it is with those traits that CA holds a high advantage over SA (ie, you have a high likelihood ratio). You write:

    ===
    You seem to be at pains to avoid the fact that Sober explicitly defined p as pr(Z=1). so p, the likelihood of CA, is only low because pr(Z=1) is low. and pr(Z=1) is only low when considering a deleterious/neutral trait.
    ===

    Of course, that's the point. I have written about this several times.

    ===
    but this has nothing to do with CA, and everything to do with the adaptiveness or non-adaptiveness of the trait.
    ===

    Of course, it is the neutral and especially deleterious traits that are selected for the CA proof.

    ===
    it is not possible to formulate a hypothesis that has high probability when the trait is deleterious or neutral.
    ===

    CA has never been shown to have high probability. The compelling arguments for CA use contrastive reasoning, as Sober illustrates, which show it has a high likelihood ratio when compared with SA.


    ===
    and CA has high probability when the trait is adaptive. why do you ignore this point?
    ===

    No, CA has a low likelihood ratio for adaptive traits.


    ===
    and why do you not point out that CA only has low probability when the trait is deleterious or neutral?
    ===

    Because that would be a misrepresentation.

    ReplyDelete
  56. CH,

    Substitute "likelihood" for probability in my post. CA has a high likelihood when traits are adaptive.

    ReplyDelete
  57. CH,
    "CA has never been shown to have high probability. "
    what, exactly do you mean by "probability" here? it seems from the following that you are using "probability" and "likelihood ratio" interchangeably.

    "and CA has high probability when the trait is adaptive. why do you ignore this point?
    ===

    No, CA has a low likelihood ratio for adaptive traits."

    ReplyDelete
  58. CGH: "Well I'm glad that finally has your "OK."
    ======

    I think there is some nuance in presentation, intent, and conclusions that are certainly not OK.

    REC: Cornelius ignores the demonstration, invokes that the probability of common ancestry is small (how?), and concludes the only support for evolution is contrastive reasoning that makes separate ancestry look worse.
    ======

    CGH: More strawmen. I of course said no such thing.

    So lets Break that down:

    Cornelius ignores the demonstration....
    Yeah, that was in the ellipses of the original post. Convenient omission.

    ....invokes that the probability of common ancestry is small....
    Sorry, do you believe it is large?
    "it doesn’t matter that common descent is not a good theory." (since we're apparently evaluating probability, not good=poor).
    "CA has never been shown to have high probability."

    ...and concludes the only support for evolution is contrastive reasoning that makes separate ancestry look worse.
    "It must be true because the alternative is even worse."

    Strawman, or summary or your position?
    ++++++++++++++++

    CGH: On the other hand, it is true that contrastive reasoning is where most of the powerful metaphysics comes from.

    I don't remember contrastive reasoning being fallacious on face. It seems an important part of hypothesis testing. Take drug testing-treatment a vs treatment b or placebo. I certainly am at a loss as to how hypothesis testing is "powerful metaphysics."

    There is just no meat here. Your take on the sixth grade level presentation of rabbit forearms and Venus flytraps is just uninformed, and I'm at a loss as to what the gripe with Sober is. He presents a rational argument, with support.

    Unless you think that as the probability of X falls, the ratio of probability X to the probability of Y must always fall? My commute example disproves this.

    So what is there?

    Huff and puff and ......

    ReplyDelete
  59. nano:

    ===
    Substitute "likelihood" for probability in my post. CA has a high likelihood when traits are adaptive.
    ===

    OK, sure, but contriving a theory for which we can compute nice likelihood values is not particularly noteworthy, as you suggest. We can hypothesize CA, and then state that conserved, adaptive traits have a pretty high probability *if* CA is true. We have, of course, skipped over all the problems with CA, in the first place. The calculation of the likelihood value for conserved, adaptive traits is trivial. All you need do is assume three values:

    i) the probability that the trait exists in their common ancestor
    ii) the probability that the trait persists from the common ancestor to an extant species
    iii) probability that there is a switch to the trait, from the common ancestor to an extant species.

    Armed with these three numbers, we can then compute the likelihood value. So for example, for an adaptive trait let's assume that the trait has a .95 chance of existing in the ancestor. So p = 0.95. Then, let's assume that since the trait is adaptive, it most likely will persist. So Pr(1 -> 1) is 0.90, and Pr(0 -> 1) is, let's say pretty high as well, say 0.5. Then the CA likelihood for the shared adaptive trait between the two species is:

    (.05) * [ 0.5 ]^2 + (.95) * [ 0.9 ]^2 = 0.78

    So if I've done this correctly, the CA likelihood is 0.78. This is not particularly newsworthy.

    What is newsworthy is that even by the evolutionist's reckoning there are plenty of observations that are of low probability, given the assumption CA is true. And furthermore, it is precisely these cases that evolutionists have relied upon for their apologetics. The reasoning is that such cases drive down SA even more. In other words, the evolutionists are crucially reliant on the SA model having a bad showing. It is this contrastive thinking, with all of its embedded metaphysics, that fuels the evolution argument. Even though it is here that CA has such a bad showing.

    Now you argue we ought to tout the cases where CA has a better likelihood, such as the adaptive traits. It is true that the flat earth model, geocentrism, CA, etc, have their predictive successes. But what is so often interesting is where they breakdown. The retrograde motion and ship over the horizon cases tell us much about the models. The fact that evolution relies on these cases for its apologetic adds an interesting twist.

    ReplyDelete
  60. RobertC:

    ===
    and I'm at a loss as to what the gripe with Sober is. He presents a rational argument, with support.
    ===

    Agreed, Sober has done a good job analyzing evolutionary arguments. Please see:

    http://darwins-god.blogspot.com/2009/06/evolutions-religion-revealed.html

    ReplyDelete
  61. rpvicars,

    I don't quite understand your two-step model, but I these point may bring some clarification:

    - Mutations don't necessarily occur in zones of the DNA that translate into protein.

    - Mutation in the translated zones do not necessarily modify the amino acid sequence.

    - Mutation needs not happen as a "re-ordering" of DNA (e.g. it can be a single nucleotide substitution).

    - Amino acid sequence and molecular environment directly determine protein folding (they do not change in separate "steps"). But,

    - Changes in the amino acid sequence do not necessarily affect protein folding importantly.

    - Proteins can tolerate a fair amount of change in both sequence and shape and still be functional.

    - That's because molecular interactions in biology rarely work by perfect-fit. Chemistry is much fuzzier than the nice textbook diagrams show.

    - I can't summarise the ways new protein function evolves here. Go to the books.

    Finally, evolution is much more than protein change (see what happened to Cornelius!). Buy a good introductory Biology book and get the whole picture.

    ReplyDelete
  62. Cornelius:
    Derived from a common ancestral form? And how do evolutionists know these radically different designs evolved from a common ancestor? Well, because they are homologous, that’s how. And after all, homologous structures share a common ancestor. Amazing.

    Others already noted it, but it's a dishonest attempt to present the evolutionary argument as a tautology. The notion of homology predates the evolutionary explanation for it. Cornelius knows it. I mentioned it in the previous post.

    Nowadays homology is understood as an inference from hierarchical patterns of similarity to be tested. Several independent series of similarity patterns (selected by stringent criteria of position, form, development, &c) congruent with a single hierarchy are best explained as series of homologies.

    ReplyDelete
  63. RobertC,

    Are they? Humerus, radius and ulna, carpal bones. Might be harder to interpret without other species: Ancanthostega, Tiktaalik, Ichtyostega, Limnoscelis-but it seems like there is a pretty nice record of modification with descent of these homologous structures. No?

    http://www.devoniantimes.org/opportunity/tetrapodsAnswer.html


    I should note that the figure of the Panderichthys forelimb there is outdated. The actual structure is even more tetrapod-like.

    http://www.nature.com/nature/journal/v456/n7222/fig_tab/nature07339_ft.html

    Of course, this won't stop Cornelius from not looking what he doesn't want to see.

    And anyway, all of this is still an argument from incredulity.

    ReplyDelete
  64. Nowadays homology is understood as an inference from hierarchical patterns of similarity to be tested. Several independent series of similarity patterns (selected by stringent criteria of position, form, development, &c) congruent with a single hierarchy are best explained as series of homologies.

    I shall anticipate misrepresentation. Some characters look similar but don't fit the overall hierarchical distribution (homoplasies). Again, that's because homology is an inference. It is tested.

    ReplyDelete
  65. CH,
    "
    So if I've done this correctly, the CA likelihood is 0.78. This is not particularly newsworthy.

    What is newsworthy is that even by the evolutionist's reckoning there are plenty of observations that are of low probability, given the assumption CA is true."

    the text after this statement makes me think you are referring to likelihood, not probability. if not, correct me. the traits are of low likelihood under CA (or any other hypothesis) because the traits under consideration themselves are unlikely. if you start with a p of 0.1 for a deleterious trait, any subsequent calculations can only keep it at 0.1 or make it lower. so it is not a reflection of CA that the observations are of low probability, but of the traits themselves.so it is misleading to say CA is a "bad hypothesis" because some traits have low likelihood under it. they would have low likelihood under any hypothesis.

    ReplyDelete
  66. Zachriel, the basis for building an objective, nested hierarchy based on your previous criteria of parsimony, etc has failed.

    http://www.evolutionnews.org/2011/02/for_darwin_day_false_facts_and043691.html

    ReplyDelete
  67. Geoxus:

    ===
    Others already noted it, but it's a dishonest attempt to present the evolutionary argument as a tautology. The notion of homology predates the evolutionary explanation for it. Cornelius knows it. I mentioned it in the previous post.

    Nowadays homology is understood as an inference from hierarchical patterns of similarity to be tested. Several independent series of similarity patterns (selected by stringent criteria of position, form, development, &c) congruent with a single hierarchy are best explained as series of homologies.
    ===

    So after protesting that the homology argument certainly is no tautology, the evolutionist then presents ..., a tautology. Now perhaps we should not read it as a tautology, perhaps it is merely question-begging. The problem is, as always, the argument is not fully presented. Then I get the blame for not "knowing what evolutionists really mean."

    Yes, the notion of homology predates the evolutionary explanation for it, but that, in itself, does not justify evolutionary arguments that homologies are powerful evidence for evolution. What is needed is a non tendentious, non tautological, non selective, non metaphysical explanation for why this is so. Evolutionists have never presented one.

    It is little wonder that the argument from homology is presented in textbooks and web sites, like this one from Berkeley, with such brevity. The argument, from Darwin up to today, is deeply metaphysical. That is not controversial. If evolutionists are to persuade people that this is the powerful, compelling *scientific* evidence for evolution they claim it is, then they need to explain why.

    ReplyDelete
  68. nano:

    ===
    the traits are of low likelihood under CA (or any other hypothesis) because the traits under consideration themselves are unlikely.
    ===

    Rationalism is oblivious to its own assumptions. Like a fish that doesn't know it is in an ocean, rationalists think their axioms are universal. There is no other way. They are immersed in their metaphysics but they think they are objective.

    Here the evolutionist explains, as though it is a scientific fact, that deleterious traits are of low probability. That is an evolutionary concept, with all of the metaphysics that evolution entails.

    And so these evolutionary proofs are circular. They are based on axioms that derive from evolutionary thought, though evolutionists present them as objective and universal.

    ReplyDelete
  69. CH,
    "Here the evolutionist explains, as though it is a scientific fact, that deleterious traits are of low probability. "

    and CH dodges the point once again. all along he has agreed (or at least seemed to agree, based on his assignment of p values for traits) that deleterious traits are low probability (btw, i never said this was a fact). then when it becomes inconvenient, he suddenly accuses me of metaphysics for using assumptions that he has agreed to all along. truly pathetic.
    so, CH, do you agree, given the assumption that deleterious traits are unlikely, that any hypothesis about their origin in extant species has low probability?

