Monday, January 10, 2011

New Genes: Putting the Theory Before the Evidence

Imagine that you have been falsely accused of a crime. The police department has identified you as the prime suspect and they are busy gathering as much evidence against you as possible. They have constructed a theory of your motivations and actions, and as they gather the evidence they interpret it according to their theory. Their process of working from a preconceived notion of your guilt leads the police investigators to explain even ambiguous or contradictory evidence in ways that support their theory. And so it is the theory that is informing the evidence, rather than the evidence informing the theory. As crazy as it sounds, this approach is standard for evolutionists and here are three recent examples dealing with protein evolution.

Example 1: Evolving a virus

In this study evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host. Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory.

But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology.

Did the evolutionists conclude that proteins did not evolve? Did they suggest their findings are a problem for evolution? Did they even do so little as discuss the possibility that this one particular protein they studied may not have evolved?

No. There is not even a hint from the evolutionists there is a problem. In fact, the results are, in typical fashion, interpreted according to evolution. As usual, the evolutionists simply explained that evolution must have, somehow, solved the problem:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

But other mechanisms, such as homologous recombination, do not help. Homologous recombination, or any other mechanism that evolutionists can imagine, does not provide some ingenious end around the problem. Evolution cannot somehow brilliantly find the one in 10^70 long shot. The evolutionists rosy report is not data-driven, but theory-driven.

Example 2: Evolving a simple function

In this study evolutionists attempted to evolve a protein that binds to a simple, common chemical group. This function is so simple even random polypeptides sometimes have slight binding affinities. Using their laboratory process the evolutionists were able to evolve minor improvements to a random polypeptide’s binding affinity. But these small binding levels are hardly detectable. So not only is the function trivial (in order to improve fitness a protein needs to do more than merely bind to a chemical), but the levels observed are likely too small to make a difference anyway.

As with Example 1 the evolved amino acid sequences showed no similarity to nature’s sequences and when the evolutionists tried using a larger number of trials there was no sign of improved results.

Despite these feeble results the evolutionists made remarkable conclusions:

The ease of the functional development within a small sequence variety implies that enzyme evolution is prompted even within a small population of random polypeptides. … These results mark the implementation of Darwinian evolution in the system.

There is no comparison between the evolution of an enzyme and their polypeptides with minor binding affinities. And there certainly was no Darwinian evolution demonstrated in their results, for such evolution requires tangible fitness improvements which can be selected. It was good research work, but the interpretation was according to evolution.

Example 3: New genes


This example deals with new genes. When a gene is found in a large number of species, evolutionists assume it came from the common ancestor of those species, which would date far back into evolutionary history. But when a gene is found in only one or a few species, evolutionists must conclude it arose in the common ancestor of only those few species, and therefore more recently.

But how can a new gene arise so quickly? Genes that code for proteins are difficult to evolve in any case (see here and here), but the problem is accentuated when the time frame is shortened.

How a gene could have evolved is not the only problem with new genes. Such new genes, however they were supposed to have evolved, were expected to be less important. But in this study evolutionists noticed this wasn’t so.

The evolutionists compared what they assume to be new and old genes, and found no statistical difference in the importance of their functions. Knockout a new gene, and you are just as likely to kill the organism as when you knockout an old gene. In fact, the proportion of genes that are essential is similar in every assumed evolutionary age group they examined.

But once again, evolutionists do not hesitate in fitting awkward results into their framework. “These data,” the evolutionists deftly concluded, “suggest that new genes frequently and rapidly evolve essential functions and participate in development.”

In fact, outside of evolutionary theory, there is no reason to think these genes are any newer than other genes. And inside of evolutionary theory there is no scientific explanation of how proteins arise in the first place. Evolutionists are hardly in a position to assert that these data, or any other data for that matter, suggest new genes frequently and rapidly evolve, period. With little more than a bare assertion the evolutionists convert yet another unexpected finding into an evolutionary proclamation.

Evolutionists are bound to the preconceived notion that evolution must be a fact. It drives their thinking in spite of the scientific evidence, and they interpret any and all evidence in this light. It may sound crazy, but it is the theory that informs the evidence, rather than the evidence that informs the theory.

206 comments:

  1. Thanks one again for the work you do Dr. Hunter:

    I find the last study particularly revealing.

    ORFan Genes Challenge Common Descent - Paul Nelson - video
    http://www.vimeo.com/17135166

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  2. A recent review in Nature Reviews Molecular Cell Biology, by Romero and Arnold:

    Exploring protein fitness landscapes by directed evolution

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997618/

    wipes the floor with this post.

    Enjoy!

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  3. Institutional conformity can be seen in other endeavors as well. The military is one glaring example. People will literally line up and risk getting shot following authority. Evolutionists must make the sort of decision, are the consequences of conformity more beneficial than not? Those in authority control the consequences. We need to understand how the scientific elite functions to alter their behavior if the truth of evolution will ever be taught. The question of evolution after all is not scientific, but religious as your detractors prove everyday. Blogs are important, but real political pressure needs to be used.
    .

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  4. Cornelius Hunter: Example 1: Evolving a virus

    Cornelius Hunter: What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host.

    The function increased by orders of magnitude.

    Cornelius Hunter: Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved.

    Well, no. Previous work has already shown that the fitness landscape can be quite rugged, and that there may be multiple paths to a given function. The purpose of the experiment was to explore the fitness landscape.

    Cornelius Hunter: But other mechanisms, such as homologous recombination, do not help.

    Of course they do. It's easy to show that evolutionary algorithms that include recombination are much more powerful than evolutionary algorithms using point-mutation alone.

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  5. Cornelius Hunter: Example 2: Evolving a simple function

    Cornelius Hunter: In this study evolutionists attempted to evolve a protein that binds to a simple, common chemical group.

    It was also a hydrolase, one of the primary enzymatic functions.

    Cornelius Hunter: This function is so simple even random polypeptides sometimes have slight binding affinities.

    Nearly all enzymatic activity is comprised of 'simple' binding, splitting or joining.

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  6. Cornelius Hunter: Example 3: New genes

    Cornelius Hunter: When a gene is found in a large number of species, evolutionists assume it came from the common ancestor of those species, which would date far back into evolutionary history.

    Having already established the nested hierarchy, we can then make predictions concerning relationships about particular genes. These predictions can then be tested against other evidence.

    Cornelius Hunter: But when a gene is found in only one or a few species, evolutionists must conclude it arose in the common ancestor of only those few species, and therefore more recently.

    If it evolved more recently, then those "few species" will be likely be closely related.

    Cornelius Hunter: The evolutionists compared what they assume to be new and old genes, and found no statistical difference in the importance of their functions.

    That's not correct. They found that new genes caused problems *later* in development than old genes. This is consistent with diversification from a common ancestor with newer genes responsible for the differences among more closely related taxa.

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  7. excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal stage and also found in the larval stages.

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  8. Age doesn't matter: New genes are as essential as ancient ones - December 2010
    Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked."
    http://www.sciencedaily.com/releases/2010/12/101216142523.htm

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  10. Cornelius Hunter:

    They have constructed a theory of your motivations and actions, and as they gather the evidence they interpret it according to their theory.

    I'm eagerly awaiting the day when a lawyer can use the "an unidentified designer did it" argument when defending his/her client. The judge presiding over the case would immediately proclaim: "well, yes. This alternative hypothesis is possible. Any claim otherwise is pure metaphysics. Case dismissed".

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  11. bornagain77: Age doesn't matter: New genes are as essential as ancient ones - December 2010

    From the same cite: Intriguingly, in the new study, deleting many of the new genes causes flies to die during middle or late stages of development, while older genes were lethal during early development. So while ancient genes essential for the early steps of development are shared, newer genes unique to each species may take over the later developmental stages that make each species unique. For example, many new genes in the study were found to be involved with metamorphosis, the mid-life stage that drastically transforms the body plan in animals.

    In other words, the results are consistent with diversification from common ancestors.

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  12. It is much more likely that a gene has been eliminated than a gene has been formed. Why don't they simply take the 'missing gene' and add it to the one missing it. Wouldn't it be interesting if the addition caused the species with the one gene to now act like one of the species with both?

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  13. Cornelius Hunter: Example 1: Evolving a virus

    Cornelius Hunter: What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host.

    Zachriel:The function increased by orders of magnitude.


    So, let's see: The function starts out at zero. I.e., 0. Then it becomes 0.000001 of the native function. Then it becomes 0.00001. Then it becomes 0.0001. What do you know: an increase in function of two orders of magnitude!!

    Zachriel, you're being simplistic here.

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  14. Cornelius Hunter: Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved.

    ZachrielWell, no. Previous work has already shown that the fitness landscape can be quite rugged, and that there may be multiple paths to a given function. The purpose of the experiment was to explore the fitness landscape.


    And, of course, the most that happened was substitution of 3 a.a.s.

    We've been down this road before. What "evolution" did is basically trivial. What it needs to do is insurmountable---your vaunted "evolution" needs to be assisted by a library of size 10^70; that is, 10^70 different sequences derived through an error-prone PCR process (basically a random sequence generator). Tell me, Zachriel, how do you propose to "build" this size library? What resources would you use exactly? Remember that in the experiment the most they could generate was a library of 10^13. So, now, if only you could do that 10^57 times, "evolution" will be at your fingertips.

    Cornelius Hunter: But other mechanisms, such as homologous recombination, do not help.

    ZachrielOf course they do. It's easy to show that evolutionary algorithms that include recombination are much more powerful than evolutionary algorithms using point-mutation alone.


    You've used this line before. In silica experiments may or may not be realistic, by definition. And "much more powerful" is a relative term, as in: "a water pistol is a much more powerful ejector of water than a mouth-blown straw." But you're not going to kill a grizzly bear with it, are you?
    January 10, 2011 6:18 AM

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  15. I like the police analogy given that, unfortunately, they often do things in that exact way no matter how foolish and a lot of innocent persons end up in jail while the true culprit laughs it all off; And of course Darwinian dupes always do this!

    Evolutionary theory is truly the modern Alchemy.

    Circular reasoning is their most visible fallacy but seeing they accept circular reasoning as "correct reasoning" they eventually equivocate the fallacy with the correct reason process!

    Once that occurs they are almost beyond hope of remedy since acute cognitive dissonance short circuits their brains ability to distinguish circular reasoning from correct reasoning. The 2 are henceforth conflated.

    Thereafter, as we witness here with every new post, they chase their tails and go round and around the mulberry bush; interpreting the data by the theory instead of the judging the theory by the data. They go on endlessly begging the question, and never awaken to the flaws involved. Flaws that are glaring to any unprejudiced party.

    Darwinian "thought" creates a cognitive illness, as Hoyle astutely stated.

    And sadly, as Zachriel, and so many other Darwinian fundamentalist dupes show us here every day, as above.

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  17. Imagine that you have been falsely accused of a crime.

    Cornelius,

    It's likely your analogy sums up your position on evolution quite nicely.

    For example, it starts out supposing to know the accusation was false. And it does so by appealing to a source (the accused) which bypasses need to interpret evidence. It also points to the emotional outrage of those who supposedly know the accused is innocent. (Of course it would seem "crazy" from their perspective due to the knowledge they possess.)

    Furthermore, it suggests we should make an exception to how we interpret evidence due to knowledge obtained without the need to do just that: interpret evidence.

    Last, it assumes bias against this source (the accused) which is the means by which the bypass occurred.

    However, when we attempt to apply this analogy to evolutionary theory there is one significant problem. We need a way to bypass the need to interpret evidence. But this doesn't exist as science is limited by the problem of induction. Right?

    Or, in presenting this particular analogy, does this mean you do think there is a solution to the problem of induction? If so, what is it?

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  18. lino235: The function starts out at zero.

    The initial defective phage showed limited infectivity, then increased in function by 17000-fold.

    lino235: you're being simplistic here.

    Rather, you have an erroneous view of how evolution works, and the meaning of fitness.

    In regione caecorum rex est luscus. — Erasmus

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  19. lino235: What "evolution" did is basically trivial.

    Infectivity is not trivial to the virus — or to the host.

    lino235: Remember that in the experiment the most they could generate was a library of 10^13. So, now, if only you could do that 10^57 times, "evolution" will be at your fingertips.

    There was evolution using the 10^13 library.

    Zachriel: It's easy to show that evolutionary algorithms that include recombination are much more powerful than evolutionary algorithms using point-mutation alone.

    lino235: In silica experiments may or may not be realistic, by definition.

    The claim concerns the general evolutionary process, and is true whether or not it applies specifically to biological evolution. That would depend on whether recombination occurs in nature. It does.

    lino235: And "much more powerful" is a relative term, as in: "a water pistol is a much more powerful ejector of water than a mouth-blown straw." But you're not going to kill a grizzly bear with it, are you?