    ReplyDelete
  70. Cornelius,
    So after protesting that the homology argument certainly is no tautology, the evolutionist then presents ..., a tautology.

    No. You put it as:

    1. Homologous structures share a common ancestor.

    2. We know these structures share a common ancestor because they share a common ancestor.

    That's true, but it's not the real argument. The argument is:

    1. We see independent series of characters that present specific similarity patterns.

    2. Those series similarities fit a common hierarchical structure explained as series of transformations.

    3. Those series of characters are evidence for evolution.

    3'. The characters in each series are referred to as homologous to each other.

    Characters that are homologous are evidence for evidence for evolution, but not just because we call them homologous. They are evidence for evolution because they show similarity patterns consistent with common descent.

    ReplyDelete
  71. Rationalism is oblivious to its own assumptions. Like a fish that doesn't know it is in an ocean, rationalists think their axioms are universal. There is no other way. They are immersed in their metaphysics but they think they are objective.

    Hubris, thy name is Cornelius.

    ReplyDelete
  72. Hunter:

    It is little wonder that the argument from homology is presented in textbooks and web sites, like this one from Berkeley, with such brevity. The argument, from Darwin up to today, is deeply metaphysical. That is not controversial. If evolutionists are to persuade people that this is the powerful, compelling *scientific* evidence for evolution they claim it is, then they need to explain why.

    It's not that hard to understand. Common ancestry is a hypothetical framework (a web of guesses about genealogy) that explains similarities in biological structures, developmental pathways, and genes. Those similarities make sense in light of the hypothesis, but they are unfathomable otherwise. Without evolutionary theory posing questions to be answered, collecting biological data would be like collecting stamps

    ReplyDelete
  73. nano:

    ===
    i never said this was a fact
    ===

    OK, sorry, I thought you were asserting that.

    ===
    do you agree, given the assumption that deleterious traits are unlikely, that any hypothesis about their origin in extant species has low probability?
    ===

    Yes, I agree with that. That's a helpful point, but common descent, nonetheless, has these many low likelihood cases. In other words, even according to evolutionary assumptions, common descent has low likelihood cases. The fact that all models, according to evolutionary assumptions, also have low likelihood does not help.

    ReplyDelete
  74. Cornelius:

    DATA HAS LIKELIHOOD. HYPOTHESES (LIKE COMMON ANCESTRY) DO NOT. LIKELIHOOD IS DEFINED AS THE PROBABILITY OF THE OBSERVATIONS GIVEN THE HYPOTHESIS. THAT'S WHAT P(D|H) MEANS. IF ONE HYPOTHESIS CONFERS A HIGHER LIKELIHOOD ON THE DATA THAN A SECOND HYPOTHESIS, THE FIRST HYPOTHESIS IS FAVORED (ASSUMING EQUAL DEGREES OF FREEDOM; IF NOT, USE AIC).

    SO THE LOW PROBABILITY OF A PARTICULAR DNA ALIGNMENT UNDER COMMON ANCESTRY IS *NOT* A STATEMENT ABOUT THE PROBABILITY OF COMMON ANCESTRY. IT'S A STATEMENT ABOUT THE PROBABILITY OF THAT DNA ALIGNMENT. THE "LOWNESS" OF THE PROBABILITY IS JUST A PRODUCT OF THE LENGTH OF THE ALIGNMENT. FOR EVERY NEW BASE ADDED, YOU ARE MULTIPLYING BY A FRACTIONAL PROBABILITY, BECAUSE YOU HAVE FRACTIONAL PROBABILITIES OF OBSERVING A, C, G, OR T. AN ALIGNMENT 100000 BASES WIDE WILL BE ABOUT (AVERAGE FRACTIONAL PROBABILITY PER SITE)^1000 LOWER LIKELIHOOD THAN AN ALIGNMENT 100 BASES WIDE.

    AS IT TURNS OUT, ALTHOUGH BOTH LIKELIHOODS ARE "LOW", THE LIKELIHOOD OF OBSERVED DNA ALIGNMENTS IS WAY WAY HIGHER UNDER COMMON ANCESTRY THAN UNDER SEPARATE ANCESTRY. THIS IS BECAUSE GETTING A PARTICULAR OBSERVED SIMILARITY THROUGH COMMON ANCESTRY REQUIRES THAT THAT CHARACTER STATE ONLY ARISE ONCE, BUT SEPARATE ANCESTRY REQUIRES THAT YOU GET THE SAME CHARACTER STATE MANY MANY TIMES, BY CHANCE, INDEPENDENTLY.

    I SUPPOSE YOU COULD SAY YOUR HYPOTHESIS IS THAT GOD WANTED ALL THE DNA TO BE THE WAY IT IS, THEREFORE THE DATA HAS A SUPER-HIGH LIKELIHOOD, BUT THEN YOUR HYPOTHESIS HAS AS MANY DEGREES OF FREEDOM AS THERE ARE DATA POINTS, AND A.I.C. WOULD PRETTY MUCH NUKE THAT IN A MODEL SELECTION FRAMEWORK.

    BASICALLY, YOU HAVE NO IDEA WHAT YOU ARE TALKING ABOUT, AND SHOULD RE-READ SOBER'S BOOK, PARTICULARLY CHAPTER 1 WHERE HE GOES THROUGH ALL THESE BASICS.

    ReplyDelete
  75. Geoxus:

    ===
    The argument is:

    1. We see independent series of characters that present specific similarity patterns.

    2. Those series similarities fit a common hierarchical structure explained as series of transformations.

    3. Those series of characters are evidence for evolution.

    3'. The characters in each series are referred to as homologous to each other.

    Characters that are homologous are evidence for evolution,
    ===

    If that's true then evolution is false. If your hypothesis, H, predicts E, then ~E implies ~H, by modus tollens. The great many violations of the hierarchical structure (which even evolutionists admit to) are also evidences. So if you're going to say that your theory predicts a hierarchical structure, then you must agree your theory is false.

    But instead you argue this is compelling evidence for your theory. So you are either selectively culling the evidence, or if not then you have some explanation that renders the unexpected evidences inconsequential. Obviously it is the latter that is needed, but evolutionists have never presented a non tendentious explanation.

    ReplyDelete
  76. Oops, instead of:

    AN ALIGNMENT 100000 BASES WIDE WILL BE ABOUT (AVERAGE FRACTIONAL PROBABILITY PER SITE)^1000 LOWER LIKELIHOOD THAN AN ALIGNMENT 100 BASES WIDE.

    ...I meant to say:

    AN ALIGNMENT 100000 BASES WIDE WILL BE ABOUT (AVERAGE FRACTIONAL PROBABILITY PER SITE)^99900 LOWER LIKELIHOOD THAN AN ALIGNMENT 100 BASES WIDE.

    ReplyDelete
  77. Cornelius, if you had understood what I just said in caps, you would never have said, as you did at the beginning, that common ancestry gets less probable as the likelihood goes down. Game over. Surrender that point and rational discussion can commence.

    ReplyDelete
  78. NickM:


    ===
    DATA HAS (sic) LIKELIHOOD.
    ===

    Oh no, Matzke has gone all-caps in defending his Berkeley website


    ===
    BASICALLY, YOU HAVE NO IDEA WHAT YOU ARE TALKING ABOUT,
    ===

    This coming from a theologically-driven evolutionist.


    ===
    DATA HAS LIKELIHOOD. HYPOTHESES (LIKE COMMON ANCESTRY) DO NOT.
    ===

    Of course hypotheses have likelihoods.


    ===
    YOU ...SHOULD RE-READ SOBER'S BOOK, PARTICULARLY CHAPTER 1 WHERE HE GOES THROUGH ALL THESE BASICS.
    ===

    No Nick, I'm not the one here who needs to read Sober's book.

    ###
    Fisher dubbed Pr(O|H) the likelihood of H. Because Fisher's terminology has become standard in statistics, I will use it here. However, this terminology is confusing, since in ordinary English, "likely" and "probably" are synonymous. So beware! You need to remember that "likelihood" is a technical term. [9]
    ###

    ReplyDelete
  79. "If that's true then evolution is false. If your hypothesis, H, predicts E, then ~E implies ~H, by modus tollens. The great many violations of the hierarchical structure (which even evolutionists admit to) are also evidences. So if you're going to say that your theory predicts a hierarchical structure, then you must agree your theory is false."

    This is like saying that occasional instances of things moving uphill disprove gravity. Phylogenetic trees from different sources are very commonly statistically significantly very similar, despite occasional instances of incongruence, which are also known to be due to various identifiable processes.

    ReplyDelete
  80. CH,
    "The fact that all models, according to evolutionary assumptions, also have low likelihood does not help. "

    it's one of the many reasons that you can't evaluate a hypothesis in the absence of alternatives. a low or high likelihood by itself doesn't tell you much. for example, one of your protein models may predict structure with 60% accuracy, but how does this compare to another model? if a null model predicts structure with 55% accuracy, then your model is not too impressive, regardless of its accuracy observed in isolation.

    ReplyDelete
  81. NickM:

    ===
    "If that's true then evolution is false. If your hypothesis, H, predicts E, then ~E implies ~H, by modus tollens. The great many violations of the hierarchical structure (which even evolutionists admit to) are also evidences. So if you're going to say that your theory predicts a hierarchical structure, then you must agree your theory is false."

    This is like saying that occasional instances of things moving uphill disprove gravity.
    ===

    Except that you quote-mined me again. What you selectively omitted was this:

    "or if not then you have some explanation that renders the unexpected evidences inconsequential." Such explanations exist for objects moving uphill.

    ReplyDelete
  82. NickM:

    ===
    Cornelius, if you had understood what I just said in caps, you would never have said, as you did at the beginning, that common ancestry gets less probable as the likelihood goes down. Game over. Surrender that point and rational discussion can commence.
    ===

    I'd gladly surrender that point except that I didn't say common ancestry gets less probable. (if I did that was a mistake, and I'd appreciate knowing so I can fix it).

    ReplyDelete
  83. Suppose we flip a coin N times. Under the hypothesis that the coin is fair (i.e. pr(heads)=pr(tails)=1/2), the likelihood of any sequence of N flips equals (1/2)^N. Which approaches zero monotonically from above as N becomes larger.

    Therefore, according to Cornelius' "logic", the hypothesis that the coin is fair gets worse the more often you flip it.

    In other words, ignorance is bliss.

    ReplyDelete
  84. Hunter:

    If your hypothesis, H, predicts E, then ~E implies ~H, by modus tollens.

    Again, Hunter's confuses deductive logic with hypothesis testing. In deductive logic ~E falsifies H unequivocally. In inductive hypothesis testing one weighs the evidence and does not rush to throw the baby out with the bathwater.

    The great many violations of the hierarchical structure (which even evolutionists admit to) are also evidences.

    Indeed. And many of those exceptions are explained as lineage-specific, rather than as core features, such as those that are conserved throughout the bilateria. (But one has to read the literature to learn that.)

    ReplyDelete
  85. @ Cornelius Hunter
    Here

    http://darwins-god.blogspot.com/2010/12/it-didnt-begin-or-end-with-darwin.html?showComment=1293736319059#c6192767175217098057

    you said:
    “Of course natural selection and common descent are important parts of the idea, but they can be forfeited. There could be drift, there could be multiple ancestors, etc. None of this goes agaisnt the over arching idea of evolution.”

    So I still don't understand that you argue so vehemently about common descent if you think that common descent is a dispensable asset. I think what you say is quite right. Common descent is not a dogma. If the data would support multiple ancestry than that would be fine to.

    ReplyDelete
  86. troy:

    Suppose we flip a coin N times. Under the hypothesis that the coin is fair (i.e. pr(heads)=pr(tails)=1/2), the likelihood of any sequence of N flips equals (1/2)^N. Which approaches zero monotonically from above as N becomes larger.