    The problem with evolution by point-mutation alone is that it tends to become stuck on a local fitness peak. If we start the process from a different point on the landscape, it may find a different local peak. If we have many trials, starting at different points, we can explore more of then landscape, but many peaks may still remain outside a reasonable search. Recombination avoids this problem and can harness intrinsic structure in landscapes to find global or near global fitness.

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  21. New genes in Drosophila quickly become essential. - December 2010
    Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
    http://www.ncbi.nlm.nih.gov/pubmed/21164016

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  22. This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show 'exceedingly rare' beneficial morphological changes from mutations to the DNA code.

    The Origin of Biological Information and the Higher Taxonomic Categories - Stephen Meyer
    "Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion."
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    Stephen Meyer - Functional Proteins And Information For Body Plans - video
    http://www.metacafe.com/watch/4050681

    This following video and article are much more clear for explaining exactly why mutations to the DNA do not control Body Plan morphogenesis, since the mutations are the ‘bottom rung of the ladder’ as far as the 'higher levels of the layered information’ of the cell are concerned:

    Stephen Meyer on Craig Venter, Complexity Of The Cell & Layered Information
    http://www.metacafe.com/watch/4798685

    Getting Over the Code Delusion (Epigenetics) - Talbot - November 2010 - Excellent Article for explaining exactly why epigentics falsifies the neo-Darwinian paradigm of genetic reductionism:
    http://www.thenewatlantis.com/publications/getting-over-the-code-delusion

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  23. Meyer: "Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text."

    Not true. Selection acts on expressed characteristics (phenotypes), that give some individuals advantages that others don't have. The difference might be due, ultimately, to a genetic difference, but evolution is blind to such.

    Meyer: "Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine."

    Of course. The phenotype is a combination of several factors, including genes and environment. Are you sure that "neo-Darwinists" did not know that?

    Meyer: "Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan."

    Wrong, that DNA might not be "wholly" responsible for morphogenesis does not mean that mutations cannot result in a new body plan. It only means that it is very hard to predict which mutations, and how, will result in new body plans.

    Meyer: "Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion."

    Sure, start with straw-men, follow up with non-sequiturs, and conclude whatever you want Meyer. Add "Cambrian Explosion" for dramatic effect, please.

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  25. bornagain77: "Excellent Article for explaining exactly why epigentics falsifies the neo-Darwinian paradigm of genetic reductionism"

    Reductionism is an approach of work. The idea is that you might be able to understand a whole by studying the parts. This is not always true because of the possibility for emerging properties, which are frequent in biological systems. Epigenetics does not falsify anything. It just adds insight as to why reductionism alone might not help us completely understand how life and evolution work.

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

    Dr. Don Johnson explains the difference between Shannon Information and Prescriptive Information, as well as explaining 'the cybernetic cut', in this following Podcast:

    Programming of Life - Dr. Donald Johnson interviewed by Casey Luskin - audio podcast
    http://www.idthefuture.com/2010/11/programming_of_life.html

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  27. Evolution Vs Genetic Entropy - Andy McIntosh - video
    http://www.metacafe.com/watch/4028086

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit')
    http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010
    http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00

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  28. This is the falsification of ‘reductive materialism”:

    The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/releases/2009/07/090722142824.htm

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  29. This is the falsification of non-reductive materialism:

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    BRUCE GORDON: Hawking irrational arguments – October 2010
    Excerpt: The physical universe is causally incomplete and therefore neither self-originating nor self-sustaining. The world of space, time, matter and energy is dependent on a reality that transcends space, time, matter and energy. This transcendent reality cannot merely be a Platonic realm of mathematical descriptions, for such things are causally inert abstract entities that do not affect the material world. Neither is it the case that “nothing” is unstable, as Mr. Hawking and others maintain. Absolute nothing cannot have mathematical relationships predicated on it, not even quantum gravitational ones. Rather, the transcendent reality on which our universe depends must be something that can exhibit agency – a mind that can choose among the infinite variety of mathematical descriptions and bring into existence a reality that corresponds to a consistent subset of them. This is what “breathes fire into the equations and makes a universe for them to describe.,,, the evidence for string theory and its extension, M-theory, is nonexistent; and the idea that conjoining them demonstrates that we live in a multiverse of bubble universes with different laws and constants is a mathematical fantasy. What is worse, multiplying without limit the opportunities for any event to happen in the context of a multiverse – where it is alleged that anything can spontaneously jump into existence without cause – produces a situation in which no absurdity is beyond the pale.
    For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.

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  30. This is the falsification of non-reductive materialism:

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    BRUCE GORDON: Hawking irrational arguments – October 2010
    Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com/news/2010/oct/1/hawking-irrational-arguments/

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  31. Proof That God Exists – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.
    http://www.faqs.org/periodicals/201008/2080027241.html

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  32. bornagain77,

    Let me get this straight. I show you that citations to cdesign proponentsists are useless except to show that they misrepresent science, and your answer is more of those citations?

    If you paid attention, the answers I gave you should give you a clue. It is up to you to detect the problems with the rest. A few very short points: I don't have any reason to define information to a creationist liking, nor do I have any reason to trust their biased, quote-mined, cherry-picked "data." I know little about cosmology and quantum mechanics. But given how easily I spot misrepresentations in the things I do know, I see no reason to trust a creationists/cdesign proponentsists on things I don't know. I am pretty sure that those who do know about cosmology and quantum mechanics can spot the misrepresentations there.

    Have a good week.

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  33. Believe what lie you want you will anyway

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  34. So Cornelius, I assume you must be busy preparing three comments for peer-review at the moment - or is a blog a sufficiently rigorous forum, do you think?

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  35. Hi guys.

    It is sort of really fascinating that this sort of discussions is going on and going on and going on while going nowhere.

    I just explained my own kids a couple of days ago why religion, evolution, creationism, and real science go very well with one another. There is not contradition and there is no having to choose one and reecting the other. It was so easy for them to understand that they looked at me like I must be stupid that this needs to be explained since it is a no-brainer. So, what I wonder is if kids can understand this as somethng naturally, why do adults have trouble with it?

    Sorry, this might sound sort of provocing for some I imagine. However, I think the world would be a much friendlier and better place if those people who make a big fuzz out of it would manage to realize that Religion and Science are two completely different things and that each of them has a different very valuable function, that they can exist next to one another without the the other one suffers any losses and that by realizing this, people will gain a tremendeous amount of freedom of thought, freedom of curiosity, freedom ot be open for new things, an unquestioned solid ground to stand on, and many other great things that will greatly increase the quality of live.

    Well, the backdraw is unfortunately that then relition can no longer be misused as a tool of power nor can science - instead, both become ultimate source of pleasure and serve the natural needs of our minds and much more.

    Everybody who thinks now: "What is she talking about?": stop stinking complicated. It is so easy that no complicated words are needed for that one - other than: think about it, open your eyes, and you will see.

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  36. Zach:"The problem with evolution by point-mutation alone is that it tends to become stuck on a local fitness peak. If we start the process from a different point on the landscape, it may find a different local peak. If we have many trials, starting at different points, we can explore more of then landscape, but many peaks may still remain outside a reasonable search. Recombination avoids this problem and can harness intrinsic structure in landscapes to find global or near global fitness"

    Ok. but recombination is a complez mechanism, not just an alleatory one. How do you reach recombination without recombination?

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  37. Zachriel:

    Infectivity is not trivial to the virus — or to the host.

    This forms the basis of our disagreement.

    From what I can see of the experiment, they took random sequences and looked to see what the phage could do with these sequences. From what the authors report, it appears that with all of these sequences, they ended up with new sequences differing mostly at one a.a., with some differing at up to 3 a.a. When they compared one sequence that reached, per their logarithmic scale, 52% infectivity and then compared the sequences, there was no similarity whatsoever.

    These are meager, almost inconsequential developments, comparable to the 2 to 3 a.a. ability of putative natural selection to change an organism's genome as Behe determines in his Edge of Evolution, and as becomes apparent in his latest article in QRB.

    If you take two data points: (1) a man jumps over a two-foot tall bench, (2) a man jumps over a bar six feet in the air, and then extrapolate, you'll have him "able to leap tall buildings in single bound" before you know it.

    The results are unimpressive. They confirm what we already know: organisms have the ability to adapt to environments.

    If someone is not wedded to Darwinian orthodoxy, I think the unimpressive nature of these results is obvious. Again, this is Dr. Hunter's main point in all of this.

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  38. Negative Entropy:

    Not true. Selection acts on expressed characteristics (phenotypes), that give some individuals advantages that others don't have. The difference might be due, ultimately, to a genetic difference, but evolution is blind to such.

    Speaking of phenotypes, within animals the same DNA results in very different types of cells; that is, they have different, let us say, 'phenotypes'. Is recombination and mutations the cause of these? Of course not. So how did this come about? Can we say, as in standard Darwinian thought, that this variety of 'phenotypes' is the result of competition? Where was selection in all of this?

    Wrong, that DNA might not be "wholly" responsible for morphogenesis does not mean that mutations cannot result in a new body plan. It only means that it is very hard to predict which mutations, and how, will result in new body plans.

    There hasn't been the emergence of a new body plan since the Cambrian Period over 550 mya. Isn't that long enough for mutations/recombination/natural selection to come up with something new?

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  39. Interesting. When evolutionists do more than shoehorn a mountain of data into their theory using all manner of subjective interpretation, they run to the edge of evolution.

    If new genes are said to evolve rapidly, and independent evolution is frequent, what basis do evolutionists have in saying that common genes are due to descent? Why not believe the shared genes evolved independently over and over again? Their criteria for building a phylogenetic tree based on parsimony and shared traits is suspect. Again, they are trying to have it both ways.

    For example, their theorized phylogenetic tree (based on the above criteria) for the sea squirt was a complete failure.

    Like the man who spent 30 years in prison because of evidence that shoehorned him into the crime scene, but was later vindicated by DNA evidence. This man even had witnesses that said he did it! These witnesses were just as certain as evolutionists are today of their interpretation!

    DNA will prove to be the demise of evolutionists. The theory of common descent will be relegated to the section of textbooks dealing with predicting the future based on interpreting bird poop.

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  40. Blas: Ok. but recombination is a complez mechanism, not just an alleatory one. How do you reach recombination without recombination?

    Recombination is the primitive condition. A complex mechanism is required to minimize errors during replication and to limit horizontal transfer.

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  41. Hahaha, another blow for Cornelius and his creationist fans:

    http://www.sciencedaily.com/releases/2011/01/110106145311.htm

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  42. Neal Tedford: If new genes are said to evolve rapidly, and independent evolution is frequent, what basis do evolutionists have in saying that common genes are due to descent?

    Remember! Nested hierarchy.

    Neal Tedford: Why not believe the shared genes evolved independently over and over again?

    Convergence can occur, but there is usually evidence of the history supporting the nested hierarchy. Genetics are particulate, so you have to account for that, as well, but it doesn't preclude best fit phylogeny in most cases.

    Neal Tedford: Like the man who spent 30 years in prison because of evidence that shoehorned him into the crime scene, but was later vindicated by DNA evidence. This man even had witnesses that said he did it! These witnesses were just as certain as evolutionists are today of their interpretation!

    Irony of ironies. You appeal to DNA evidence to vindicate the man, the same DNA evidence that reveals the relationships between organisms.

    Neal Tedford: DNA will prove to be the demise of evolutionists. The theory of common descent will be relegated to the section of textbooks dealing with predicting the future based on interpreting bird poop.

    Which brings to mind, did you ever support your posited objective, best fit iPod taxonomy?

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  43. Hello lino235,

    I hope you are not missing the point of my answers: Meyer misrepresented what evolution is and does. That is plainly clear, and your points don't change that, not even one little bit.

    As for your points:

    Speaking of phenotypes, within animals the same DNA results in very different types of cells; that is, they have different, let us say, 'phenotypes'. Is recombination and mutations the cause of these? Of course not. So how did this come about? Can we say, as in standard Darwinian thought, that this variety of 'phenotypes' is the result of competition? Where was selection in all of this?

    I don't see the relevance of mistaking the process of development with evolution.

    There hasn't been the emergence of a new body plan since the Cambrian Period over 550 mya. Isn't that long enough for mutations/recombination/natural selection to come up with something new?

    I guess you have a problem defining "body plan." However, if what you said were true (again, it might be, depending on your definition of "body plan"), then what was S. Meyer complaining about?

    (On the other hand, you might have the wrong idea about what evolved during the Cambrian.)

    Have a good week.

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  44. Zachriel: Infectivity is not trivial to the virus — or to the host.

    lino235: This forms the basis of our disagreement.

    Rather odd to disagree on that point. From a biological standpoint, if you produce 17000 more children than your competitors, then your descendents will overwhelm the population.

    lino235: From what the authors report, it appears that with all of these sequences, they ended up with new sequences differing mostly at one a.a., with some differing at up to 3 a.a.

    Hayashi et al., Time Series of Fitness and Amino Acid Sequence
    http://tinyurl.com/6kz7acn

    ReplyDelete
  45. lino235: When they compared one sequence that reached, per their logarithmic scale, 52% infectivity and then compared the sequences, there was no similarity whatsoever.

    Do you mean no similarity to the native strain? That is correct. So? There are apparently many possible sequences that are functional.

    lino235: The results are unimpressive. They confirm what we already know: organisms have the ability to adapt to environments.

    The experiment didn't mean to demonstrate the ability for phage to jump over the moon. And yes, it showed that viruses can *evolve* to adapt to their environments. The experiment was designed to explore the foot of the fitness slope.

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  46. lino235: So how did this come about? Can we say, as in standard Darwinian thought, that this variety of 'phenotypes' is the result of competition? Where was selection in all of this?

    There are still open questions about the origin of metazoa, but cooperation is a powerful adaptation which is found even in bacteria.

    lino235: There hasn't been the emergence of a new body plan since the Cambrian Period over 550 mya.

    Because humans are just modified deuterostomes, tubes with appendages to stuff food into one end. You know, microevolution.

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  47. In regard to phenotype and genotype. Different cells within a body might have different functions and morphologies. However, they do not have different phenotypes. This is calles specification. this is due to that different genes are turned on/off. The mechanisms behind this is highly comples and it would take a whole book to cover it all that we know about this.

    We speak of different phenotypes if a whole organism is morphological or functional different from another one that has the same genomic setup (same genes). This as well is highly complex and it would take another book to cover everything that we know about that. Many species have mechanism that lead to different phenotypes and it is in many cases possible to "controle" a specific phenotypic change/development within a lab. That can be nutritional, temperature, and many other things.

    Then, in regard to macro/microevolution. Current investigations show that a advanterous change of the genome is not (always) dependent on a accumulation of many small changes. There are examples where small changes lead to great changes. Also, there are parts of the genome that are more prone to mutations than others. With this, changes of the genome (mutations) happen more likely in some parts than in others. With this, the whole math behind calculating the likelyhood of changes within the genome due to mutations/recombinations and others is simple false.

    There are so many fascinating things that are currently under investigation and most of them actually point toward finding an explanation why and how the "seemingly impossible" is actually pretty reasonable and not a surprise. I am sorry...:)

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  48. Neal Tedford: DNA will prove to be the demise of evolutionists. The theory of common descent will be relegated to the section of textbooks dealing with predicting the future based on interpreting bird poop.

    1860: The
    1880: theory
    1900: of
    1920: evolution
    1940: will
    1960: fall
    1980: any
    2000: day
    2020: now...

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  49. Zachriel, DNA is forcing evolutionists to make up more stories to give it cover for its failed predictions.

    What about the little sea squirt? What happened to your phylogenetic tree? A theory that fails to make accurate predictions is worthless. Your nested hierarchy criteria failed to accurately define the sea squirt. What happens to your "objective" nested hierarchy for the sea squirt?

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  50. Neal Tedford: A theory that fails to make accurate predictions is worthless.

    Neal, what about theories that fail to make any predictions?

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  51. Neal Tedford: For example, their theorized phylogenetic tree (based on the above criteria) for the sea squirt was a complete failure.


    Can you provide a reference for this?

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  52. Oh come one. The phylogenetic tree changes faster than any printer can print out the current one. Is this alone evidence that evolutions is false? I don't think so. It is evidence for that scientist are doing their job. They change their minds if new evidence is found that shows that whatever they thought was currect is no longer valid. And there are things that we don't know (yet). Well, this exactly is the difference between scientists and creationists. Scientists change their mind according to knew findings and they admit if there is something that they don't know, chreationists don't. This is why chreationism is a Religion in contrast to Science which is NOT.

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  53. Neal Tedford: What about the little sea squirt?

    There is tentative evidence of a hybridization event during its evolution.

    Neal Tedford: What happened to your phylogenetic tree?

    The phylogenetic tree has always had exceptions. Darwin devoted an entire chapter of Origin of Species to hybridization.

    Neal Tedford: A theory that fails to make accurate predictions is worthless.

    There is a strong correlation to the nested hierarchy. Do you understand what is meant by a correlation? Does the Earth follow an elliptic orbit about the Sun?

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  54. Neal Tedford: For example, their theorized phylogenetic tree (based on the above criteria) for the sea squirt was a complete failure.

    Derick Childress: Can you provide a reference for this?

    Syvanen & Ducore, Whole genome comparisons reveals a possible chimeric origin for a major metazoan assemblage. J. Biol. Systems 2010.

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  55. emil, sure scientists change their mind, but this kind of a reply is typically used by evolutionists when they don't have a good story as to why their prediction failed.

    Somehow evolutionists are never able to link the failed predictions to actually questioning whether evolution itself is a failed hypothesis.

    Zachriel, the placement of the sea squirt originally and the genetic sequencing did not fit. Criteria for building phylogenetic trees and cladograms failed.

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  56. Neal Tedford: Criteria for building phylogenetic trees and cladograms failed.

    Try responding to the points raised. The nested hierarchy has never been predicted to be perfect. Darwin devoted an entire chapter of Origin of Species to hybridization.

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  57. Hi Neal,

    What about the little sea squirt? What happened to your phylogenetic tree?

    So, failing to notice, when data was not available to notice, that some organisms are the result of associations and/or hybridizations makes evolution false? That not every organism will trace back thus to a single lineage (but two instead) makes evolution false?

    A theory that fails to make accurate predictions is worthless.

    Do you mean to say that if I can't predict 100% of species to be traceable to single ancestries then the theory is worthless? I guess then that the theories that help make your computer work are worthless despite they, well, help design computers that work. After all, they don't predict which, nor how many circuits will make a mistake with 100% accuracy.

    Your nested hierarchy criteria failed to accurately define the sea squirt. What happens to your "objective" nested hierarchy for the sea squirt?

    I don't see how if we have a proper explanation of how this happened then evolution is false. Can you find the logical path from evolutionary theory to "no organisms are allowed to be the result of hybridizations." Just remember that creationist propaganda and straw-men are not evolutionary theory.

    Somehow evolutionists are never able to link the failed predictions to actually questioning whether evolution itself is a failed hypothesis.

    Those are not predictions from evolutionary theory, but hypotheses made by people working, often not even in evolution, to know whether a process runs one way or another. When those particular scientists thought it would go one way, Cornelius pretends that such was a prediction of evolution (but somehow he fails to show how exactly those are predictions of evolution, rather than hypotheses of particular scientists about something somewhat related to evolution), then, if the scientists found the opposite, Cornelius triumphantly claims that thus evolution is false.

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  58. Bravo Dr Hunter!!! You are a beacon of light among the smoke and mirrors of evolutionists.

    God Bless

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  59. hardy said: "Bravo Dr Hunter!!! You are a beacon of light among the smoke and mirrors of evolutionists.

    God Bless"

    One thing that I love about this blog is that I have no idea whether that comment was meant sarcastically or not.

    ReplyDelete
  60. Derick Childress said...

    hardy said: "Bravo Dr Hunter!!! You are a beacon of light among the smoke and mirrors of evolutionists.

    God Bless"

    One thing that I love about this blog is that I have no idea whether that comment was meant sarcastically or not.


    Poe's Law:

    "Without a winking smiley or other blatant display of humor, it is impossible to create a parody of Fundamentalism that SOMEONE won't mistake for the real thing."

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  61. Zachriel said, "The nested hierarchy has never been predicted to be perfect."

    The sea squirt fit nicely into your "objective" nested hierarchy, until it didn't. Your selection criteria for putting the sea squirt into it's "objective" classification was flawed and it failed. Your "objective" organizational structure is a human construct built in the imaginations of evolutionists based on selection criteria that has proved to be suspect.

    So much for the "objective" Nested Hierarchy.

    Next question to Derick: Is the Sea Squirt classified as a Chordate. Why?

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  62. Neal Tedford: So much for the "objective" Nested Hierarchy.

    So Neal, sea squirts don't fit into an objective nested hierarchy, but iPods do? Is that correct?

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  63. Neal Tedford: Next question to Derick: Is the Sea Squirt classified as a Chordate. Why?

    The short answer is that I'm not an expert on sea squirts, so I'm still researching this. As a general principle, I refrain from commenting on things I know little about. It's a good policy; I recommend you try it out some time.

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  64. Neal Tedford: Criteria for building phylogenetic trees and cladograms failed.

    Zachriel: Try responding to the points raised. The nested hierarchy has never been predicted to be perfect. Darwin devoted an entire chapter of Origin of Species to hybridization.

    Neal Tedford: Your selection criteria for putting the sea squirt into it's "objective" classification was flawed and it failed.

    Are you refusing to address the point, or don't you understand the point raised?

    Did you know that the human genome includes what are apparently fragments of viruses?

    Does the planet Uranus follow an elliptical orbit about the Sun?

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  65. Neal,

    If I remember correctly, sea squirts are in the phylum Chordata because their larval form, a swimming thing with bilateral symmetry, has a notochord.

    But somehow I doubt you really care about sea squirts. So, how do problems for a universal tree, such as horizontal gene transfer, endosymbiosis, and hybridization, change the fact that life forms evolve from previous life forms, and that, thus, we share ancestry with chimps and bonobos, among many other organisms? How do any horizontal heritage acquired at different stages in our evolution, like the inserted viruses mentioned by Zachriel, help you in whatever you do care about? (I don't know what you think, so I rather not venture a bad guess--What do you think? God-did-it? Flat Earth? 6000 year old Earth? Billions-of-years-old-Earth? Evolution-guided-by-some-god? Some combination of the above? Is it OK for you to tell?).

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  66. (There were other characteristics besides the notochord, but I have forgotten. I learned these things too long ago.)

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  67. All the following per Zachriel:

    Zachriel: Infectivity is not trivial to the virus — or to the host.

    lino235: This forms the basis of our disagreement.

    Zachriel: Rather odd to disagree on that point. From a biological standpoint, if you produce 17000 more children than your competitors, then your descendents will overwhelm the population.

    But not if it has to compete with someone who can produce a million. (I.e., the native strain) And 1.7 x 10^4 x 0.00000001 isn't much.

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  68. I'm having to post this response piece-by-piece. I've been trying to post it for three days now. What fun!

    Here goes:


    lino235: From what the authors report, it appears that with all of these sequences, they ended up with new sequences differing mostly at one a.a., with some differing at up to 3 a.a.

    Zachriel: Hayashi et al., Time Series of Fitness and Amino Acid Sequence
    http://tinyurl.com/6kz7acn


    You understand, of course, that this experiment is an experiment of basically artificial selection, and only minimally is it of natural selection. It was the experimenters who decided what would be cloned in each subsequent generation. They were breeders, basically. NS only notched up the intervening generations. And, of course, each of these "generations", IIRC, had "libraries" of PCR induced sequences added to them. We're dealing with huge numbers of replications, and a relatively small string of a.a.s.

    lino235: When they compared one sequence that reached, per their logarithmic scale, 52% infectivity and then compared the sequences, there was no similarity whatsoever.

    Zachriel: Do you mean no similarity to the native strain? That is correct. So? There are apparently many possible sequences that are functional.

    There are apparently many possible sequence that are minimally functional.

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  69. This is the third of probably five posts:


    lino235: The results are unimpressive. They confirm what we already know: organisms have the ability to adapt to environments.

    Zachriel: The experiment didn't mean to demonstrate the ability for phage to jump over the moon. And yes, it showed that viruses can *evolve* to adapt to their environments. The experiment was designed to explore the foot of the fitness slope.

    That's your take on it, but this is how the authors conclude their abstract:

    Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

    ReplyDelete
  70. The last part (hopefully--the last effort got me the response that I don't own my username):


    lino235: So how did this come about? Can we say, as in standard Darwinian thought, that this variety of 'phenotypes' is the result of competition? Where was selection in all of this?

    Zachriel: There are still open questions about the origin of metazoa, but cooperation is a powerful adaptation which is found even in bacteria.

    So competition is how NS is supposed to work, but we’ll insist on cooperation if need be. Is that how it works? Notice, though, that the bacteria that ‘cooperate’ don’t have the exact same genome, whereas the genome is exactly the same for all of these different cell types.

    lino235: There hasn't been the emergence of a new body plan since the Cambrian Period over 550 mya.

    Zachriel: Because humans are just modified deuterostomes, tubes with appendages to stuff food into one end. You know, microevolution.

    Well, of course, a soapbox racer and a Porsche share a similar ‘body plan’. Let’s not confuse complexity with body plan. And you’re using the assumption THAT evolution, and only evolution, could produce higher organisms--which is what is at odds, to then form the basis of your attempt to prove that evolution is therefore not trivial. You can’t have it both ways.