    Therefore, according to Cornelius' "logic", the hypothesis that the coin is fair gets worse the more often you flip it.


    By Jove, I think you've got it!

    ReplyDelete
  87. @Neal Tedford

    That's really cute. Expectedly the discovery institute is not quite update as you can see here:

    http://www.ncbi.nlm.nih.gov/pubmed/20591845

    Surprisingly the authors of the paper are not concerned that the ToE could be wrong.

    ReplyDelete
  88. All quotes from Cornelius.

    DATA HAS (sic) LIKELIHOOD

    http://www.merriam-webster.com/dictionary/data

    If that's true then evolution is false. If your hypothesis, H, predicts E, then ~E implies ~H, by modus tollens.

    Modus tollens does not apply for probabilistic hypotheses.

    The great many violations of the hierarchical structure (which even evolutionists admit to) are also evidences.

    Yes, they are evidences, and should be considered duly weighed with the fitting data. Of course, I don't expect to convince you that you over-weigh it, but can you give an estimation of the fitting/not-fitting series ratio for an allegedly well-resolved phylogeny? Can you refute the statistical support of it?

    So you are either selectively culling the evidence, or if not then you have some explanation that renders the unexpected evidences inconsequential.

    Yes, there are explanations for data not fitting the hierarchical pattern, but again, the departures are not enough to render the fitting data insignificant.

    ReplyDelete
  89. Homology proves nothing about common descent, because common descent is a formal principle or axiom of the system. On the basis of this axiom, other individual propositions can be constructed and tested.

    There is no probative element to homology, an elastic concept that has had different explanations and justifications over the last hundred years. At the time of Darwin and for some decades after, phylogenies were derived based on comparative anatomical and embryological data that relied heavily on a concept of homology that was defined by the axioms of phylogenetic and ontogenetic continuity.

    This well-known quote illustrates but one of the insurmountable problems with the concept of homology: "Structures as obviously homologous as the alimentary canal in all vertebrates can be formed from the roof of the embryonic gut cavity (sharks), floor (lampreys, newts), roof and floor (frogs), or from the lower layer of the embryonic disc, the blastoderm, that floats on top of heavily yolked eggs (reptiles, birds)" (Gavin de Beer, , Oxford Biology Readers No. 11, eds. J.J. Head and O.E. Lowenstein [Oxford: Oxford University Press, 1971] p. 13.)

    John I.

    ReplyDelete
  90. So Cornelius, teach us the homology inference of the vertebrate forelimb is wrong. Let's be sure of not culling the evidence, and include Eusthenopteron, Panderichthys, Acanthostega, Tiktaalik, Tulerpeton, Limnoscelis, and Cacops besides as many other taxa you like.

    ReplyDelete
  91. Geoxus:

    ===
    If that's true then evolution is false. If your hypothesis, H, predicts E, then ~E implies ~H, by modus tollens.

    Modus tollens does not apply for probabilistic hypotheses.
    ===

    That rationalization only works if you are close.


    ===
    "The great many violations of the hierarchical structure (which even evolutionists admit to) are also evidences."

    Yes, they are evidences, and should be considered duly weighed with the fitting data.
    ===

    I'm glad to see an evolutionist agreeing that the unexpected data should be considered. They are routinely ignored when evolutionists present the "evidences" for evolution.


    ===
    Of course, I don't expect to convince you that you over-weigh it,
    ===

    The problem is not that I over-weigh contradictory evidences, the problem is that evolutionists under-weigh them, or to be more precise, evolutionists give them zero weight (ie, do not consider them when presenting the evidence).

    (cont)

    ReplyDelete
  92. Geoxus:
    (cont)

    ===
    but can you give an estimation of the fitting/not-fitting series ratio for an allegedly well-resolved phylogeny? Can you refute the statistical support of it?
    ===

    Let's take some examples. The evolutionary expectation is that if a pair of species shares a trait, then they likely will share other traits. And if a pair of species have a different trait, then they likely will not share other traits as well. In other words, there should be a correlation between how species compare, across different traits, as a consequence of common descent. If species share a relatively recent common ancestor, then the two species should be similar in many ways. If species share a very distant common ancestor, then the two species should be different in many ways.

    But the data are in violent disagreement. We're not talking about statistical or biological "noise." There are striking similarities in distant species, and there are striking differences in cousin species. The problem is evolution is protected for all of this by various unlikely, but unquestioned, escape hatches. For instance, in the first case, evolutionists say the striking similarities in distant species are a consequence of "convergence." The same designs independently evolved.

    In the second case, evolutionists say the striking differences in cousin species are a consequence of temporarily rapid evolution, or some such. A different design just happened to arise for some unknown reason.

    These many evidences are then discounted, because they are "explained," and you end up with a filtered data set consisting of the agreeable data. Of course within this filtered data set there are smaller disagreements. Here, evolutionists can appeal to "noise" and castigate skeptics as ignorantly naive of such vital statistical concepts.

    An example at the morphological level of a striking similarity in distant species is the vision system in the squid and human. You have an incredibly detailed design arising twice, in completely different environments, and from completely different initial conditions. The convergence escape hatch is simply a just-so story. Random, unguided biological variation must have twice created these two instances of this incredibly detailed design. No, selection doesn't help. It doesn't guide the biological variation. These designs must arise on their own, one small step at a time.

    An example at the molecular level are the UCEs (ultra conserved elements). Here evolutionists would say these long, practically identical, stretches of DNA are for some reason conserved in certain species, even though the stretches don't seem very important for fitness.

    An example at the morphological level of a striking different designs in cousin species are embryological development pathways. To the surprise of evolutionists, profoundly different pathways are found in otherwise similar species. Yes frog A and frog B, according to evolution, share a relatively recent common ancestor, but for some reason one of them swapped in a completely different development pathway.

    An example at the molecular level of a striking different designs in cousin species are the different genes that are found. One example is the growing list of ORFans that are found.

    These examples are not "in the noise." Can evolutionists come up with creative explanations for them? Sure, a bunch of mutations just happened to occur in the right place, etc. But this doesn't mean these data get a pass.

    (cont)

    ReplyDelete
  93. Geoxus:
    (cont)

    ===
    Yes, there are explanations for data not fitting the hierarchical pattern, but again, the departures are not enough to render the fitting data insignificant.
    ===

    What if every once in awhile your pencil floated in mid air? Compared to all the measurements of objects falling to the ground, all over the world, year after year, your pencil would be statistically insignificant. But it's just bad, protectionist science to use that as a reason to ignore the data. It is precisely in these odd ball cases where scientists must explore, and where striking advances are sometimes made.

    ReplyDelete
  94. Hunter quoting Geoxus:

    Modus tollens does not apply for probabilistic hypotheses.
    ===
    That rationalization only works if you are close.


    It isn't a rationalization; it's a plain statement of fact. Hunter denies the difference between deductive and inductive reasoning! Talk about equivocation.

    Amazing!

    ReplyDelete
  95. Hunter:

    An example at the morphological level of a striking similarity in distant species is the vision system in the squid and human. You have an incredibly detailed design arising twice, in completely different environments, and from completely different initial conditions.

    That ain't the half of it. What about the compound eyes of arthropods? But wait, the developmental genetics of beetle, squid and human eyes all involve the Pax6 gene, which is highly conserved among all bilaterian species.

    Coincidence? I think not!

    Pax-6 in vertebrates and its homolog eyeless in Drosophila are known to be essential for eye development. Here we investigate the role of Pax-6 in eye development in another major systematic group, molluscs. We demonstrate that alternatively spliced RNAs derived from a single Pax-6 gene in the squid (Loligo opalescens) are expressed in the embryonic eye, olfactory organ, brain, and arms. Despite significant sequence differences between squid Pax-6 and Drosophila eyeless in the region outside the paired- and homeodomains, squid Pax-6 is able to induce the formation of ectopic eyes in Drosophila. Our results support the idea that Pax-6 related genes are necessary for eye and olfactory system formation throughout the animal kingdom.

    http://www.ncbi.nlm.nih.gov/pubmed/9122210

    ReplyDelete
  96. @Cornelius Hunter

    But why then don't you take this paper for example:

    http://www.ncbi.nlm.nih.gov/pubmed/20591845

    and show us on detail where the authors sanitized the data?

    ReplyDelete
  97. Cornelius:

    "For instance, in the first case, evolutionists say the striking similarities in distant species are a consequence of "convergence." The same designs independently evolved."

    Typical. You pretend as if "evolutionists" explain the similarities by simply inventing a fancy term ("convergence") and leave it at that. But of course there is more to it than that. E.g., the similarity in body shape between dolphin and shark is explained by similarity in selection on swimming speed. Do you have a better explanation?

    ReplyDelete
  98. CH,
    "It is precisely in these odd ball cases where scientists must explore, and where striking advances are sometimes made. "

    I'm glad you agree that investigating evolutionary theory can (and has) provided striking advances in other fields, esp. when researchers investigate anomalies. just last week provided a nice example:

    http://www.sciencemag.org/content/331/6018/753.short

    ReplyDelete
  99. troy asked Hunter:

    Do you have a better explanation?

    A foolish question. Hunter doesn't DO explanations.

    ReplyDelete
  100. Me:

    Yes, they are evidences, and should be considered duly weighed with the fitting data.

    Cornelius:

    I'm glad to see an evolutionist agreeing that the unexpected data should be considered. They are routinely ignored when evolutionists present the "evidences" for evolution.

    Routinely ignored? There is a little word for that kind of data. It's homoplasy, which is thoroughly discussed in the literature. Entry level texts routinely discuss a particular kind of homoplasy: convergence.

    http://evolution.berkeley.edu/evolibrary/article/0_0_0/similarity_hs_06

    Cornelius:

    The problem is not that I over-weigh contradictory evidences, the problem is that evolutionists under-weigh them, or to be more precise, evolutionists give them zero weight (ie, do not consider them when presenting the evidence).

    Cornelius, meet the Consistency Index; one of the most used estimators of clade support in cladistic analysis.

    http://books.google.cl/books?id=Enuaxb9FymEC&pg=PA36&lpg=PA36&dq=consistency+index+homoplasy&source=bl&ots=olGEgFrUNB&sig=-QiHpesZYU1yD3ycX1wz4pi4new&hl=en&ei=iqNZTevlKsT0gAeGrL2EDQ&sa=X&oi=book_result&ct=result&resnum=10&ved=0CGAQ6AEwCQ#v=onepage&q=consistency%20index%20homoplasy&f=false

    ReplyDelete
  101. Blogger is becoming a bit naughty again, it deleted my last post.

    ReplyDelete
  102. This comment has been removed by the author.

    ReplyDelete
  103. "A foolish question. Hunter doesn't DO explanations."

    Sadly, it seems that way. Cornelius could have been a productive member of society. Instead, he attacks science in the name of superstition. Religion rots the brain and it matters.

    ReplyDelete
  104. All the quotes from Cornelius:

    What if every once in awhile your pencil floated in mid air? Compared to all the measurements of objects falling to the ground, all over the world, year after year, your pencil would be statistically insignificant.

    False analogy. Homoplasy does not support common descent, but it doesn't represent evidence against it either. Homoplasy is no hovering pencil.

    It is precisely in these odd ball cases where scientists must explore, and where striking advances are sometimes made.

    If you think evolutionary biologists do not research the causes of homoplasy, it is evidence of an enormous ignorance of evolutionary literature from your part. I know you scan it, but do you read it?

    ReplyDelete
  105. This comment has been removed by the author.

    ReplyDelete
  106. "An example at the morphological level of a striking similarity in distant species is the vision system in the squid and human."

    Wired different (photoreceptors forward vs backward), develops different, structural differences, rods and cones vs rhabdomeres, different G-proteins, dark activated vs. light activated.

    Striking similarity at a trivial level.