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  71. lino235:

    I'm having to post this response piece-by-piece. I've been trying to post it for three days now. What fun!
    ...
    This is the third of probably five posts:
    ...
    The last part (hopefully--the last effort got me the response that I don't own my username):


    Why are creationists so inept?

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  72. lino235,

    lino235 to Zachriel: When they compared one sequence that reached, per their logarithmic scale, 52% infectivity and then compared the sequences, there was no similarity whatsoever.

    Where exactly do the authors say that their sequence should become similar to the natural sequence? Where exactly does the theory of evolution say that newly evolved sequences towards some function should produce the same sequences again and again?

    Lino235 to Zachriel:That's your take on it, but this is how the authors conclude their abstract:

    But science is not based on abstracts, let alone abstracts from a single article. Science is based on evidence.

    The authors clearly stated that their aim was to explore a fitness landscape starting with random sequences. They did so with point mutations over a randomly generated aa sequence. They got what they could get given their particular conditions. After all, it is you who said:

    You understand, of course, that this experiment is an experiment of basically artificial selection, and only minimally is it of natural selection. It was the experimenters who decided what would be cloned in each subsequent generation. They were breeders, basically. NS only notched up the intervening generations.

    So then, if you understand the limitations, why are you so bent over about their results?

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  73. Zachriel,

    I would not continue the discussion where lino235 mistakes development for evolution (which continues in lino235's January 12, 2011 2:11 PM comment). It will lead you nowhere. By the time you notice that you are talking about a very different thing than what lino235 is arguing about, the whole thing will be so confused that it will be impossible to clarify anything.

    Best!

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  74. Negative Entropy:

    lino235: Speaking of phenotypes, within animals the same DNA results in very different types of cells; that is, they have different, let us say, 'phenotypes'. Is recombination and mutations the cause of these? Of course not. So how did this come about? Can we say, as in standard Darwinian thought, that this variety of 'phenotypes' is the result of competition? Where was selection in all of this?

    NE: I don't see the relevance of mistaking the process of development with evolution.

    I'm not "mistaking" the one with the other, but rather comparing them. They bear this comparison: evolutionary theory posits that the differences in physical structure seen in organisms (i.e., the phenotype) can be traced to changes in the genetic make-up, changes brought about through random mutation/gene duplication/recombination (fill in the blank). Yet, we differently organized cells--which correspond to different body-plans--that have very different physical/structural appearances, and which, nevertheless, have the very same DNA; the very same!

    Further, these cells are not in competition with one another, but, rather, work in harmony with one another such that if certain types fail, life ceases. That's a selection factor of 1.0, BTW. How do you explain this development using your idea of what evolution is. I await your explanation.

    I'm posting one thing at a time because of all the problems I've had posting here.

    ReplyDelete
  75. Negative Entropy:
    I guess you have a problem defining "body plan." However, if what you said were true (again, it might be, depending on your definition of "body plan"), then what was S. Meyer complaining about?

    If more precision is required (those who are evasive by nature seek an overly precise meaning so as to find, let us say, "escape routes". I hope that doesn't apply here.), then let me phrase it this way: 40 of the 41 known phyla existed by the end of the Cambrian.

    I posit the question again: Isn't this sufficient time for NS to have evolved entirely new body-plans/phyla? Would you care to comment?

    As to Steven Meyer, what complaint do you speak of?

    Negative Entropy:(On the other hand, you might have the wrong idea about what evolved during the Cambrian.)

    I think I have a pretty good idea of what appeared during the Cambrian. Maybe you can explain to me what "evolved" during the Cambrian. I await.

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  76. Pedant:

    Why do you assert that I am a Creationist? Do you know me? Have I stated anything in these posts that betrays this? Or is it simply because I choose to question Darwinian orthodoxy?

    What a great light you are for your side: no evidence for your characterization of me, yet you just jump to conclusions.

    Not only do you claim that I'm a Creationist, but I'm an 'inept' Creationist. Upon what basis do you make such a claim. Do you have any idea at all of the problems I had to deal with? Again, without any basis, you jump to a conclusion.

    And, of course, you're crass and rude. Wonderful. Your side must be proud.

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  77. Negative Entropy:

    I would not continue the discussion where lino235 mistakes development for evolution (which continues in lino235's January 12, 2011 2:11 PM comment). It will lead you nowhere. By the time you notice that you are talking about a very different thing than what lino235 is arguing about, the whole thing will be so confused that it will be impossible to clarify anything.

    You're asking Zachriel to avoid answering: is this because you have no answer? You'll notice I've asked you the same question in a more precise form.

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  78. Negative Entropy:
    Where exactly do the authors say that their sequence should become similar to the natural sequence? Where exactly does the theory of evolution say that newly evolved sequences towards some function should produce the same sequences again and again?

    They don't say that; but nature requires it---else we would be seeing something different in the native protein.

    And the authors tells us that a random sequence library of 10^70 is required to arrive at the native protein fitness.

    Would you like to tell me--and those who are looking on---why this is so, and what the implications are?

    NE:So then, if you understand the limitations, why are you so bent over about their results?

    Because you're misrepresenting the results, that's why.

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  79. This comment has been removed by a blog administrator.

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  80. Steven Meyers (quoted by bornagain77):

    Meyer: "Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text."

    Negative Entropy:
    Not true. Selection acts on expressed characteristics (phenotypes), that give some individuals advantages that others don't have. The difference might be due, ultimately, to a genetic difference, but evolution is blind to such.

    So, then, you're positing the possibility of a non-genetic evolutionary path. What might that look like? Or should we just believe that this can happen?

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  81. lino235: But not if it has to compete with someone who can produce a million. (I.e., the native strain)

    That's right, but the claim was that what "evolution" did was basically trivial. In fact, evolution dramatically increased infectivity starting from a randomized protein domain.

    lino235: So competition is how NS is supposed to work, but we’ll insist on cooperation if need be.

    Cooperation between related organisms can be a very effective evolutionary strategy.

    lino235: Notice, though, that the bacteria that ‘cooperate’ don’t have the exact same genome, whereas the genome is exactly the same for all of these different cell types.

    Precisely. The more closely related they are, the more likely cooperation will be an effective evolutionary strategy. This can be understood in the mathematics of game theory.

    lino235: Let’s not confuse complexity with body plan.

    You introduced the vague term "body plan". According to your claim of no new body plan since the Cambrian Explosion, a lamprey and a sparrow are the same body plan.

    lino235: And you’re using the assumption THAT evolution, and only evolution, could produce higher organisms--

    Why would you say that? Rather ,the position is that the evidence strongly supports historical evolution, not that no other mechanism, such as highly technological hominoids, couldn't produce complex organisms.

    lino235: which is what is at odds, to then form the basis of your attempt to prove that evolution is therefore not trivial. You can’t have it both ways.

    Not sure how to parse that. Trivial is often used qualitatively. There are profound differences between a primitive vertebrate from 525 million years ago, and a frog. Perhaps you don't consider an amnion or hands to be part of a body plan, in which case, frogs and humans are just modified deuterostomes, tubes with appendages.

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  82. lino235: I'm not "mistaking" the one with the other, but rather comparing them.

    Thought you were asking how they evolved.

    lino235: Yet, we differently organized cells--which correspond to different body-plans--that have very different physical/structural appearances, and which, nevertheless, have the very same DNA; the very same!

    Yes, it's an effective evolutionary strategy. Remember, all that matter is the hereditary line. If a trillion cells die to ensure continuation of the line, then it will persist in nature.

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  83. Negative Entropy:

    I know creationists love equivocation fallacies, but that's another story.

    Well, I see the invective is coming. This is a sure sign that you have lost the argument.

    As to being aggressive, I was born in New York. What do you want?

    NE:an you explain how to manufacture a computer using your idea of gravitational forces?

    Clever. But this won't work. Electro-magnetic forces are not the same as those of gravity. But here we're dealing with the very same elements: DNA, cells, cell factories, mutations, death (NS), etc. You might like to think that we're dealing with apples and oranges, but we're not.

    All of this gets right back to what Steven Meyer wrote (quoted by BA77 up above)--something you took exception to:

    "Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion."

    You see, the answer to the question: what came first, the 'chicken' or the 'egg'? is: the 'egg'.

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  84. lino235: Isn't this sufficient time for NS to have evolved entirely new body-plans/phyla?

    There were already three billion years of evolution that preceded the Cambrian Explosion. Evidence indicates that cells were already communicating and cooperating in colonial form. The emergence of larger organisms was probably slowed by the lack of free oxygen. Once this evolution began, we see a rapid radiation, exactly what one expects when a new niche becomes available, followed by a pruning of the less successful and less lucky adaptations.

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  85. OFF-TOPIC

    lino235: Not only do you claim that I'm a Creationist, but I'm an 'inept' Creationist.

    There's a known problem with blogspot where posts that appear will then disappear. You might want to save your posts in a notepad.

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  86. lino235: All of this gets right back to what Steven Meyer wrote (quoted by BA77 up above)

    Stephen Meyer's text has substantial problems. But your argument seems to be that simple changes at the lower level can't result in higher level organization. Is this correct?

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  87. Ups, sorry, I erased my answer thinking it was duplicated.

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  88. Negative Entropy:

    venturous answer to the phyla thing (venturous because I son't know if you are looking for an answer or for a gap) is as follows: What today are phyla, by the Cambrian might have been orders, or families, or genera (I don't know). This would look as if the Cambrian had representatives of many more "phyla" than those existing today. However, no all of these groups left descendants all the way to the present. In other words, given the process of evolution, we can only expect current life forms to converge into a few past forms, thus few phyla. There is also the little detail about mass extinctions that erase many organisms (and their phyla with them), and let a few (representing few phyla) evolve and conquer vacated niches. So, both, because of the catastrophic history of the planet, and because of the nature of evolution itself. Let me know if the explanation is not too clear. I suspect I assumed too much knowledge of taxonomy and biology on your part.

    I didn't know that Charles Darwin was still alive. This is exactly how he would talk and describe things.

    There's just this one, great big problem: a phyla is not an order. Don't you know that? And a body-plan is a body-plan. Don't you know that either?

    The problem with the Cambrian Explosion---which, to Darwin, would have been the Silurian Explosion---is precisely that: Darwin expected that the fossil record was incomplete and that with further investigation a whole new extended period of time would show up prior to the Silurian (Cambrian), which earlier period, per your explanation above, would contain all these "orders" on their way to becoming "phyla". (But, of course, why stop there? Why not keep going and have Phyla turn into Kingdoms? What explanation does Darwin give for everything stopping at the level of a Class? None.) Well, as I say, he stops at classes. So maybe that's why you used "Orders"---just below "Classes"---and want to stay away from "Phyla" and "Body-Plans". But here's news: there isn't any evidence that all these Phyla came about other than in a very short period of time; that is, in an explosive manner. And other than in the Phylum of Chordata and in the case of insects, nothing much has happened with those other 38 Phyla.

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  89. Negative Entropy:

    I just lost a post because of size. I don't care to reconstruct it. So here it is in its nub:

    About your venturesome explanation of the origin of Phyla: it's as though Darwin has risen from his grave.

    But, of course, we know that he was looking for an extended period before the Silurian (Cambrian in our geology), and expected that further investigation of the fossil record would show that it existed. Of course, the "pre-Silurian", as he called it, is now completely ruled out. He was wrong.

    As to the Cambrian and now: other than in the Phylum Chordata, and the insects, not a whole lot has happened. When people talk about the "tree of life", they're basically talking about Chordate evolution (evolution, as in a 'change of form', mechanism unknown).

    You're peddling a 150 year-old theory. That won't fly.

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  90. Tanks lino235 for posting almost my entire answer. I thought I lost it. As you see, not only creationists can be inept. (Yes you are a creationist, why the pretence?)

    There's just this one, great big problem: a phyla is not an order. Don't you know that?

    Not today. And if you prefer not to understand, well, then don't ask.

    And a body-plan is a body-plan. Don't you know that either?

    Again, depends on your definition. See if you find a primate body-plan in the Cambrian, then we can exchange a series of "Don't-you-know-that?" more properly.

    Why not keep going and have Phyla turn into Kingdoms?

    Oh! So you got it. Good. Thanks. I "stopped" at phyla because I try to keep it short. Otherwise I get into posting trouble (like you did). But keep guessing my malevolent motives (and Darwin's). I will stop at Order! Muahahahahahahahahahahahahaha!

    there isn't any evidence that all these Phyla came about other than in a very short period of time; that is, in an explosive manner.

    Well, if you want to ignore all evidences newer than wherever the cdesign proponentsists stopped looking, plus whatever they overlooked for some mysterious reason. Maybe. We also seem to have a different idea of what a "very short period of time" is.

    And other than in the Phylum of Chordata and in the case of insects, nothing much has happened with those other 38 Phyla.

    Again, we seem to have a different definition of "nothing much."

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  91. Zachriel:There were already three billion years of evolution that preceded the Cambrian Explosion. Evidence indicates that cells were already communicating and cooperating in colonial form.