    ReplyDelete
  107. Me:

    but can you give an estimation of the fitting/not-fitting series ratio for an allegedly well-resolved phylogeny? Can you refute the statistical support of it?

    Cornelius:
    Let's take some examples. The evolutionary expectation is that if a pair of species shares a trait...

    LOL, I asked for a simple number very easy to obtain from any published analysis and all you provide are words like "violent" and "striking". If you feel so confident about your ability to evaluate morphological data, present a concrete example. Take responsibility of the one you already mentioned: show how the case for limb homology of Eusthenopteron and tetrapods is wrong. Don't forget not to cull the data by omitting the relevant transitional taxa I mentioned before.

    ReplyDelete
  108. I reposted my last comment because of a typo.

    ReplyDelete
  109. Pedant: "A foolish question. Hunter doesn't DO explanations."

    Better yet, Hunter refuses to respond to direct questions regarding explanations.

    01. Has science explained anything at all?

    02. Is the biological complexity we observe beyond explanation by human reason and problem solving?

    03. Do you think there is an answer to the problem of induction? If so, what is it?

    It's as if Hunter thinks not disclosing this information somehow means he has no position on these issues, in realty, which somehow makes him immune from bias.

    I wrote: For example, you've quoted people who's statements you interpret as *representing* a religious belief about God's nature. But, surely, you're not suggesting the act of writing or verbalization represents your real criteria? A person who holds any view need not necessarily express it publicly, yet it can still influence their interpretation of evidence.

    Of course, my multiple attempts to clarify his criteria were ignored. I guess he's taking the 5th.

    What I can't figure out is why Cornelius expects anyone to take him seriously. It's as if he thinks his evolutionary objections exist in a vacuum in that they'd have no implications on other fields. Things just don't add up.

    ReplyDelete
  110. second opinion, your link stated, "These global processes may have triggered the rapid diversification of placental mammals... However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression. These speciation-related processes led to a mosaic genome and conflicting phylogenetic signals. Split network methods are ideal for visualizing these problematic branches and can therefore depict data conflict and possibly the true evolutionary history better than strictly bifurcating trees. "

    ----

    "May have"... "possibly". Again, it is all based on an assumption that universal common descent is a fact. It was the nice and tidy branching Darwinian tree of life that was supposed to be strong evidence for evolution. What happened? We have "webs" not only at the bacterial level but even at the mammalian level. "Mosaic genomes" is not really conducive to evolutionary descent, is it? The mixing and matching of genes was not part of the objective nested hierarchy argument. Pinning evolutionists down on their expectations and predictions is like nailing Jello to a wall.

    This has got to be driving evolutionists nuts, as Darwin thought his whole theory could just about stand on the nested hierarchy and homology argument.

    ReplyDelete
  111. Geoxus:

    ===
    Routinely ignored? There is a little word for that kind of data. It's homoplasy, which is thoroughly discussed in the literature.
    ===

    Which is why I was careful to say "when evolutionists present the "evidences" for evolution."


    ===
    Entry level texts routinely discuss a particular kind of homoplasy: convergence.

    http://evolution.berkeley.edu/evolibrary/article/0_0_0/similarity_hs_06
    ===

    That's encouraging, but the limbs of the octopus, sea star and grasshopper make for a convenient example. In fact the page says: "Simple observation tells us that these limbs are probably not homologous to the tetrapod limb, because they have such different structure." Biology is full of structures that are not so different.


    ===
    Cornelius, meet the Consistency Index; one of the most used estimators of clade support in cladistic analysis.
    ===

    No, CI is not used to explain why we need not worry about ORFans, radical differences in development pathways, etc. Measures of phylogenetic fit, such as CI, are generally used by evolutionists to compare different evolutionary trees, and decide which is better, according to traits that can be quantitatively compared.


    ======
    "What if every once in awhile your pencil floated in mid air? Compared to all the measurements of objects falling to the ground, all over the world, year after year, your pencil would be statistically insignificant."


    False analogy. Homoplasy does not support common descent, but it doesn't represent evidence against it either. Homoplasy is no hovering pencil.
    ======

    This is wonderful clarity. Astonishing, but with great clarity.

    First, this is a universal claim for evolutionists. Similarities between species that can, according to the assumptions of evolution, be explained by common descent are viewed as powerful, compelling evidence. But similarities between species that *cannot,* according to the assumptions of evolution, be explained by common descent are not a problem. The long list of incredible, profound similarities which, even by evolutionists' own reckoning, cannot be explained by common descent, are simply written off as lightning striking twice. Without the slightest of a blush evolutionists tell you the 2nd category of similarities is not a problem while the 1st category is powerful evidence. Random biological variation just happened independently to produce the striking vision system in the squid and human, and so what? Yet a similarity between more closely related species, that's powerful evidence for evolution.

    Second, there is the problem of striking differences in otherwise similar species. New genes arose, perfectly good development pathways suddenly switched to something completely different. So what?

    Evolutionists tout the similarities between species as though they are powerful evidences for evolution, but the pattern is all over the map. It does not *fit* evolution, rather, it is interpreted according to evolution.


    ===
    LOL, I asked for a simple number very easy to obtain from any published analysis and all you provide are words like "violent" and "striking". If you feel so confident about your ability to evaluate morphological data, present a concrete example.
    ===

    That's strange, I presented four examples. Examples for which evolution has no explanation beyond non scientific speculation. You want numbers? There are plenty of numbers for ORFans or UCEs. Thousands of DNA bases with an identical sequence between, say mouse and human, with hundreds of experiments showing no fitness impact. An evolutionist once told me evolution would be flat out falsified if highly similar, unconstrained sequences were discovered. Well that is exactly what UCEs are. (of course, he is still an evolutionist -- that "falsifiable prediction" was conveniently forgotten). There's no lack of numbers if that is what you want. The problem is there is no evolutionary explanation, beyond speculation, not even close.

    ReplyDelete
  112. Cornelius Hunter:

    "What if every once in awhile your pencil floated in mid air?"

    According to the theory of gravity a feather should fall to the ground with the same speed as a stone. So I guess the theory is falsified then?

    ReplyDelete
  113. @Neal Tedford

    What you still don't get is that common descent does not predict that the tree of life must be 100 % bifurcated. We have observed hybridization and ring species for example. What common descent does predict is that the further you go back in time the more closely related the species should become. And that is what is observed.

    ReplyDelete
  114. @ Cornelius Hunter

    Similarities in morphology and embryological development are proxies for the underlying genetics. Nobody halfway reasonable expects these proxies to the completely accurate and convergence is a very reasonable explanation for deviations.

    Only the UCEs are an example of something that is a problem for ToE.

    ReplyDelete
  115. Hunter:

    There are plenty of numbers for ORFans or UCEs. Thousands of DNA bases with an identical sequence between, say mouse and human, with hundreds of experiments showing no fitness impact.

    No fitness impact? From the abstract of an open-source review (published July 2008):

    "Although our knowledge of UCEs is limited, most recent studies suggest that UCEs play a functional role in vertebrate genomes, such as serving as long-range enhancers of flanking genes, regulating splicing and epigenetic modifications, and functioning as transcriptional coactivator. Most recent studies show that expression of UCEs is consistently altered in tumors, strongly suggesting these elements may also be involved in human disease such as cancer development."

    http://www.ncbi.nlm.nih.gov/pubmed/18708752

    ReplyDelete
  116. Second Opinion said, "What you still don't get is that common descent does not predict that the tree of life must be 100 % bifurcated."

    ---

    So how low can the percentage go? 95%... 51%....10%? I don't believe there is a specific percentage, correct? So whatever the changing estimate is will still be good enough for your theory because the validity of evolution doesn't really ride on it.

    Other than finding multiple herds of buffalo fossils in various Cambrian rock, I'm hard pressed to think of anything that would cause evolutionists to give it up. Well, even then, someone would probably come up with something imaginative. I know... "we certainly didn't expect the herds of buffalo, but we don't know everything and there's still lots of other evidence for evolution". Presto.

    ReplyDelete
  117. Neal Tedford: So how low can the percentage go?

    You're living in upside-down world. There *is* a nested hierarchy. Just like planets trace elliptical orbits. The patterns don't go waway because the nested hierarchy is not perfect, or because planets don't trace perfect ellipses. And it's these patterns that science attempts to explain.

    As for the Theory of Evolution, it never posited a perfect nested hierarchy. Darwin discussed hybridization and convergence, among other difficulties, way back in 1859.

    ReplyDelete
  118. Zachriel, we certainly can draw nested hierarchies of nature, but the results depend on the selection criteria used. For example, your original selection criteria using parsimony, etc failed many times to yield the same results as genetic sequencing does. You can always pass it off as hybridization or convergence or whatever, but is that just another guess?

    Even a broken clock is right twice a day.

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  119. Cornelius,

    In an attempt to determine the best explanation of your selective objections of science, I'm trying to clarify the explanations you provide. However, this has proved difficult as you seem to be unwilling to answer relevant questions or quantify your criteria. 

    For example, in the case of Soble's quote, it seems we can sum up your objection as follows...

    if you can't claim evidence that a specific outcome of an evolutionary process with common descent has a low likelihood also represents evidence that common decent is a bad explanation for those features, then we cannot claim any evidence that suggests a specific outcome of an evolutionary process with common descent has a high likelihood is evidence that common decent is a good explanation for those features. 

    In other words, if common decent as an explanation for all features (outcomes) of a species is insulated from outcomes of low probabilities, then it's also isolated from outcomes of high probabilities. 

    Is this an accurate summary?

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  120. Neal Tedford: we certainly can draw nested hierarchies of nature, but the results depend on the selection criteria used.

    It's difficult to believe you are still stuck on this, when it's easy enough to show that the nested hierarchy is not an artifact of the selection criteria, but has real empirical implications.

    We tried this before, but let's objectively categorize a few examples, basing our categorization on the panoply of traits.

    dolphin, cat, fish

    Which two should be grouped together?

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  121. Zachriel,

    Actually, it's not difficult to explain Neal being stuck on this.

    We can explain his refusal as Neal holding a belief that the biological complexity we observe is beyond human reasoning and problem solving. In other words, he's taken it off the table. Period.

    Furthermore, Neal can simply affirm or deny if he holds this view. Of course, I've asked him this question several times, but he has yet to reply.

    Neal, to repeat my question...

    Do you believe that the biological complexity we observe in nature is beyond human reasoning and problem solving?

    This is really a simple, relevant question, so it's unclear why neither Neal or Cornelious have answered it.

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  122. Zachriel and Scott, your dancing around the problems.

    Zachriel, your categorization on the "panoply of traits" yielded a different outcome than when genetic sequencing criteria was used. This criteria has shown to be flawed and inconsistent. Look at the link from second opinion... what happened to your tidy cladograms? The webs of life look like a vain attempt to hold together a supposed phylogenetic relationship when the mosaic of life is screaming mixing and matching of genes by design.

    Scott, the biological complexity we observe in nature is beyond Darwinian mechanisms to explain. The digital information originates by an intelligence being. We know enough about nature and chemistry to know that purely natural processes can not account for the biological complexity we see. Earthquakes and lightning have a better chance at duplicating a Mount Rushmore. By analogy to your thinking, since an earthquake can create a rock that looks like a nose, then just keep at it and presto we have a Mount Rushmore.

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  123. Neal,

    You're not under oath. I'm not a layer. This is not a trial.

    But this in no way prevents me from noting that you didn't answer the direct question I asked you.

    In other words, you can refuse to answer the question I asked, because your under no obligation to do so. However, you can't say your response *was* an answer to the question I asked.

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  124. Neal,

    what happened to your tidy cladograms?

    They hold quite well at shorter phylogenetic distances, such as humans and the other apes.

    The webs of life look like a vain attempt to hold together a supposed phylogenetic relationship when the mosaic of life is screaming mixing and matching of genes by design.

    No it is not screaming such thing. For one, there is plenty of evidence that common descent is a main mechanism in evolution. What the data show is that there is more to evolution than just common descent. For instance, horizontal gene transfer seems to be so prevalent in microbes that it competes a lot with common ancestry as a source of new species. However, we still need common ancestry for there to be some population to receive the genes. That genes are transferred we knew already, we had discovered plasmids, virus, and transposons well before knowing they played such a big role in microbial evolution. We see that non-shared genes within a single species occur in genomic islands, and that they are surrounded by sequences that betray their transference by transposons, viruses, and plasmids (if they are not in plasmids). Thus, there is no need to talk about designers doing the mixing nor the transfer. We know of natural mechanisms doing the job. Furthermore, the problems arise so infrequently at other levels of life-forms that it fits with evolution in the sense that we expect catastrophes to happen with a higher probability among long-separated lineages. Hybridization is a well known genetic mechanism, virus integration too, transposons, and such. We see such signatures, thus no need to add anything to understand what's going on. How would things happening by natural mechanisms scream of designers?

    Furthermore, if there were designers, you should be able to show them to exist and do their work. After all, you claim that the whole thing screams of design, then, if the designers are acting at so many points in time, why don't they leave any evidence of their existence? Where are their hardware (such as tools) and their niches? Where do they live? Where do they hide while not at work? Without that, and having natural explanations for everything, why would we invoke designers?

    the biological complexity we observe in nature is beyond Darwinian mechanisms to explain

    Agreed. But it is not beyond natural mechanisms to explain. Life forms are not static rocks by the way. Thus, your Mount Rushmore fails as counterexample for anything.

    Have a great week!

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  125. Negative Entrophy, your criteria for seeking the existence of the creator is too narrow otherwise you would have found Him already. If you really want to find God, make it a very serious effort, and you will most certainly find Him.

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  126. By Cornelius question about a floating pencil. We would have to study what's going on. Would we stop thinking that gravitational theory explains gravity? Since there is so much evidence for gravitational forces, nope. But we might find another thing thanks for the pencil. In the evolutionary scenario, this is what happens with horizontal gene transfer, endosymbiosis, hybridizations, polyploidy, and et cetera. Mechanisms that contribute to common ancestry and smaller mutational events to the whole evolutionary process.

    I truly don't see why would evolution be false. It is richer than we thought, richer than our most common explanations might be able to convey. But false? Come on!

    But far from showing any failed predictions, what Cornelius does is to claim that anything where scientists claim to find something they did not expect, they have proven a "prediction from evolution" to be false. No matter if he can show such to truly be a prediction from evolution rather than a hypothesis about a particular mechanism that however it went, is not a prediction of evolution, but a detail about how some process goes (evolutionary or otherwise).

    But he does not care. Religion drives his pseudoscience, and it sure matters.

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  127. Neal,

    Negative Entrophy, your criteria for seeking the existence of the creator is too narrow otherwise you would have found Him already. If you really want to find God, make it a very serious effort, and you will most certainly find Him.

    My sincere thanks Neal. It is good to know what this is about in your case. I am not seeking for the existence of anything, let alone a creator. Hypocrites try and disguise their seeking as if it were science, and I am truly glad to know you are not one of them. Given that, look at my answer(s)/Comment(s), plus whatever trustable source of information about evolution (not a cdesign proponentsist one). If you were not biased towards trying to find a creator, what would you think?

    For as long as natural processes can account for what we see, for as long as nature shows that we share ancestors with the other apes. It is so. It would take some real evidence, rather than the pseudoscience of the cdesign proponetsists, to convince me that evolution is false. Evolution is science and it is a fact beyond reasonable doubt. Believing in a particular sort of god, with a particular means for creating life forms, is not reasonable doubt Neal. It is putting the conclusions before the facts. Sorry to tell you.

    Best again, and see you much later.

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  128. Zach:"dolphin, cat, fish

    Which two should be grouped together? "

    Depends on the grouping criteria.

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  129. Blas: Depends on the grouping criteria.

    Objective consideration of the panoply of traits.

    Neal Tedford: your categorization on the "panoply of traits" yielded a different outcome than when genetic sequencing criteria was used.

    As our readers can see, you didn't answer the question. Nor is anyone claiming a perfect nested hierarchy, certainly not Darwin.

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  130. Negative Entrophy, lets start at the beginning. You have a warm puddle of goo and no life. What natural process have you observed to spontaneously form life? Scientists have put all the compounds necessary for life together and they haven't seen life form. Natural selection is powerless. Chemical properties just don't come together and form life. Life has the property of containing highly complex and specified information.

    You said, "For as long as natural processes can account for what we see". That's hogwash. If you know how life originated via natural processes, don't hold back, there's a nobel prize waiting for you.

    We know too much about nature just to chalk it all up to some warm little pond fairy tale.

    Design is the best explanation at hand. I looked at this many years ago and didn't buy the warm little pond fairy tale and it led me to faith in a Creator, not vice versa.

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  131. Zachriel, so what degree of perfection in nested hierarchies still qualifies Darwinism to be valid? There is no objective degree and hence no way to falsify yet another Darwinist claim.

    We've beat up the dolphin, cat and fish hierarchy enough. Again, do you know for sure that the multitude of conflicting data coming from genetic sequencing is due to HGT, convergence, and even global warming (no joke, it's in second opinions link). When you and Derick were analyzing the Apple ipod hierarchy you didn't hold back on emphasizing exceptions. What about the sea squirt? Do we chalk up the phylogenetic conflicts with the sea squirt to global warming or what?

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  132. Great post with the usual lucid observations by Dr. CH.

    Its just hilariously reading the evolutionists comments as they continue to supply proof to what CH is saying.

    I feel almost like when I'm watching Islamic fundamentalists rioting, calling for executions and violence, just after someone publishes a remark on how violent they are.

    Unreal, they prove it every time and Darwinists are just as self-contradictory.

    Its truly hard to believe anyone could be so willfully blind or adamantly obstinate as to continue on "believing" the inane Darwinian "hypothesis" -it doesn't actually qualify as a valid theory.

    Belief is the key word for Darwinians since their "mountains of overwhelming evidence", once dissected by a scrutinizing logical mind, always end up being rather mountains of overwhelming just-so stories, wishful thinking and incredibly naive gullibility.

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  133. CH: There are two problems here. First, the claim affirms the consequent. If a hypothesis successfully makes a prediction, that does not mean the hypothesis is correct.

    Cornelius, unless you have a solution to the problem of induction, we can't know that any hypothesis for any phenomena is correct at the level you're alluding to. But what we can know is that one explanation is superior for any particular group of phenomena. And we can know this as a fact.

    For example, take chemical reactions. From Wikipedia…

    "When a chemical substance is transformed as a result of its interaction with another or energy, a chemical reaction is said to have occurred. Chemical reaction is therefore a concept related to the 'reaction' of a substance when it comes in close contact with another, whether as a mixture or a solution; exposure to some form of energy, or both. It results in some energy exchange between the constituents of the reaction as well with the system environment which may be a designed vessels which are often laboratory glassware. Chemical reactions can result in the formation or dissociation of molecules, that is, molecules breaking apart to form two or more smaller molecules, or rearrangement of atoms within or across molecules. Chemical reactions usually involve the making or breaking of chemical bonds. Oxidation, reduction, dissociation, acid-base neutralization and molecular rearrangement are some of the commonly used kinds of chemical reactions."

    Can we say chemical reactions as described in this definition is a fact?

    What we observe are chemicals being transformed. Our explanation for this phenomena is that they react to each other. However, we cannot know if the changes we observe actually occur because they react to each other, rather than demons intelligently choosing to act on these substances when they are in close proximity.

    Despite this limitation, we accept the former because it's a superior explanation of the observations. And we can know this as a fact.

    This is because, merely saying "demons did it" doesn't explain why these particular transformations occur, rather than some other transformation we do not observe. Essentially, we can distill the demon-based explanation of these transformations down to…

    Demons intelligently choose to act on chemicals as if they were reacting to each other.

    Her'e the demon's actions are explained by the prevailing theory: the substances are reacting to each other. What's missing is an explanation as to why the demon performs these particular transformations when these substances are in proximity of each other, rather that performing some other transformation when they are away from each other, etc. Adding a demon to the mix doesn't add to the explanatory power.

    It's a convoluted elaboration of the theory that chemicals react to each other.

    As such, we know for a fact the explanation of chemicals reacting to each other is the best explanation of the transformations we observe. This is because any explanation of the transformations we observe is independent of any state of affairs in reality. Furthermore, it's independent of any sort of hierarchy, such as mathematical deduction, induction or philosophy.

    I'd also note that un-conceived explanations cannot be defended as an explanation because, well, they do not explain anything.

    So, unless you have some way around the problem of induction, then it would appear that your objection is dependent on your definition of science or it would render in the entirety of science as unscientific.

    Of course, attempts to clarify this issue have gone ignored.

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  134. Zach: "Objective consideration of the panoply of traits"

    Then you will have three groups of shared traits. One for each couple of animals.

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  135. Scott, again your analogy is flawed. We have not observed universal common descent, but we observe chemical reactions. Your analogy would be valid if we saw life spontaneously arise from chemical mixtures, or if we saw new phyla forming. All we see are small scale changes and evolutionists holding onto ungrounded assumptions.

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  136. second opinion:

    ===
    Similarities in morphology and embryological development are proxies for the underlying genetics. Nobody halfway reasonable expects these proxies to the completely accurate and convergence is a very reasonable explanation for deviations.

    Only the UCEs are an example of something that is a problem for ToE.
    ===

    No, the unexpected developmental pathways are not examples of convergence. These unexpected findings are *differences* in otherwise similar species. With evolution what we must imagine is that over millions of years you have embryonic development evolving (somehow) leading up to, say, a frog. Then it splits giving rise to two descendant frog species. Except that in this relatively short time, with relatively little evolutionary change occurring, you have a major development pathway radically switching to a different pathway. This makes no sense. It is not uncommon, and was a major failed prediction of evolution.

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  137. Pedant:

    ======
    There are plenty of numbers for ORFans or UCEs. Thousands of DNA bases with an identical sequence between, say mouse and human, with hundreds of experiments showing no fitness impact.

    No fitness impact? From the abstract of an open-source review (published July 2008):

    "Although our knowledge of UCEs is limited, most recent studies suggest that UCEs play a functional role in vertebrate genomes, such as serving as long-range enhancers of flanking genes, regulating splicing and epigenetic modifications, and functioning as transcriptional coactivator. Most recent studies show that expression of UCEs is consistently altered in tumors, strongly suggesting these elements may also be involved in human disease such as cancer development."

    http://www.ncbi.nlm.nih.gov/pubmed/18708752
    ======

    What I was referring to is more than a hundred tests of fitness that showed now perceptible difference in mice with UCEs removed. That doesn't mean there is literally zero function, but the function difference would be difficult for natural selection to filter.

    Furthermore, even if natural selection could somehow filter on this small fitness difference, it nonetheless makes no sense. With evolution, what we must imagine is that incredibly long DNA segments are strongly selected with literally 100% sequence identity in many cases, and close to 100% in other cases. This would be astonishing and makes evolution ludicrous.

    In other words, for a 1,000 base DNA segment, there are 4^1000, or 10^602 (a 1 followed by 600 zeros) different possible DNA sequences. And evolution needs to find one of those!? This makes creating proteins seem trivial.

    The escape hatch for evolutionists here is to say that, well, there isn't just 1 sequence out of those 10^602. There are actually a great many of them. But each one is a spike in the fitness landscape, so you don't see one evolving to another. When evolution finds one of them, then it can't move. Any move degrades fitness radically.

    But even with this explanation, we must imagine that evolution finds a unique sequence where there is no gradual slope leading to it. It is a spike in the fitness landscape, so evolution simply has to get lucky, very, very lucky. The theory is ludicrous.