    "He who lives by the sword, dies by the sword."

    Yes, bacterial life is believed to have been around since 3 billion years ago, or so. So, then why did it take so long to become more complex? Remember: it has a smaller genome, and it replicates faster. Why two billion years before we some some kind of colonial life form (which is: [1] controversial, and [2] right before the Ediacaran/Cambrian)? What was your vaunted NS doing all those years? Was it asleep like Rumpelstiltskin?

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  92. lino 235,

    About your venturesome explanation of the origin of Phyla: it's as though Darwin has risen from his grave.

    Thanks you! This made my day! (I wish I could add this to my C.V.)

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  93. Zachriel:

    Stephen Meyer's text has substantial problems. But your argument seems to be that simple changes at the lower level can't result in higher level organization. Is this correct?

    Yes.

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  94. Negative Entropy:

    (Yes you are a creationist, why the pretence?)

    You can't know how happy it makes me that you know exactly what I am!!

    You're using a lower-cased 'c' for 'creationist'. One would suppose that this stands in contradistinction with the upper-case variety of 'Creationist', thus allowing you to lump the one with the other. This is evasion.

    Not today. And if you prefer not to understand, well, then don't ask.

    One isn't required to understand the incoherent. You're passing off sophistry.

    See if you find a primate body-plan in the Cambrian, then we can exchange a series of "Don't-you-know-that?" more properly.

    This appears to be gross ignorance on your part, either willful or otherwise.

    I don't have to show you a "primate" 'body-plan' in the Cambrian; I only have to show you a "chordate" 'body-plan' in the Cambrian---which is easily done.

    Well, if you want to ignore all evidences newer than wherever the cdesign proponentsists stopped looking, plus whatever they overlooked for some mysterious reason. Maybe. We also seem to have a different idea of what a "very short period of time" is.


    This is all weasel-wording. Honestly, "we have a different idea of what a 'very short period of time' is." Wow.

    You mean it "all depends on what your meaning of is is!"

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  95. lino 235,

    They don't say that; but nature requires it---else we would be seeing something different in the native protein.

    Nature requires it? If newly evolved proteins with similar functions didn't look like existing ones then the existing ones would be different? Maybe you want to rethink this.

    And the authors tells us that a random sequence library of 10^70 is required to arrive at the native protein fitness.

    But you knew abut the limitations of the experiments, so this is irrelevant whether I buy it or not.

    Would you like to tell me--and those who are looking on---why this is so, and what the implications are?

    These were the calculations of these guys. So I don't really know if this "is so." Still, these experiments have their limitations, you said it yourself.

    NE:So then, if you understand the limitations, why are you so bent over about their results?

    lino: Because you're misrepresenting the results, that's why.


    Am I? Is it me who is misrepresenting the aim of the study and compounding it with a series of assumptions about what should happen "if evolution were true" according to creationist cartoons and misconceptions, rather than according to evolutionary theory?

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  96. lino235: Yes, bacterial life is believed to have been around since 3 billion years ago, or so. So, then why did it take so long to become more complex?

    Eukaryotes are highly complex cells compared to bacteria. Precambrian organisms developed complex communication and colonial structures. A prevalent theory is that lack of oxygen prevented more concentrated structures from emerging. In any case, it's not apparent why you would think millions of years is too fast.

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  97. Zachriel: But your argument seems to be that simple changes at the lower level can't result in higher level organization. Is this correct?

    lino235: Yes.

    The evolution of tetrapod legs is certainly a higher level organization, yet we can see how it occurred in incremental and selectable steps.

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  98. lino235,

    Please forgive my ignorance of the existence of a lower case and an upper case of "creationist." I hope I will be able to make amends sometime in my low-life. (More malevolent laughter in the background, of course: "I will lump Creationists with creationists. Muahahahahahahaha!")

    One isn't required to understand the incoherent. You're passing off sophistry.

    Seems like I am not. After all you later showed that you got it.

    I don't have to show you a "primate" 'body-plan' in the Cambrian; I only have to show you a "chordate" 'body-plan' in the Cambrian---which is easily done.

    If so, then there is no reason to act surprised that there are no new "body plans." But we already went through the phyla thing. No need to extend on this side.

    This is all weasel-wording. Honestly, "we have a different idea of what a 'very short period of time' is." Wow.

    There is little I can do if you think that millions of years is "a very short period" of time, and if you prefer to ignore all the evidence of previous life forms. So I rather ask if we understand the same thing. Otherwise we go back and forth uselessly as with the body-plans.

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  99. lino235,

    I didn't know that Charles Darwin was still alive. This is exactly how he would talk and describe things.

    You sure find ways of making a commenter happy. Thanks a lot for the evening conversation. Have a great rest of the week if I have no chance of coming back sooner.

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  100. Negative Entropy:

    Nature requires it? If newly evolved proteins with similar functions didn't look like existing ones then the existing ones would be different? Maybe you want to rethink this.

    If I had a million dollars, I'd be rich. Sophistry. Is that all you're capable of?

    We KNOW what nature has come up with; we can only conjecture as to what may have been. The task for evolutionists is to figure out how, via Darwinian mechanisms, these proteins came about. Waving away these difficulties by saying, essentially, that, well, it could of been different is just that: hand-waving.

    These were the calculations of these guys. So I don't really know if this "is so." Still, these experiments have their limitations, you said it yourself.

    I don't think you've fully grasped the work of these researchers. What these "guys" did was to simply extrapolate their data using the formulas they devised. Do you think they lied? Do you think it was really only 10^15 libraries they needed instead of 10^70?

    I'm not going to continue this discussion unless the quality of the responses is able to improve.

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  101. Zachriel:

    Eukaryotes are highly complex cells compared to bacteria. Precambrian organisms developed complex communication and colonial structures.

    Sorry. This is just pablum. Yes, eukaryotes are highly complex cells. Thank you for telling me this. I would have never known!

    And the chordate body-plan is more complex than yeast. So why did it take so long to form the one, and not the other?

    The evolution of tetrapod legs is certainly a higher level organization, yet we can see how it occurred in incremental and selectable steps.

    I don't think that is what Meyer meant. He's talking about body-plans (higher level), not what eventually happens to a part of the body-plan (lower-level).

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  102. Negative Entropy:
    Seems like I am not. After all you later showed that you got it.

    It's hard to come to understand incoherence, but if one applies oneself, it is possible. That doesn't mean it is no longer incoherent; only that it is understood to be incoherent.

    Here's what a contemporary said of Darwinism:

    "Where it is unoriginal, it is correct; where it is original, it is wrong."

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  103. This comment has been removed by a blog administrator.

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  104. Hey lino235,

    I was about to leave.

    Me: Nature requires it? If newly evolved proteins with similar functions didn't look like existing ones then the existing ones would be different? Maybe you want to rethink this.

    Lino: If I had a million dollars, I'd be rich. Sophistry. Is that all you're capable of?


    This was your sophistry then. That is what you said. Not what I said. I just rephrased. If that is not what you meant say so, and say what you truly meant. Here what you originally said:

    They don't say that; but nature requires it---else we would be seeing something different in the native protein.

    ---

    We KNOW what nature has come up with; we can only conjecture as to what may have been. The task for evolutionists is to figure out how, via Darwinian mechanisms, these proteins came about.

    Explaining "how" does not mean that it should include an exact "what." There is no reason to expect the very same protein to evolve every time an experiment is made (as in to have the very same, or very similar, sequence).

    Waving away these difficulties by saying, essentially, that, well, it could of been different is just that: hand-waving.

    There is no reason why the evolutionary process should repeat the very same steps nor aim to get the very same results. What you are implying is that, according to your cartoon of evolution, a planet similar to ours should have humans, plus nothing else but whatever we see in our planet today, after about 4.5 billion years.

    What these "guys" did was to simply extrapolate their data using the formulas they devised. Do you think they lied?

    Nope. I just don't know how they made their extrapolation, nor if it is valid the way they did it. Sometimes limited data might give the wrong impression of the kind of relationships between variables. But, again, does not matter. Their experiments were limited as you have attested.

    I'm not going to continue this discussion unless the quality of the responses is able to improve.

    Fine by me. After all, I was close to Darwin. Once again, thanks for the evening conversation, and have a great rest of the week.

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  105. lino235: You're using a lower-cased 'c' for 'creationist'. One would suppose that this stands in contradistinction with the upper-case variety of 'Creationist', thus allowing you to lump the one with the other. This is evasion.

    What is the difference between a Creationist and a creationist?

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  106. Negative Entropy:
    Where exactly do the authors say that their sequence should become similar to the natural sequence? Where exactly does the theory of evolution say that newly evolved sequences towards some function should produce the same sequences again and again?


    lino235:They don't say that; but nature requires it---else we would be seeing something different in the native protein.

    lino235, if you're saying what it sounds like you're saying, then you've don't have even the most rudimentary grasp of the theory of evolution. Barring a misunderstanding of what you're saying on my part, that's one of the most absurd things I've ever heard on the subject.

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  107. Derick:

    Barring a misunderstanding of what you're saying on my part, that's one of the most absurd things I've ever heard on the subject.

    Yet, the idea that experimental evolution should yield exact replicas of the products of historical evolution has precedent. From Hunter’s OP:

    They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

    Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved.

    As with Example 1 the evolved amino acid sequences showed no similarity to nature’s sequences and when the evolutionists tried using a larger number of trials there was no sign of improved results.


    And from Hunter’s previous post:

    Such experiments reveal what seemed rather obvious from biochemistry: evolutionary schemes are not likely to find the highly complex protein designs we find in nature. The results of such experiments fall short of anything close to the real thing. The resulting sequences of amino acids look nothing like what we find in nature, and the resulting functions are orders of magnitude short of what real proteins do.

    "Replay the tape a million times ... and I doubt that anything like Homo sapiens would ever evolve again"

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  108. Far above, troy said...

    Hahaha, another blow for Cornelius and his creationist fans:

    http://www.sciencedaily.com/releases/2011/01/110106145311.htm


    From the ScienceDaily story:

    In a series of experiments exploring the role of differing proteins, the scientists showed that several different strains of bacteria that should have died were rescued by novel proteins designed in the laboratory. "These artificial proteins bear no relation to any known biological sequences, yet they sustained life," Hecht said.

    Another “trivial” result.

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  109. Pedantski

    for a good post vous gagnez une chanson


    Enjoy old buddy!

    Don't forget to learn lyrics. Link is at bottom left.

    ReplyDelete
  110. lino235: What these "guys" did was to simply extrapolate their data using the formulas they devised. Do you think they lied? Do you think it was really only 10^15 libraries they needed instead of 10^70?

    Do you think they lied when they said that other mechanisms, such as recombination, would resolve the issue, but that it wasn't relevant to their particular study, which was to examine the foot of the fitness landscape?

    lino235: Yes, bacterial life is believed to have been around since 3 billion years ago, or so. So, then why did it take so long to become more complex? A prevalent theory is that lack of oxygen prevented more concentrated structures from emerging.

    Zachriel: Eukaryotes are highly complex cells compared to bacteria. Precambrian organisms developed complex communication and colonial structures.

    lino235: Sorry. This is just pablum.

    Sorry, but with all due respect, you have your pablum misplaced. You wondered why there was no significant evolution in the three billion years preceding the Cambrian Explosion. The evolution of complex cells, including eukaryotes with organelles, intracellular and intercellular communication, primitive forms of colonial behavior and organization is very significant evolution.

    lino235: And the chordate body-plan is more complex than yeast. So why did it take so long to form the one, and not the other?

    Did you choose to ignore the answer (twice now), or did you just not understand it? Oxygen levels may have been too low to allow the density of cells required for metazoan development.

    Zachriel: The evolution of tetrapod legs is certainly a higher level organization, yet we can see how it occurred in incremental and selectable steps.

    lino235: I don't think that is what Meyer meant. He's talking about body-plans (higher level), not what eventually happens to a part of the body-plan (lower-level).

    So you don't consider the evolution of legs and hands, feathers and wings, to be a higher level of organization? As for primitive architecture, there are important clues to this in the evolution of Hox genes, which regulate segmentation and appendages. This was preceded by the development of adhesion and intercellular communication, which was preceded by intracellular communcation.

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  111. lino235: The task for evolutionists is to figure out how, via Darwinian mechanisms, these proteins came about.

    Start with the nested hierarchy. Though, there is no single, accepted phylogenetic tree for all proteins, they do form very large families and superfamilies, supporting common descent within these groupings. There are various ideas how these larger groupings may also be related.

    lino235: Here's what a contemporary said of Darwinism: "Where it is unoriginal, it is correct; where it is original, it is wrong."

    Heh. Darwin's theory is considered the foundation of all the biological sciences, while the contemporary, what was his name again?