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  138. This comment has been removed by the author.

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  139. Cornelius Hunter:

    And what determines the developmental pathways? Genes?

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  140. Hunter:

    What I was referring to is more than a hundred tests of fitness that showed now perceptible difference in mice with UCEs removed.

    Were you referring to this paper?

    Deletion of Ultraconserved Elements Yields Viable Mice

    http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050234

    The authors, who are not as tendentious as Hunter, wrote:

    “All four elements examined in this study demonstrated in vivo enhancer activity when tested in a transgenic mouse assay (Figure 1) [6], which would suggest regulatory element redundancy as another possible explanation for the lack of a significant impact following the removal of these specific elements. Just as gene redundancy has been shown to be responsible for the lack of phenotypes associated with many seemingly vital gene knockouts, regulatory sequence redundancy [22] can similarly provide a possible explanation for the lack of a marked phenotype in this study.”

    That caution, in addition to the subsequent of studies revealing functions for many UCEs, renders your claim that they falsify evolution something less than a slam dunk.

    That doesn't mean there is literally zero function, but the function difference would be difficult for natural selection to filter.

    That would depend on the environment, populations, and time. The natural environment for wild mice is not the same as the laboratory environment.

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  141. Hunter, having shot his bolt on UCEs, reverted to his well-worn tornado in a junkyard argument, so loved by anti-evolutionists:

    In other words, for a 1,000 base DNA segment, there are 4^1000, or 10^602 (a 1 followed by 600 zeros) different possible DNA sequences. And evolution needs to find one of those!?
    ….
    But even with this explanation, we must imagine that evolution finds a unique sequence where there is no gradual slope leading to it. It is a spike in the fitness landscape, so evolution simply has to get lucky, very, very lucky. The theory is ludicrous.


    If evolution were a prospector looking for a needle in a haystack, this fistful of straws from the haystack might have purchase. But evolution is a-teleological, or so the theory goes.

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  142. Hey Neal,

    Still there?

    We know too much about nature just to chalk it all up to some warm little pond fairy tale.

    So we should go for a god-of-the-gaps fairy tale instead?

    Design is the best explanation at hand. I looked at this many years ago and didn't buy the warm little pond fairy tale and it led me to faith in a Creator, not vice versa.

    Nope, design is the laziest explanation at hand. Suppose I didn't know exactly how thunder/lightning works. Does that make Thor the best explanation at hand or could I accept that given the processes we know about processes producing electric currents and such can give me clues about thunder/lightning being a natural process? The same happens about life origins. We know enough about natural processes, energy flow, matter, et cetera, to know that life could have arisen naturally. We only not know how exactly it happened here. Given what I have learned, I don't think we will know the exact history of life's origin in our planet (clues lost in times immemorial), but I am quite convinced that we will have many possible scenarios, all well supported by scientific understanding and evidence. Only we will not know which one worked here.

    But more to the point Neal. Suppose there was no solution, that no matter how much we tried, life origin's were unexplainable. Suppose too that you knew as well as I know, that we share ancestry with the other apes, and the other primates in general. Suppose you understand the evidence for these to be irrefutable. How not knowing how life originated would invalidate that evidence? How not knowing how life originated would make our common ancestry false? If you understand my questions here, then you understand why holding to life origins and catastrophic events between long-time-separated lineages will not make evolution false. You will also understand why we see putting evolution together with origin of life and origin of the universe as nothing but a cheap trick by creationists who think that not knowing one invalidates the rest. It doesn't. Just like not knowing about quantum mechanics would not invalidate the evidence that thunder/lightning is a natural phenomenon.

    Have a great day and week, and et cetera.

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  143. Negative Entrophy said, "We know enough about natural processes, energy flow, matter, et cetera, to know that life could have arisen naturally. "

    ---

    This is on par with flies spontaneously forming from garbage. No, it just completely wishful thinking if one assumes that chemical evolution was a fact.
    ---

    Even the smallest life forms are extremely complex organisms which contain vast amounts encoded digital information. Complex, digital information is only known to arise from intelligent design. It is the best explanation.

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  144. Complex, digital information is only known to arise from intelligent design.

    And the only known source of intelligent design is human beings. Are you claiming that human beings designed life?

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  145. Pedant said, "And the only known source of intelligent design is human beings. Are you claiming that human beings designed life?"

    Are you kidding? God is a known source of intelligent design.

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  146. Neal Tedford: so what degree of perfection in nested hierarchies still qualifies Darwinism to be valid?

    Darwin didn't posit a perfect nested hierarchy. He explained the nested hierarchy, including many known exceptions.

    Neal Tedford: We've beat up the dolphin, cat and fish hierarchy enough.

    The reason why we point it out is that the vast majority of people know there is only one reasonable classification — dolphins group with cats, with fish in the outgroup. There are thousands of points of similarities in dolphins and cats that are not shared by fish, including skeletal, skin, blood, glands, brains, eyes, lungs, ears. Classification of their embryos is even more apparent. There are some points of similarity between dolphins and fish, in particular, their streamline bodies and surfaces. What you fail to realize is that this convergence is considered strong evidence for natural selection, as Darwin pointed out.

    But you're still in upside-down world. The nested hierarchy exists regardless of any scientific theory or explanation.

    Blas: Then you will have three groups of shared traits. One for each couple of animals.

    That's right. And when you look over all the traits, which two are closest in terms of observable traits; dolphin, cat or fish?

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  147. Neal:
    Are you kidding? God is a known source of intelligent design.

    So you've observed God designing things? That's great because if there's one thing ID lacks it's a mechanism. Since you've seen him in action you should be able to tell us just how it's done!

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  148. Tedford:

    Are you kidding? God is a known source of intelligent design.

    What Norm Olsen said, and this:

    That creature of your imagination is not known to have designed anything.

    First, you have to imagine that such a being exists.

    Then, you have to imagine that such a being has properties like humans only much better, including super intelligence and super magical creative power.

    Then, you have to imagine that your superhuman had desires, such as a desire to create something.

    And on and on. No end to your wishful thinking based on an inflationary projection of human behavior.

    You can't use science to prove the existence of God.

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  149. Zachriel said, "The reason why we point it out is that the vast majority of people know there is only one reasonable classification — dolphins group with cats, with fish in the outgroup."

    I'll go along with that for this simple example. Many classifications are not nearly this simple. One controversy comes when you try to force an evolutionary assumption on the classification. Conflicting data from genetic sequencing contradicts the tidy phylogenetic tree. Based on your "panoply of traits" criteria you get one result, based on genes you get a different result... The Sea Squirt, for example.

    Biological classification based on the "panoply of traits" fits better as a typology classification rather than a result of common descent. You no longer have an elegant theory, as Darwin proposed, but a tangled web.

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  150. Oh what a
    tangled web
    evolutionists weave,
    When first
    they practise to
    draw a
    tree of life!

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  151. Neal: Scott, again your analogy is flawed. We have not observed universal common descent, but we observe chemical reactions.
    Neal,

    I could respond to your objection with further details, but why should I?

    You've already demonstrated that you're not interested in having a serious discussion since you've failed to answer direct questions I've asked repeatedly.

    If I ask a question you don't like, you'll just ignore it or answer some other question I didn't ask as if you did.

    So, why should I even bother?

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  152. Zach:"That's right. And when you look over all the traits, which two are closest in terms of observable traits; dolphin, cat or fish?"

    You have to specify what do you mean by "closest".

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  153. I'd note If you do not understand a question I've asked, then you can always ask for clarification, but this has not occurred. Instead; you simply ignore them.

    On the other hand, I've repeated asked for detailed clarifications, which are often ignored.

    So, again, why should we take your objections seriously?

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  154. Sorry, I was unable to reply yesterday.

    All quotes from Cornelius.

    Which is why I was careful to say "when evolutionists present the "evidences" for evolution."

    As I already said, convergence is typically discussed in entry level textbooks. Actually, many times the concepts of homology and analogy (yes, a bit old-fashioned) are introduced together.

    ...but the limbs of the octopus, sea star and grasshopper make for a convenient example.

    Yes, it is rather simple, but I've also seen discussions with structures you consider astronomically similar; specifically the vertebrate and octopus eyes.

    No, CI is not used to explain why we need not worry about ORFans, radical differences in development pathways, etc.

    Of course CI is not supposed to explain anything. I was answering your claim that biologists ignore and give zero weigh to the data that doesn't fit CA. CI quantifies the support for a specific CA hypothesis (the sister-group relationships of the cladogram topology).

    The long list of incredible, profound similarities which, even by evolutionists' own reckoning, cannot be explained by common descent, are simply written off as lightning striking twice.

    No, total evidence is considered. Nothing is written off, I've already shown that the amount of homoplasy is considered into the evaluation of phylogenetic hypotheses. You just don't like the fact that despite all the homoplasy there might be, you can recover high support for the CA hypothesis.

    There's no lack of numbers if that is what you want.

    I know, but I didn't ask for a number of "contradictory evidence". I asked for a ratio considering the whole evidence, supporting and not supporting common descent (how many synapomorphies/how many homoplasies are required to explain the dataset), for a phylogeny that is considered to be well supported by the scientific community, but you consider to be wrong. Discuss the reported support for the tree.

    You accuse scientists of culling the data, but you only present isolated characters in isolated taxa. I put forward the challenge of total evidence. If you don't take it, say it so.

    That's strange, I presented four examples.

    Sorry, I chose words poorly. It wasn't about being "concrete", but to discuss the issue in reasonable terms. Not just cherry picking a single pair of characters. A reasonable character matrix including relevant taxa. And stick to structural characters this time, that was the topic of your post, don't get so divergent. Rant about molecular data later (but, ORFans... really?).

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  155. Cornelius,

    You should address the forelimb homology example you dismissed. This time, no arguments from incredulity, take a careful look to all the characters and the relevant taxa we presented before

    If it was such a silly example, it should be easy, shouldn't it?

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  156. Cornelius is trying to have his cake and eat it too. He has realised that a hypothesis that makes correct predictions is not necessarily right. But he also throws a hissy fit when it is pointed out that a hypothesis that makes less than correct predictions can also be correct. Wrote he in response to this:

    Bad predictions don't matter anymore.

    This goes to show that Cornelius doesn't understand likelihood arguments. Consider this: Pr(Polar bears|CA) and Pr(Polar bears|SA) are both incredibly small. According to Cornelius, this means that neither CA nor SA are very good explanations for the existence of polar bears. I.e. the probabilities of CA and SA are crap since their respective likelihoods are. But this is simply false. Knowing the likelihood of a hypothesis says nothing about it's probability. I think we can all agree that evolution of any sort would be unlikely to produce polar bears. But why would this automatically mean that polar bears were not produced by evolution?

    Cornelius also bemoans the fact that lowering the likelihood of a hypothesis can sometimes make it more favorable (via his highly disliked contrastive thinking). Well, consider this: Pr(Polar bears & grizzly bears & cats|CA) and Pr(Polar bears & grizzly bears & cats|SA) are even more incredibly small. Here, the likelihoods of both CA and SA are lower than in the example with only polar bears. But the likelihood of SA has shrunk more than has the likelihood of CA. Therefore, we conclude that CA is a better explanation than is SA. I fail to see why Cornelius has a problem with this sort of thinking.

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  157. Zachriel: The reason why we point it out is that the vast majority of people know there is only one reasonable classification — dolphins group with cats, with fish in the outgroup.

    Months later ...

    Cornelius: I'll go along with that for this simple example.

    Good. Now add frogs and dogs, larks and sharks.

    Cornelius: Many classifications are not nearly this simple.

    Quite so! Nevertheless, there is a very clear nested hierarchy across many taxa and structures. This is true regardless of any theory or explanation.

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  158. The irony about the imperfect nested hierarchy is that most of us know what Neal would claim if the nested hierarchy was absolutely perfect. “It is so perfect it must have been... .”