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  112. Zachriel said, "Start with the nested hierarchy. Though, there is NO SINGLE, ACCEPTED phylogenetic tree for all proteins, they do form very large families and superfamilies, supporting common descent within these groupings."


    ----
    So much for the "objective" nested hierarchy evidence. I must give you credit for at least being forthright about it.

    Wasn't support for common descent based on the "objective" quality of the nested hierarchy?

    That was supposed to be the big difference between evolution and human designs according to you and Derick.

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  113. Neal Tedford: So much for the "objective" nested hierarchy evidence.

    As you have repeatedly shown, you don't understand the nested hierarchy, and won't support your claim concerning iPods, so it's not clear what your point might be.

    Concerning proteins, we have several large limbs, each with many branches. Concerning morphology and genomes, we have nearly complete trees. What's interesting is that these hierarchies match, that is, where we have data, the hierarchies are in very good alignment. This strongly indicates a common origin for the patterns.

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  114. Neal Tedford: That was supposed to be the big difference between evolution and human designs according to you and Derick.

    Funny, I don't remember discussing evolution with you in a long while, Neal. What I do remember is your proposal that iPods form an objective nested hierarchy, and your months-long failure at demonstrating this. (I mean, you never even elucidated what criteria one would use to group iPods - do we group by model number, or by number of components, or by type of components, or something else?)

    And if memory serves, Zachriel was trying to explain to you the nested hierarchy of species before, whereas in the snipped you quoted, he was talking about a nested hierarchy of proteins.

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  115. @Zachriel
    "Concerning proteins, we have several large limbs, each with many branches. Concerning morphology and genomes, we have nearly complete trees. What's interesting is that these hierarchies match, that is, where we have data, the hierarchies are in very good alignment. This strongly indicates a common origin for the patterns."

    I don't think it is quite accurate to argue this way. Proteins and morphology are dependent on the genome (phenotype follows genotype which is known also from independent experiments like cloning), so this is not really independent evidence. Also fossils are only independent in so far as they are from a different time.

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  116. Negative Entropy:
    This was your sophistry then. That is what you said. Not what I said. I just rephrased. If that is not what you meant say so, and say what you truly meant. Here what you originally said . . .

    It appears I didn't see the second question mark. So I misunderstood you. My apologies.

    However, you're suggesting that nature, and NS (remember, "nature" is a part of "natural"), is indifferent to the sequence.

    To a degree---a very SMALL degree---this is true. But the fact that NS can't walk up the rugged landscape unless its aided by 10^70 libraries of already prepared random sequences, suggest that, realistically, NS is helpless to climb the landscape.

    Why? Because specificity is needed. And not just any old kind of specificity, but functional specificity.

    Another way of saying this is this: unless you have the right sequence, it won't fully function the way the native protein does.

    This probably means that this sequence stretch is involved with multiple tasks, and has multiple entanglements, and to "fully" function, all of those needs must be met. The net result of these layered entanglements is a highly specified sequence, one that NS is incapable of achieving.

    To all the others:

    Most of you comments strike me as nit-picking silliness; so you'll understand if I'm not interested enough to reply.

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  117. Zach "Evidence indicates that cells were already communicating and cooperating in colonial form. The emergence of larger organisms was probably slowed by the lack of free oxygen."

    More difficult to explain is why the new enviroment could not be occupied by the procariotic cells, faster in replicating and adapting than the eucariotic cell.

    Just curious which is the evidence of cooperation between cells in that period?

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  118. Blas: More difficult to explain is why the new enviroment could not be occupied by the procariotic cells, faster in replicating and adapting than the eucariotic cell.

    That's sort of like asking why if humans evolved from monkeys why there are still monkeys. Or if happen to be a metazoa to think that there was no evolution of consequence before the origin of metazoa.

    It's a mistake to equate primitive with simple. The primordial world was highly complex with many types of niches. Prokaryotes and the ancestors of eukaryotes were highly diversified.

    The origin of eukaryotes is still a bit of a mystery, but the advantage of cooperation between mitochondria and the larger cell seem apparent.

    Blas: Just curious which is the evidence of cooperation between cells in that period?

    Well, sponges predate the Cambrian Explosion. Due to common descent, a good way to try to further explore the question is to study extant organisms that bridge the boundary between metazoa and the single-celled world, such as sponges or choanoflagellates.

    Nichols et al., Early evolution of animal cell signaling and adhesion genes, Proc Natl Acad Sci 2006.

    King & Carroll, A receptor tyrosine kinase from choanoflagellates: Molecular insights into early animal evolution, PNAS 2001.

    El Albani et al., Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago, Nature 2010.

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  119. Zachriel, yes the primordial world was complex from the get go. Like bacteria utilizing quantum mechanics.

    You said that "the origin of eukaryotes is still a BIT of a mystery".

    There you go again with minimizing the problems.

    Geocentric math encountered a BIT of mystery also.

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  120. lino235:
    "To a degree---a very SMALL degree---this is true. But the fact that NS can't walk up the rugged landscape unless its aided by 10^70 libraries of already prepared random sequences, suggest that, realistically, NS is helpless to climb the landscape. "

    Do you really think NS is only acting on random de novo sequences?

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  121. Zach:"It's a mistake to equate primitive with simple. The primordial world was highly complex with many types of niches. Prokaryotes and the ancestors of eukaryotes were highly diversified. "

    Well if you stick at the theory that is a fact NS "keep" the genes that had advantages, the problem is wich advantages NS keeps as old and news remains.

    Zach:"Well, sponges predate the Cambrian Explosion. Due to common descent, a good way to try to further explore the question is to study extant organisms that bridge the boundary between metazoa and the single-celled world, such as sponges or choanoflagellates.

    Nichols et al., Early evolution of animal cell signaling and adhesion genes, Proc Natl Acad Sci 2006.

    King & Carroll, A receptor tyrosine kinase from choanoflagellates: Molecular insights into early animal evolution, PNAS 2001.

    El Albani et al., Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago, Nature 2010."

    So the evidence is assuming Common descent true, and actual genes were similar to precambrian, unicelalular pre cambrian could interact.

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  122. Hey lino235,

    However, you're suggesting that nature, and NS (remember, "nature" is a part of "natural"), is indifferent to the sequence.

    NS is completely and absolutely indifferent to sequence. NS only acts on function. So, for NS it is inconsequential whether it was sequence X or sequence Y. Now, of course, not every sequence will provide a function. But there is no reason to think that only the sequences we see in nature would have done. There is a lot of data suggesting the opposite though.

    To a degree---a very SMALL degree---this is true.

    I don't see how you would know if the degree is small or incommensurable.

    But the fact that NS can't walk up the rugged landscape unless its aided by 10^70 libraries of already prepared random sequences, suggest that, realistically, NS is helpless to climb the landscape.

    Well, for one it is not a fact, but a calculation by some guys about a particular experimental setting (whether I buy it or not). For another, there is no reason to think that this experimental setting represents all that is available for NS to act upon.

    Why? Because specificity is needed. And not just any old kind of specificity, but functional specificity.

    It all depends on who are your competitors. If a function is just arising, then it is enough with an incipient function. Again. I don't see any reason why this would require the sequence to evolve into a similar one to those existing in nature.

    Another way of saying this is this: unless you have the right sequence, it won't fully function the way the native protein does.

    There is no data to suggest that only the sequences existing in nature would do. So, the "right sequence" should read "any of the right sequences."

    This probably means that this sequence stretch is involved with multiple tasks, and has multiple entanglements, and to "fully" function, all of those needs must be met. The net result of these layered entanglements is a highly specified sequence, one that NS is incapable of achieving.

    I don't see how incipient functions and incipient entanglements would not have done to begin with, and thus no reason why they could not arise by NS and co-evolve into sequences, that, given each other, only seem to be "highly specified." But you tell me, how would you distinguish highly specified sequences from co-evolved to the point of high interconnectedness? (Have you heard of compensatory mutations?).

    G'night!

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  123. Zachriel: Concerning proteins, we have several large limbs, each with many branches. Concerning morphology and genomes, we have nearly complete trees. What's interesting is that these hierarchies match, that is, where we have data, the hierarchies are in very good alignment. This strongly indicates a common origin for the patterns.

    second opinion: I don't think it is quite accurate to argue this way. Proteins and morphology are dependent on the genome (phenotype follows genotype which is known also from independent experiments like cloning), so this is not really independent evidence. Also fossils are only independent in so far as they are from a different time.

    Many aspects of the genome are independent of the phenome and proteome. These independent traits also support the nested hierarchy.

    Blas: So the evidence is assuming Common descent true, and actual genes were similar to precambrian, unicelalular pre cambrian could interact.

    There are multiple lines of evidence (including possible direct evidence of colonialism preceding the Cambrian Explosion), but the fact that unicellular organisms have proteins that fit the nested hierarchy which can act as precursors for functions essential to multicellularity, is significant support for the hypothesis.

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  124. If I'm not mistaken a number of proteins are necessary to allow for multicellularity. So you have to change a number or precursors at once.

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  125. And to go from a prokaryote to a eukaryote you have to do more than just add mitochondria. There the nuclear membrane, chromosomes, etc.

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  126. natschuster: If I'm not mistaken a number of proteins are necessary to allow for multicellularity. So you have to change a number or precursors at once.

    It's a gradual process with adhesion and intercellular communication finding roles even in single-celled life.

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  127. Pedant: "Hahaha, another blow for Cornelius and his creationist fans."

    The discovery of another intelligently designed protein?

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  129. Why do I bother?

    Well, doing real biology is impossible without at least considering evolution. Many might not realize this. However, regardless if it comes to conversation biology, genetics, molecular biology, you name it, one automatically runs into evolution with any kinf of research that is done.

    Examples: Why and how does an introduced species at some point become invasive (destructive) to the environment into which it was introduced? Well try to do this without evolution and you get stuck in nowhere land. However, finding answers to this question might allow us to prevent (further) damages and this might well be vitally important for our existence on this world.

    Another example: Why and how do viruses and bacteria change over time so they become immune against existing drugs? Same thing.

    Another one: Will and if yes how will organisms and their communities change with the currently occurring climate change? Good luck without evolution.

    Somehow it seems to me that creationists would like to get over with evolution and everything that has to do with it. I don’t understand why but if this is what they want then if they would succeed then that means no biological research any more that might actually help us.

    It would much be like in the old days: not allowing the idea that the earth might be round and forbidding to go out onto the see with a ship trying to get around the world.

    It is just sad that there are people in our modern world that still go such a way even though we really should know better by now.

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  130. John wrote:

    The discovery of another intelligently designed protein?

    It seems you exhibit a common, implicit assumption with many who post here.

    For example, the researchers who created the proteins in question had knowledge of their actions, which bypassed the need to interpret empirical evidence in regards to their origin. No discovery actually occurred, yet you suggested this represented "The discovery of another intelligently designed protein."

    However, when we attempt to apply this to proteins supposedly designed by non-human designers, we cannot bypass the need to interpret empirical evidence due to the problem of induction. Some implied assumption seems to be missing from your comment.

    The question becomes: do you think there is an answer to the problem of induction? If so, what is the solution? Otherwise, it's unclear how you could consider this "The discovery of another intelligently designed protein."

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  131. Scott, I am not the one who you asked but the implied assumptions that is missing is (or a problem of induction):

    A Non-human creator exists

    With this the following fallacy was then formed to explain the existance of the protein:

    Since we have no explanation for how this protein could have been evolved, the non-human creator must have created it.

    There is not only a problem with induction and implied assumption...

    Formal logic, that was a long time ago... but if I would write my computer programs according to that kind of logic. OH MY GOSH....

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  132. The discovery was Pedants when he read the article. Of course, I don't think the word discovery threw you off, but more likely, "another". The point is, his link is hardly a "blow for Cornelius and his creationist fans", but rather it reinforces the fact that proteins require ingenuity, foresight, and skill to design.

    It was a blow similar to that felt from the metaphor to human technology last week. I'm still curious who is represented by the human designers in this type of reasoning.

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  133. John, the interesting thing is that troy linked the paper because he thinks it is supporting his position. So we have two different interpretations here. Yours was one that I could have predicted because it is along known lines of ID interpretation. I'm just wandering why you think he linked the paper in the first place? Do you think he is stupid? What other reason could there be?

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  135. John,

    How do they train you to be this cynically dishonest? Do they test you for a basic tendency towards these "talents"?

    I would appreciate it if you told me exactly when did I present the metaphor as a blow to Cornelius and fans, rather than as an intent at explaining something to you. This would be an opportunity to show some decency. If you have any left.

    The metaphor is about how as backgrounds increase, the probability for something arising using such backgrounds increases. Natural processes would have build such backgrounds, not "human designers." But you knew that the metaphor was about this.

    The article pointed by Pedant is a blow to Cornelius and fans because they demonstrate that there is no need for sequences to be similar to natural ones to have a functioning protein. But you knew this too.

    Happy?

    (What about you tell us what kind of a creationist you are? Do you accept an evolution "guided" by an "intelligent designer"? It is fair for you to tell, right? Or you rather keep it to yourself to be able to shoot the fallacy of the designer at will, no matter how much evolution you are implied to be accepting? So, come to terms, young earth? old earth? flat earth? guided evolution? Let us know, please.)

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  136. Negative Entropy: The article pointed by Pedant is a blow to Cornelius and fans because they demonstrate that there is no need for sequences to be similar to natural ones to have a functioning protein. But you knew this too.”

    I cannot find this claim by Cornelius that they had to be similar to function. Also, when he says natural, he’s referring to things he thinks were designed. So when you post an article that says you can design things that don’t seem similar to what exists in nature, to us it just means you designed something new, not that existing proteins weren’t designed themselves. Because I can create a bicycle does not mean God did not create camels. I felt the reason he was talking about similarity was because we took the virus from a KNOWN state of MUCH higher fitness and were testing to see if there might be incremental fitness gains within this particular segment. An increase in similarity would indicate that evolution was progressing stepwise back to the known function that was closeby. Another fair result, would be if the function was restored but with a different sequence or structure - another peak in the landscape. Little headway was made in each case, and while it might not be the nail in the coffin for the powers of random mutation, the results seem more compatible with a “design inference”. The link that was brought up was not only about designed proteins, but about entirely new proteins who’s function was able to replace enough of what was knocked out for an organism to survive. In the original experiment, that would be like the scientists restoring the original sequence themselves, or designing one of their own to replace the original function. In no sense would it be random or natural in the way you mean natural.

    Negative Entropy: “Happy?”

    I’m happy in general, but in regards to your reply, let’s say I’ll always try to be optimistic.

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  137. Negative Entropy: “(What about you tell us what kind of a creationist you are?
    It seems you would most likely refer to me as a “YEC fundy”.
    Negative Enropy: “Do you accept an evolution "guided" by an "intelligent designer"?”
    I believe in de-evolution. Dust has much higher fitness. It can tolerate higher and lower temperatures, has a longer lifespan, requires no nutrients, etc.. We seem to be evolving toward becoming dust. The reason we see dust now is because of all the different types of arrangements of dust that have been available to select from over time, the types that have been able to remain as dust are still visible today. As for it being guided, I’m Molinistic about that. If God knows everything, he knows about every cosmic ray and every mutation that will ever happen. So in that sense, by allowing this or that, you might say it’s guided. But for our purposes, the word random still has value. All energy in the universe may never theoretically be able to be described by an algorithm and so could be considered random and DNA and its repair mechanisms orderly and designed to illustrate order on a backdrop of chaos, but on the other hand you might describe every quanta of energy ever propogated as precisely designed and the purpose of the DNA machinery is to show that order on a canvas of life when no signal would otherwise ever be able to be detected. As far as origins, I see no better explanation than Genesis. If some piece of evidence comes along that invalidates years of research on my part, while disappointed, I would turn to Visnu, then maybe to Odin, then maybe to something like Xeno (nah just kidding). Still, any yet nameless supernatural being would be a better explanation than the traditional form of common decent from what I can see.

    Negative Entropy: “It is fair for you to tell, right? Or you rather keep it to yourself to be able to shoot the fallacy of the designer at will, no matter how much evolution you are implied to be accepting?”
    Sure it’s fair. But up to this point, I’m pretty sure I haven’t been shooting the ‘fallacy of the designer”.
    Negative Entropy: “So, come to terms, young earth? old earth? flat earth? guided evolution? Let us know, please.)”
    Young life, either/or on the age of earth, oblately spherical, and special creation.

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  140. I'm sure I'll come back later and all the repeats I deleted will be necessary again. :D

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  141. emil:

    ===
    I agree, it is fascinating ...
    ===

    Post deleted. Please, no language or abbreviations.

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  142. troy:

    ==============
    A recent review in Nature Reviews Molecular Cell Biology, by Romero and Arnold:

    Exploring protein fitness landscapes by directed evolution

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997618/

    wipes the floor with this post.

    Enjoy!
    =========

    http://darwins-god.blogspot.com/2011/01/hierarchy-of-evolutionary-apologetics.html

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  143. Paul:

    ===
    So Cornelius, I assume you must be busy preparing three comments for peer-review at the moment
    ===

    No Paul, religion trumps science.

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  144. John:
    ====
    I believe in de-evolution.
    ====

    Now you're talking!

    youtube.com/watch?v=DCpxSzacbyc

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  145. John,

    I cannot find this claim by Cornelius that they had to be similar to function.

    Then you should read his last three or four OPs (plus others). Such idea is the basis for the fallacy of improbabilities that he repeats in his latest OP (next to this one).

    Also, when he says natural, he’s referring to things he thinks were designed.

    I know. My guess is that this is why he thinks that he should present them as if they were the only possible solutions. (Though he sure knows much better than that.)

    So when you post an article that says you can design ...

    But that was not the point. So nothing else here for me to say.

    You forgot to show me when I used that metaphor as a blow to Cornelius and fans, rather than as an intent at explaining something to you. But I guessed you wouldn't.

    See ya.

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  146. John,

    Thanks for explaining your beliefs. I guessed you would not answer that one either. This means I still have to learn a lot more about you YEC fundies. Are you a Calvinist? (Might be another bad guess.)

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  148. John wrote:

    The discovery was Pedants when he read the article. Of course, I don't think the word discovery threw you off, but more likely, "another".

    John,

    I wasn't thrown off. I was pointing out how your comment was ambiguous and represented equivocation based on the specific details of the article Pedant referenced. This includes your supposed clarification regarding "another" discovery.

    Pendant was informed about the origin of the proteins in question by the author of article. And the author was informed of the proteins origin by researchers who actually created them. In other words, the origin of the proteins was not discovered by the interpretation of empirical observations.

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  149. -- continued --

    However, If by 'another' you're refereeing to supposedly non-human designed proteins, this would be equivocation since we have no way of bypassing the need to interpret evidence. That is, unless you think there is an answer to Hume's problem of induction - and that answer was used to determine the origin of supposedly non-human designed proteins.

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  150. John wrote:

    The point is, his link is hardly a "blow for Cornelius and his creationist fans", but rather it reinforces the fact that proteins require ingenuity, foresight, and skill to design.

    Please show where the researchers intepreted empirical observations which indicated design was *necessary* for proteins to sustain the bacteria that was mutated.

    Also, to reference Cornelius' first example, the researched discovery that artificially designed proteins that "showed no similarity to the native sequence" could replace a protein "which is supposed to have evolved."

    I'd also note the artificial proteins in question were not designed for any particular function. Instead, they were designed to fold in stable three-dimensional structures. To quote the article...

    Hecht and his research group set about to create artificial proteins encoded by genetic sequences not seen in nature. They produced about 1 million amino acid sequences that were designed to fold into stable three-dimensional structures.

    Specifically, the intelligence your'e appealing to was blind to protein function. Again, to quote the article…

    Once the team had created this new library of artificial proteins, they inserted those proteins into various mutant strains of bacteria in which certain natural genes previously had been deleted. The deleted natural genes are required for survival under a given set of conditions, including a limited food supply. Under these harsh conditions, the mutant strains of bacteria died -- unless they acquired a life-sustaining novel protein from Hecht's collection. This was significant because formation of a bacterial colony under these selective conditions could occur only if a protein in the collection had the capacity to sustain the growth of living cells.

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  151. -- continued --

    Given that it's likely your position assumes intelligence, in the case of the concrete biological complexity we observe, was *not* blind to protein fitness, it's unclear how this actually represents "the discovery of another intelligently designed protein" either.

    It's logically possible that protein folding was inevitable due to some design applied to the laws of physics or the resulting chemical elements which they inevitably formed, but this falls outside the theory of evolution. Nor does the theory exclude the logical possibility that the concrete functions of proteins we observe in nature were miraculously brought about by a supernatural agent.

    Instead, evolutionary theory suggests it wasn't necessary.

    Just as the claim that one can drive a car from NYC to San Francisco doesn't exclude optionally traveling across a body of water in a ferry, being towed behind a train while traveling though Nebraska, being transported across Wyoming in the cargo hold of an airplane, or even being supernally levitated over potholes or road construction. While they are logically possible, none of these things are excluded by the claim.

    Perhaps God wanted us to have five fingers, rather than four, six or some other number that would have naturally appeared otherwise. If God is omniscient and omnipotent, he could have flipped the right switches in our genome and we'd be none the wiser. Evolutionary theory doesn't rule this out either. However, we lack an explanation as to why a supernatural agent would create the specific concrete biological complexity we observe. We have five fingers because - that's just what the designer must have wanted.

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  152. Sorry Negative Entropy, the first post I made disappeared. Here it is;

    Negative Entropy: "How do they train you to be this cynically dishonest? Do they test you for a basic tendency towards these "talents"?"

    Yes, in creation school we have a class, cynical dishonesty 101. It's about how to avoid the real issues and get at the interlocutor's style or motives. I'm so busted :D

    Negative Entropy: "I would appreciate it if you told me exactly when did I present the metaphor as a blow to Cornelius and fans, rather than as an intent at explaining something to you. This would be an opportunity to show some decency. If you have any left."

    I was referring principally to Pedant (didn’t see at first he was reposting the link from troy), but as I don't feel it to be a "blow" in the sense of a striking fist, but rather as evidence compatible with the design position, I put your metaphor in this same category regardless of the type of impact you intended it to produce.

    Negative Entropy: "The metaphor is about how as backgrounds increase, the probability for something arising using such backgrounds increases. Natural processes would have build such backgrounds, not "human designers." But you knew that the metaphor was about this."

    I certainly knew what you intended to show from the metaphor, but the problem is that the ability of "natural processes" to "build such backgrounds" is precisely what is being questioned here. The fact that human technology looks designed and is also known to have a designer is not without consequence to the point of the analogy. I could use the same metaphor to show you that, rather than reinventing a unique protein for the same task in every organism, an intelligent designer might as well reuse existing tools in each design.

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  153. John: I could use the same metaphor to show you that, rather than reinventing a unique protein for the same task in every organism, an intelligent designer might as well reuse existing tools in each design.

    But, if like human designers, wouldn't be so limited into forming a consistent nested hierarchy.

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  154. Zachriel said, "But, if like human designers, wouldn't be so limited into forming a consistent nested hierarchy."

    Consistent, except for exceptions?

    The grouping of organisms is based on criteria that is selected by humans. The criteria that is used failed, for example, to group the sea squirt consistently or objectively. The nested hierarchy is a human construct of patterns determined by the criteria selection. Change the selection criteria and you lose consistency. Evolutionists are suffering from confirmation bias. If the criteria for biological organization was strictly based on genetic sequencing, your whole tree of life would be thrown into complete confusion.

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  155. Neal Tedford: Consistent, except for exceptions?

    Sometimes, the exceptions can help demonstrate the overall pattern, such as with endogenous retroviruses. But that requires understanding the pattern we're discussing, something you have repeatedly shown you don't.

    Neal Tedford: The nested hierarchy is a human construct of patterns determined by the criteria selection.

    Neal Tedford, you have for many weeks now refused to justify your claims. Do you still say there is an objective best-fit nested hierarchy for iPods? Or have you changed your position again?

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  156. Zachriel, sure there is an best fit nested hierarchy for iPods. Nothing has changed regarding this position. Whenever you have a group of objects that share varying degrees of similarity, those objects can be grouped from least inclusive to most inclusive. But, it is all based on the selection criteria used. I have taken "best fit" to mean a component by component comparision. You and Derick make it a point to be disagreable to the point of the trivial to force your own conclusions. You are obviously capable of critical analysis, why don't you apply that same ability it to evolution???

    In reality, exceptions to the rule are a violation of consistency. You are apparently willing to live with a lot of exceptions. That's called inconsistency. It's just more subjective thinking. If a man robs a bank once a year, he may think that he is a good citizen because he is consistently not robbing a bank 364 days a year. The police have a different opinion.

    You bring up the elliptical orbit of the planets as a comparison. This is not quite the same thing. A better comparison would be like saying the planets follow a circular pattern but with some exceptions. LOL

    You can't say that the nested hierarchy is strong evidence for evolution when exceptions don't falsify that claim. You might think of explanations for the exceptions, but if evolution survives just fine with exceptions, what's your point? Is it again subjective? How many exceptions do you allow before you admit inconsistency? Is that number subjective?

    Evolutionists merely accommodate the nested hierarchy.

    The problems with your nested hierarchy go deeper though, because, as I pointed out with the sea squirt, the genetic sequencing yields a different result than a hierarchy based on morphology and parsimony, etc. Your selection criteria is suspect and therefore shewing your results as you want them. What do you say?

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  157. Neal Tedford: The grouping of organisms is based on criteria that is selected by humans.