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  160. Cornelius: Many classifications are not nearly this simple.

    Zachriel :Quite so! Nevertheless, there is a very clear nested hierarchy across many taxa and structures. This is true regardless of any theory or explanation.

    Exactly.

    Cornelius could present an explanation for this hierarchy. In fact, he may have one which he has yet to present. Or it could be that he's one of those fish who supposedly cannot tell he's swimming in an ocean.

    But, regardless of what Cornelius actually thinks or knows, providing such an explanation would be to concede the biological complexity we observe can be explained using human reasoning and problem solving. Given this is about as close as we can get to a meaningful definition of the supernatural, this must be avoided.

    The most common tactic is to deny such a pattern exists and/or suggest we cannot know what it represents.

    We can also explain Cornelius' objections on his belief in the existence of divine revelation. Cornelius has made multiple references to the traditional hierarchy of philosophy, induction and deduction, but has repeatedly ignored direct questions as to where he thinks divine revelation fits into the equation.

    Apparently, not publicly voicing his opinion on these issues magically causes his interpretation of evidence to be immune to them.

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  161. Second Opinion: The irony about the imperfect nested hierarchy is that most of us know what Neal would claim if the nested hierarchy was absolutely perfect. “It is so perfect it must have been... .”

    We can explain what appears to be a contradiction on Neal's part in his belief in divine revelation. We, as human beings, can't use reason and problem solving to draw conclusions from the hierarchy. But Neal can know life is perfect, in that it must represent God's plan, because it was revealed to him via divine revelation in the form of the particular theodicy he holds as true.

    Specifically, Christian apocalypticism is based on Jewish apocalypticism.

    The Apocalyptic explanation for suffering includes dualistic cosmic forces of good and evil. Furthermore, everyone participates on one side or the other. There is no neutral ground. So, if you do not believe in Jesus then you must be on the side of evil. If things that exist this very moment are not, ultimately, the way the should be, then God is not truly in control, etc.

    Bart Ehrman explains Apocalyptic theodicy in more detail at 23:40 in following video:

    HOW THE BIBLE EXPLAINS SUFFERING
    - - - - - - - - - - - - - - - - - - - -
    http://www.youtube.com/watch?v=y7cmUCjnCgE

    So, I'm suggesting that it's not that Neal's actions cannot be explained, it's that we cannot explain them using what Neal has intentionally reveled in his arguments against evolution.

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  162. I wrote: So, I'm suggesting that it's not that Neal's actions cannot be explained, it's that we cannot explain them using what Neal has intentionally [revealed] in his arguments against evolution.

    Of course, Neal's views on these issues would also have implications in regards to what he accepts and rejects as science, etc., which appears to explain his silence on these issues.

    To admit he thinks the biological complexity we observe is beyond human comprehension and that he does so due to divine revelation would be rather inconvenient for his argument against evolution. Yet he fails to present a better explanation of the inconsistent position he holds.

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  163. Neal:
    Scott, again your analogy is flawed. We have not observed universal common descent, but we observe chemical reactions.

    We have not observed universal common descent because universal common descent is not an observation, it's an hypothesis. The observations are (for example) patterns in the fossil record, genetic similarities, homologous structures, bio-geographic patters, etc. These observations are all consistent and consilient with the hypothesis of universal common descent, which is one of several hypotheses that fall within evolutionary theory (others being, for example, natural selection, genetic drift, etc.).

    As I understand it, "theory" is kind of a top-level explanatory framework that may incorporate numerous hypotheses, which are supported (or not) by observations (aka "facts"), i.e.:

    Theory -> Hypotheses -> Facts (Observations)

    But someone can correct me on that (and sorry if that doesn't really add to the conversation!).

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  164. Zach:"Objectivity, parsimony, predictability."

    With objectivity parsimony and predictability body shape puts fish and dolphin in one side and
    respiratory system puts cat and dolphin in one side and "moustaches" put cat and fish in one side.

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  165. Blas:

    With objectivity parsimony and predictability body shape puts fish and dolphin in one side and respiratory system puts cat and dolphin in one side and "moustaches" put cat and fish in one side.

    Don't stop there. Please go on.

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  166. Scott, the argument from design is absolutely not an argument from ignorance. When Darwin argued his theory he was ignorant of the complex, specified information of the living cell. The more we learn about the cell the more incredulous his argument becomes... not vice versa.

    We've all seen legal cases were someone was put in prison for a long time because of strong circumstantial evidence and even false testimony only to be later vindicated by DNA testing. I really believe that DNA will be the undoing of Darwinism.

    Regarding the nested hierarchy, I've stated before that it really is neither evidence for or against evolution or creation. It is just that Zachriel's claims concerning it that have shown to be seriously flawed by the results of genetic sequencing. It was a creationist who invented the biological classification system itself.

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  167. Norm, I think that the controvery is because at some slippery point evolution = universal common descent.

    On practical terms, this is how I believe evolutionists think:

    Evolution (stuff changes) = Fact
    Evolution = Univeral Common Descent
    Universal Common Descent = Fact

    Are there any evolutionists here that don't believe UCD is a fact?

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  168. hey Neal,

    Did you at least try to understand what I wrote? Did you notice that your complains, whether true or false (but false nonetheless), don;t invalidate our common ancestry with the other apes?

    Did you notice that your way of thinking mean that Thor is the best explanation for thunder/lightning?

    I ask because it seems like I explain and explain, and nothing gets there.

    ---
    This is on par with flies spontaneously forming from garbage. No, it just completely wishful thinking if one assumes that chemical evolution was a fact.

    Nope, it is not. I know enough about those things to know that natural processes can explain the origin of life. I know enough to understand how difficult it is for you to just trust me. Still, I know enough to know that from your perspective Thor would be the best explanation for thunder/lightning, even if you won't admit it.

    Even the smallest life forms are extremely complex organisms which contain vast amounts encoded digital information. Complex, digital information is only known to arise from intelligent design. It is the best explanation.

    No, it is not. If we discover that life forms contains digital information we can only conclude that thus, natural processes can produce digital information. Why should we think otherwise? Who did the research demonstrating that only intelligence can produce such kind of information? How did they rule out other possibilities?

    For instance, the first time I heard about quantum mechanics (middle school?) the prof would tell us that there is no intermediates, that if you need 1.2 quanta for something, you would use 2 quanta. That shocked me. Anyway, I digress. The point is this, quanta are "digital" Either there is a quantum or not. No divisions, no intermediates. 100% digital.

    DNA is described as "digital information" because there are no half nucleotides. It is either A, T, C, or G. No halves. Thus, it is digital "by necessity." If you observe what's happening, you will note that, given the scale, it had to be "digital." It is almost a tautology. WIth that, the word "digital" loses it magical connotations. It s obvious, and the necessity for an intelligence behind it evaporates. (In reality it is not too strictly digital, not even in the code towards proteins, but let us not complicate matters right now.)

    Again, an intelligence is the laziest explanation. ID is to biology what Thor is to thunder and lightning. Nothing but arguments from ignorance. Gods-of-the-gaps.

    Best as always!

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  169. Guess what?

    God was designed by humans:

    http://www.talkreason.org/articles/ef.cfm

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  170. "Are there any evolutionists here that don't believe UCD is a fact?"

    I believe, like any scientific hypothesis, that it could be falsified. Suppose the search for 'shadow life' pays off, and some independent life, with no biochemical features in common with normal life is found. Normal life is well evidenced to have evolved and to evolve, and shadow life likely will also. So, there could be separate common descent.

    Does this falsify evolution? No.

    This also demonstrates why questions of abiogenesis and the deepest roots of common ancestry (one life form or two or more or a pool of genes, one code or mergers and takeovers between codes, what was it like biochemically, etc) are quite distinct from the observed and well evidenced common descent of 'normal' life.

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  171. Neal:
    I really believe that DNA will be the undoing of Darwinism.

    That's funny because I consider the discovery of DNA to be one of the most breathtaking and completely unanticipated vindications of Darwin's theory. With the discovery of DNA we finally began to understand the mechanisms that produce the variation that natural selection acts upon. When you think about it, it's really a spectacular confirmation of his original theory and was the one really important piece of the puzzle that was unavailable to him.

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  172. Blas: With objectivity parsimony and predictability body shape puts fish and dolphin in one side and respiratory system puts cat and dolphin in one side and "moustaches" put cat and fish in one side.

    Yes, and cats are the cuddly kind.

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  173. Neal Tedford: Regarding the nested hierarchy, I've stated before that it really is neither evidence for or against evolution or creation. It is just that Zachriel's claims concerning it that have shown to be seriously flawed by the results of genetic sequencing.

    The Theory of Evolution never posited a perfect nested hierarchy, so pointing to supposed anomalies while ignoring the overall pattern doesn't advance your argument. Darwin specifically noted such anomalies, and indeed, showed how convergence and hybridization were critical support for his theory, not contradictory to it.

    You've demonstrated time and again that you are not willing or not able to discuss this important pattern. It took months, months, just to get you to admit that dolphins group biologically more closely to cats than fish. But we will push forward.

    So, we have {{dolphins, cats}, fish}. If we add other organisms, a pattern should become apparent.
    http://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Tree_of_life_SVG.svg/200px-Tree_of_life_SVG.svg.png

    Here's a simplified version.
    http://www.staff.fcps.net/khughes/patterns_intro.gif

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  174. Neal,

    Are there any evolutionists here that don't believe UCD is a fact?

    If by "evolutionist" you mean someone who understands and accepts evolution, then I think that UCD is a hypothesis within evolution. It may or may not be true. But common ancestry among lots and lots of life forms is evident, and our common ancestry with many other species, such as the other primates, is true beyond reasonable doubt.

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  175. Hey guys,

    I asked Cornelius a few things in this thread*, and probably he'll reply, but I'm afraid I won't be able to answer back for a few weeks (perhaps more than a month) because I have lots of work to do. Sorry about that, Cornelius. I'll check back when I can. Until then, I'm sure the other guys will continue keeping you busy as much as always (wouldn't you be bored to death if all you had here were obsessive copy-paster bornagain77s and Joe-"I-digest-my-food-with-ribosomes" Gs?).

    Cheers!

    * Specifically, to discuss the issue of morphological homology considering the whole character matrices that cladists use. Full evidence against a phylogenetic hypothesis that evolutionists consider to be well supported. Not cherry picking a couple of homoplasies and taxa as if they can't be explained from their proposed phylogenetic context (like the different forms of mollusc eye, and other characters do for the camera eye of coleoids that Cornelius mentioned) and significantly weakening the support for the CA hypothesis. (Sorry, you all know one has to be repetitive around here.)

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  176. Squish -- grammar and punctuation must be part of evolutionary theory, judging by your aversion to them.

    Mind you, you've got good typing, for someone with "bear hands".

    Nice poe.

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  177. This comment has been removed by the author.

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  178. why dont you go and kill yourselves,it was s**m like you that taught my father this rubbish in school many years ago,and in the process you ruined his life,I swear that if i could meet one of you s**m face to face,i would dismember you with my bear hands,such is my likeness for you.

    Hugs and kisses for you, m'dear Shquishy!

    ** redacted for Cornelius' language policies.

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  179. Neal: Scott, the argument from design is absolutely not an argument from ignorance.

    Neal, as much as you might want this to be my argument, it's not.

    My point is that what we accept as a fact in science represents the best explanations of phenomena. These explanations are theory laden. To quote David Deutsch,

    "That the truth consists of hard to vary assertions about reality is the most important fact about the physical world. It's a fact that is, itself, unseen, yet in impossible to vary"

    You're augment is that we have not observed evolution would also be problematic for a number of other observations which I'm guessing you accept as a scientific fact and do not conflict with your particular theodicy.

    Neal: When Darwin argued his theory he was ignorant of the complex, specified information of the living cell. The more we learn about the cell the more incredulous his argument becomes... not vice versa.

    Here's one problem with the explanatory filter: it depends on how you define intelligence. See…

    http://www.uncommondescent.com/intelligent-design/id-in-the-uk/#comment-84107

    Note how Febble was banned despite presenting clear and respectful critique of Dembski's explanatory filter. This is par for the course at UC.

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  180. squish the fools:

    ===
    you pathetic ignorant ,absurd excuse for a rational being why dont you go and kill yourselves,it was scum like you that taught my father this rubbish in school many years ago,and in the process you ruined his life,I swear that if i could meet one of you scum face to face,i would dismember you with my bear hands,
    ===

    He who is without sin, let him cast the first stone. Meanwhile, forgive and you will be forgiven. Love your enemies and pray for them. If you love only those who love you, what reward have you? And if you hate people, you are hating God's beloved creation.

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  181. appreciate the humour gary!!

    Language spelling grammar -i was too busy chasing lovely short skirt.What a gift from god!!

    Cornelius just venting a little steam, i try my best to value every being equally with love and respect.This is my 2nd and last comment on this blog, i have been following for some time and the absurdity is growing post by ridiculous post and i cant bare to read the utter gibberish these people are prepared to foster.Keep up the good work cornelius in exposing evilutionism as the great work of satan that it has always been.

    youtube poltergeist -here you will find some interesting vids that cannot be easily debunked.Not to mention the many ghost like figures caught on camera over the last century also many cannot be easily debunked.

    blessed forever YAHWEH and his begotten messiah
    YESHUA

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  182. Hey Paul,

    Thanks. Good to see that somebody's reading those comments.

    Have a great day!

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  183. Keep up the good work cornelius in exposing evilutionism as the great work of satan that it has always been.

    Meh, "exposing evolutionism a the great work of satan" / "ridding evolutionary science of its inherent metaphysics"

    You say "to-may-toe" I say "to-mah-toe"!

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  184. Hi Scott,

    I fully confess that I would like to see them answering you and finally figure out where you are going. I think I kinda known (because after getting no answers you kinda start talking any way). Definitely a different approach.

    Have a great ... almost weekend!

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  185. Negative Entropy says:"Thanks. Good to see that somebody's reading those comments."

    Sure thing - I know it doesn't always feel like people are.

    I thought that the point about "digital information" needed reiterating. It is a fundamental point and was well made.

    Now all it needs is .. answering. However, I predict it will receive ignoring instead.

    - And you have a good day, too!

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  186. Paul, the digital nature of DNA is a great discussion and one that I certainly would be glad to discuss in great length.

    I want to be sure I understand what you said about the DNA being digital as well as "all other chemical molecules and the elements themselves". Can you expand and clarify please.

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  187. Tedford:

    I want to be sure I understand what you said about the DNA being digital as well as "all other chemical molecules and the elements themselves". Can you expand and clarify please.

    Me, too!

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  188. Neal said:"I want to be sure I understand what you said about the DNA being digital as well as "all other chemical molecules and the elements themselves". Can you expand and clarify please. "

    Sure thing, Neal. DNA is digital because - and I'm just repeating why Negative Entropy already said - it comprises a discrete set of four molecules that are conveniently referred to as "letters".

    But all molecules are themselves necessarily discrete sets of elements, arranged in certain ways. They are therefore all digital. There isn't a continuum between methane and ethane - there is a modular addition that defines the difference between them. Any subset of molecules can therefore be viewed as a set of "digital" states if one finds such terminology helpful.

    The same is true of the elements themselves. There is not a smooth gradient between helium and lithium or iodine or carbon, there are only discrete additions or subtractions of whole subatomic particles.

    So, does this make the naturally occurring elements some sort of a "digital code" for molecules? Sure, perhaps so. Yet, we understand rather well how those elements form via solar nuclear fusion. We have certainly no need to invoke a 'designer' for the creation of that digital code. Its just different numbers of protons (and their concommitant neutrons and electrons). All the molecules of life and otherwise are written in that code. In fact, as you can see, there is a hierarchy of digital codes.

    But, perhaps it is also fair to say that it seems to be a trivial use of the terms 'digital' and 'code' - I think it is - as these terms are usually only applied to anthopogenic matters. But when we only apply 'digital code' to DNA, that seems rather misleading indeed, and seems like a deliberate attempt to linguistically force the appearance of design on DNA.

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  189. "But, perhaps it is also fair to say that it seems to be a trivial use of the terms 'digital' and 'code' - I think it is - as these terms are usually only applied to anthopogenic matters. But when we only apply 'digital code' to DNA, that seems rather misleading indeed, and seems like a deliberate attempt to linguistically force the appearance of design on DNA."

    You are right about digitsl, but not about code. The DNA is code as the alphabet. And all the biology agree on this when they know the protein sequence reading the nucleotide sequence.

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  190. Blas said: "The DNA is code as the alphabet. And all the biology agree on this when they know the protein sequence reading the nucleotide sequence. "

    No I don't think that's right. The alphabet is an abstract code that is used to share concepts.

    DNA is physicochemically related to amino acids via mRNA and tRNAs. ie. it is literal, physical and real, not abstract.

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  191. squish the fool,

    You would think after nearly 70 years of trying to create even the simplest forms of life in the lab,that after the first ten years being unproductive,anyone even half sane would have given up this insanity which is evo...

    Don't you mean "given up this insanity that is ID"?

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  192. This comment has been removed by the author.

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  193. Negative,

    I'm suggesting that Cornelius' metaphysics argument can be distilled down to a claim that there is a boundary where human reasoning and problem solving cannot pass. Furthermore the location of this boundary correlates with fields of science that could be interpreted as conflicting with core fundamental Christian theodicy.

    In the case of the latter. One can easily read his blog to see this correlates does indeed exist. Of course, I've invited Cornelius to list scientific conclusions he does NOT object to which do conflict with core fundamental Christian theodicy, but I'm still waiting for a reply.

    In the case of the former, to defend the existence of the supernatural is essentially claiming there is a boundary human reason and problem solving cannot pass. Again, I've asked Cornelius if he thinks this is the case, but he has yet to reply.

    How do we know where this boundary exists where he claims it does, if it even exists at all? Why here, but not there? After all, you don't need to be non-material to evade detection. You only need to be advanced enough to manipulate the material world in such a way that you appear as if you do not exist. This includes manipulating photons, atoms, neurological signals, etc.

    If this is the case, we can explain where Cornelius draws this boundary based on observations, including what Cornelius does and does not say.

    For example, as a Christian, we know Cornelius beliefs in revelation. Should Cornelius place revelation above the traditional hierarchy of philosophy, induction and mathematical deduction it could serve as justification for claiming the location of this boundary while still rationalizing a claim that human reason and problem solving cannot pass it.

    Again, I've directly asked Cornelius where revelation fits into this hierarchy, but he remains silent.

    Until Cornelius reveals how he knows if and where this boundary exists, his objection in the case of evolution doesn't add up, as it fails to explain his lack of objection to other theories.

    Of course, I'm open to some other explanation, but none seems to be forthcoming.

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  194. You might ask, how does evolutionary theory fit into this knowledge based view of reality?

    I take a knowledge based view to reality. Take Newton's laws of motion, for example. We just got around to testing these laws less than 300 years ago. However, the evidence for these laws has been falling on every square foot of the earth for billions of years, and will continue to fall for billions of years in the future. Furthermore, as far as we know, this is the case for all of the sciences, including biological complexity.

    As such, you could say we do not discover new evidence but that we conceive explanations that better fit the evidence that has been there all along. Galileo's contribution to science was that we could ask questions, which would lead to even better questions, etc.

    However, Cornelius is claiming that there is some point where there no better questions can be asked. Ever.

    To use an analogy, one can think of a lock having a combination, which is a series of numbers. Unless we know the numbers, we cannot open the lock. But the numbers really represent a part of the explanation of the lock itself.

    Just as the evidence for Newton's laws of motion has been falling for billions of years, the evidence of how the lock works has been around for billions of years and exists right in front of us in the form of the laws of physics, atomic theory, etc. which are represented in the lock's operation. We just need to know the right questions to ask. For example, we could simply x-ray the lock or use a number of other means to "ask" the lock how it works. The right explanations, when presented as a whole, acts as a key that fits just right.

    In a way, you can think of reality as a sort of puzzle, similar to combination locks used to secure bicycles, but with an infinite number of rotating discs and that opens incrementally. The position of each individual disc represents an explanation of a particular aspect of phenomena and as the distance between the correct sequences of numbers is reduced, the lock opens a bit more. While you can't tell if any single disc is in the right position in isolation, you can create a theory of the relationship between a series of discs, rotate them and note if the lock incrementally opens or closes. And you can do so for other series of discs, then theorize the relationship between these groups, etc.

    As such, we can think of scientific theories as representing a theory of the correct sequence of digits for a particular sequence of discs. As our explanations become more accurate, the more they will form a chain which is hard to vary; just as rotating each disc closer to the correct position to the disc before and after it results in opening the lock further.

    Note this matches the process we actually use today. Theories start out as conjecture of unseen explanations for seen phenomena which we then test and refine, eventually they form part of a chain which is used to make additional observations, etc.

    I'm suggesting that we are justified in considering evolutionary theory a fact not because of philosophy, induction or even deduction, but because it's the best explanation of the biological complexity we observe. This in itself represents facts about reality.

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  195. Blas: The DNA is code as the alphabet. And all the biology agree on this when they know the protein sequence reading the nucleotide sequence.

    There's more than one sense of code, and it's easy to equivocate. Code can means a system of symbols for communication, or it can simply refer to a one-to-one or many-to-one correspondence or function.

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  196. The more I think about it, the more Gravity seems to be just as silly a theory as Evolution. Micro vs Macro gravity, for example. No one has ever seen a galaxy form, so what evidence do we have that gravity even plays a role? NONE! The fact that an apple moves towards the earth when let go only proves that small things move towards large things in our general vicinity. There is no reason to believe that it affects larger objects. Heck, we don't even know if Neptune actually orbits the sun. We have yet to see it go completely around the sun even once!

    And what of all the failed predictions of gravity? For example, objects dropped from the same height are supposed to fall at the same rate, but drop a feather and a brick and guess what...they don't! And what about balloons? Some of them don't even fall at all! They float up into the air. Or how about the Pioneer 10 and 11 spacecraft? Based on what we know about gravity, they are not where they are supposed to be. Clearly predicting their position based on gravity has failed spectacularly.

    These are but a few examples out of a vast multitude of failed predictions of gravity theory. Any one of them should be enough to falsify the theory completely, but all we get from scientists are just so stories about air density and chemistry that aren't even related to gravity. Heck, in the case of the Pioneer spacecraft we don't even get that. All we get is the dogmatic response "We don't know what's happening, but gravity is still a fact." It's all just a bunch of hand waving designed to distract from the fact that the theory has failed, and continues to fail with alarming frequency.

    The universe's expansion is accelerating. Accelerating, people!!! This observation is in absolute direct contradiction to the predictions of gravity. How can any proper scientist simply ignore that fact and pretend that gravity is even remotely viable as a scientific explanation anymore? Oh wait. I get it. Gravity pulls things together...except when it pushes things apart. Yeah, that makes perfect sense. A theory that predicts everything predicts nothing, and clearly Gravity predicts everything.

    Look, I'm not saying there is no evidence for gravity. I'm just saying that we can't legitimately call gravity a fact when there is so much evidence against it.

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  197. "No I don't think that's right. The alphabet is an abstract code that is used to share concepts.

    DNA is physicochemically related to amino acids via mRNA and tRNAs. ie. it is literal, physical and real, not abstract."

    What do you mean by abstract? there is no physicochemically relation between the ink of the letters of the alphabet and what we understand? Then what are there?

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