    It is a little bit sad Neal. You were on the right track with your criticism but then screwed up badly. It is in principle a valid point to question the selection of the criteria. But this does not spare you from looking at the actual data and make your criticism concrete.

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  158. Neal Tedford: sure there is an best fit nested hierarchy for iPods. Nothing has changed regarding this position.

    Then you certainly won't mind providing the specific traits you used to arrive at that conclusion. Derick Childress was the iPod taxonomist, but it's been so long since he posed the question, he may have since retired.

    Neal Tedford: Whenever you have a group of objects that share varying degrees of similarity, those objects can be grouped from least inclusive to most inclusive.

    Books don't form a best-fit nested hierarchy. There are many different, equally consistent classification schemes.

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  159. Neal Tedford: You are apparently willing to live with a lot of exceptions... You bring up the elliptical orbit of the planets as a comparison.

    But you didn't answer the question. Does the planet Uranus follow an elliptical orbit around the Sun?

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  160. Zachriel, elliptical. An elliptical orbit is not a circle with exceptions. Furthermore, the elliptical orbit of uranus and the other planets is precise and predictable. Your analogy fails on all grounds.

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  161. Neal Tedford: Zachriel, elliptical. An elliptical orbit is not a circle with exceptions.

    It only took a few dozen attempts for you to answer the question. But no, Uranus does not follow a mathematical ellipse. When the anomaly in the orbit of Uranus was discovered, it could have meant that the Theory of Gravity was wrong. Or it could have meant there was another body affecting its orbit. Le Verrier predicted a planet, Neptune, "with the point of his pen," first observed in 1846.

    So, no. The orbit of Uranus is not an ellipse. It's very close to an ellipse though, but is affected by the gravity of the other planets, especially Jupiter and Saturn, and in this case, Neptune.

    (The Earth's solar orbit is not an ellipse either, largely because of the Moon, but the orbit *is* convex.)

    So, should they continue to teach children about elliptical orbits?

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  162. Zachriel, no. They should teach it like it really is otherwise they'll be mistaken like I was. I was aware of the effect of the other planets but not to that extent. Very important details are lost when one is not accurate, and so too with evolutionists using the nested hierarchy pattern as evidence without serious qualifications... especially when your not simply pointing out a pattern, but trying to support a hypothesis.

    But dumbing down evolution is really what is left in biology books. Deceit is probably too strong except for some of the well known evolutionary textbook examples. As CH points out in his newest article, by the time the evolutionary research reaches the kids it's pretty much an exaggerated fairy tale.

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  163. Neal Tedford: I was aware of the effect of the other planets but not to that extent.

    It's pretty close to an ellipse, and treating a planet's orbit in isolation from the rest of the universe is a good first approximation. Similarly, the biological nested hierarchy is not perfect, but it is a clearly recognizable pattern. Nor was it ever posited to be perfect, even by Darwin. He devotes an entire chapter to hybridization.

    Do you understand what is meant by a correlation?

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  164. Hey John!

    Yes, in creation school we have a class, cynical dishonesty 101. It's about how to avoid the real issues and get at the interlocutor's style or motives. I'm so busted :D

    Hum, interesting. I always thought it was more like a handbook for apologetics. Chapter one or so. Also, I thought it was more about "Moving the goalposts and sending red-herrings discretely while someone is still explaining a first answer to you" or "Keeping your interlocutor confused by adding loads of issues to avoid having to admit that you already got an answer."

    I put your metaphor in this same category regardless of the type of impact you intended it to produce

    And regardless of the misinterpretation you gave it by doing so. Again, part of that handbook I suppose (or cynical dishonesty 101, given that it might actually require a full course load).

    I certainly knew what you intended to show from the metaphor, but the problem is that the ability of "natural processes" to "build such backgrounds" is precisely what is being questioned here.

    Then the honest thing to do was say that you got the idea, but that you doubt nature can build such background. The game of "mistaking" the metaphor into an "inability" to explain things to you without a "designer example" is mere rhetoric.

    Anyway, see ya. Oh, before we forget, you are a Calvinist, right?

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  165. Scott: "I wasn't thrown off. I was pointing out how your comment was ambiguous and represented equivocation based on the specific details of the article Pedant referenced. This includes your supposed clarification regarding "another" discovery."

    Yeah, you are looking way too deeply into it. We know the scientists designed the proteins. I'm putting words in Pedant's mouth about natural proteins being designed and this one therefore being "another", but the point was obviously to elicit a response, which it did.

    Scott: "In other words, the origin of the proteins was not discovered by the interpretation of empirical observations."

    Yay! You figured it out even though I apparently made it hard for you.

    Scott: "However, If by 'another' you're refereeing to supposedly non-human designed proteins, this would be equivocation since we have no way of bypassing the need to interpret evidence."

    See, you got what I was saying. I wasn't saying this proved the already existing ones were designed, I was saying it doesn't help the case that they WEREN'T designed.

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  166. John,

    You said: I'm putting words in Pedant's mouth about natural proteins being designed and this one therefore being "another", but the point was obviously to elicit a response, which it did.

    And you don't see anything dishonest in doing that, right?

    I already know what I can expect from you, but I never dreamed of a creationist admitting that much.

    Life is full of surprises.

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  167. Scott: "Also, to reference Cornelius' first example, the researched discovery that artificially designed proteins that "showed no similarity to the native sequence" could replace a protein "which is supposed to have evolved."

    Which word in this sentence fragment is the subject? If you're wondering why he was talking about similarity, I adressed this above.

    Scott: "I'd also note the artificial proteins in question were not designed for any particular function. Instead, they were designed to fold in stable three-dimensional structures."

    At first I did not notice this from the article, but it is in the original. I will take out "foresight" from the quote that bothered you. Still, they were designed to fold and they produced 4 copies of about a million different versions about 100 in length. By the way, they tested to see if they catalyzed what the auxotrophs were missing but they did not (at least not at detectable levels). Nor did they enable bypass pathways.

    Scott: "Given that it's likely your position assumes intelligence, in the case of the concrete biological complexity we observe, was *not* blind to protein fitness, it's unclear how this actually represents "the discovery of another intelligently designed protein" either."

    Can you tell me the subject of this sentence? I think it's "this", but the commas are throwing me off the antecedent.

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  168. Negative Entropy: "And you don't see anything dishonest in doing that, right?

    No, because I'm doing it to show him what it seems he's saying. It's a perfectly honest means of discourse if people understand we are taking opposite positions.

    Negative Entropy: "I already know what I can expect from you, but I never dreamed of a creationist admitting that much."

    Spare me the drama :P

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  169. Neal wrote:

    In reality, exceptions to the rule are a violation of consistency. You are apparently willing to live with a lot of exceptions..

    And, as a someone who appeals to an all powerful and all knowing being, you seem to be unwilling to live with any exceptions. If something is prophesied, it's guaranteed to come true, or the prophecy is false. However, the predictions of scientific theories are not prophecy.

    Scientific theories are a function of the underlying explanation of the phenomena that theory encompasses. They represent potential outcomes that cannot stand alone and subject to cause and effect. This includes causes which are outside and not necessarily related to the theory itself.

    Prophecy, however, is supposedly either based of foreknowledge of what will actually occur or a supernatural ability to make that specific outcome actually occur. As such, prophecy reflects an empirical mandates of reality. If this empirical observation is not observed, the prophecy is false.

    Despite the obvious difference, Cornelius, and many other theists like yourself, seem to interpret evolutionary predictions as if they were prophecy.

    If the phylogenetic tree of life was prophecy, the outcome would be an empirical mandate of reality. God would either know life would fit the tree perfectly, based on his omniscience, or he would cause life to fit the tree perfectly using his omnipotence. As such, any variation, such as the occurrence of HGT, would have been foreknown or would be absent unless God intended it to occur.

    God can't be all knowing yet not know HGT would / did occur. God cannot be all powerful if the introduction of HGT was unintended outcome of his actions.

    But since the phylogenetic tree of life is based on the explanation of evolutionary theory, rather than prophecy, then variations of HGT are not necessarily falsifications.

    As such, we cannot evaluate predictions of scientific theories as if they were empirical mandates independent of the underlying explanations they are based on. To do so is clearly a category error.

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  172. Hey John!

    John: No, because I'm doing it to show him what it seems he's saying. It's a perfectly honest means of discourse if people understand we are taking opposite positions.

    So it is honest to misrepresent what others say because they know they did not say that, and they know that you do so only because you are taking the opposite position? Nice cop out.

    John: Spare me the drama :P

    Now being surprised is drama? Ah! Sorry, we are "taking opposite positions." Got it!

    :P

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  173. John wrote:

    Yeah, you are looking way too deeply into it.

    Are you suggesting there is no difference between a researcher concluding a protein is designed thorough the process of interpreting empirical observations and knowing a protein was designed because a researcher designed that protein as a step in an experiment? Really?

    I'm putting words in Pedant's mouth about natural proteins being designed and this one therefore being "another", but the point was obviously to elicit a response, which it did.

    So, you weren't equivocating to actually make any sort of real argument, you were equivocating to elicit a response, Right?

    I wrote: "In other words, the origin of the proteins was not discovered by the interpretation of empirical observations."

    John wrote: Yay! You figured it out even though I apparently made it hard for you.

    Yes, John. Despite your efforts to be ambiguous and disingenuous, I noticed how you cherry-picked the article and equivocated on the type of discovery that was made.

    John wrote: I was saying it doesn't help the case that they WEREN'T designed.

    Again, while presenting a knee-jerk creationist response to designed to elicit as response, you failed to notice that the intelligence you were appealing to was blind to function.

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  174. John wrote:

    Which word in this sentence fragment is the subject? If you're wondering why he was talking about similarity, I adressed this above.

    I'm sorry, John. I can't understand this paragraph because you misspelled "addressed."

    I should have wrote:

    "Also, to reference Cornelius' first example, the [researchers discovered] artificially designed proteins [which] "showed no similarity to the native sequence" [yet] could replace a protein "which is supposed to have evolved."

    This is in direct reference to Example 1: Evolving a virus in Cornelius' OP.

    John wrote:

    At first I did not notice this from the article, but it is in the original.

    Just so I'm clear, you read the article but somehow missed the primary reason the experiment was performed in the first place?

    I will take out "foresight" from the quote that bothered you. Still, they were designed to fold and they produced 4 copies of about a million different versions about 100 in length.

    So, human beings are not the product of foresight? Is this really your position? Because, again, the intelligence you're appareling to here was blind to fitness.

    John wrote: Can you tell me the subject of this sentence?

    Please see above.

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  175. Negative Entropy: "So it is honest to misrepresent what others say because they know they did not say that..."

    Strictly speaking I didn't put words in his mouth, but in the example that's bothering you right now, I stated what he might as well have said, as far as it contributed to the argument.

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  176. Scott: "Are you suggesting there is no difference between a researcher concluding a protein is designed thorough the process of interpreting empirical observations and knowing a protein was designed because a researcher designed that protein as a step in an experiment? Really?"

    Probably in your mind, but I have no idea the mental gymnastics you went through to imagine it.

    Scott: "So, you weren't equivocating to actually make any sort of real argument, you were equivocating to elicit a response, Right?"

    If natural proteins are also designed, then I wasn't equivocating. That's the point of the discussion.

    Scott: "Yes, John. Despite your efforts to be ambiguous and disingenuous, I noticed how you cherry-picked the article and equivocated on the type of discovery that was made."

    I bet the place where you are going to pin this new gold star has barely any room left!

    Scott: "Again, while presenting a knee-jerk creationist response to designed to elicit as response, you failed to notice that the intelligence you were appealing to was blind to function."

    It was a reasonable oversight from the summary, but the force of the argument from design of the structure remains as we know this is only a fraction of the sequence space and they produced over a million versions of their fold. Also the "rescue" described in the summary is quite a bit less glamorous in the original.

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  177. Scott: "I'm sorry, John. I can't understand this paragraph because you misspelled 'addressed.' "

    You can see there were multiple choices for subject which would cause you to be saying different things, so I wasn't nitpicking.

    Scott: "Also, to reference Cornelius' first example, the [researchers discovered] artificially designed proteins [which] "showed no similarity to the native sequence" [yet] could replace a protein "which is supposed to have evolved."

    I'm quite happy to agree with you that if the researchers in the article Cornelius cited tried their hands at designing a more stable protein domain, then it would be much more likely to increase infectivity.

    Scott: "Just so I'm clear, you read the article but somehow missed the primary reason the experiment was performed in the first place?"

    No, I was pretty certain that any sequences designed by the team would not be similar to anything found in nature simply because of the size of sequence space. I thought it was funny that they did an NCBI-BLAST search, you know, just to make sure!

    Scott: "So, human beings are not the product of foresight? Is this really your position? Because, again, the intelligence you're appareling to here was blind to fitness."

    No, if you examine my original quote, you will realize that by removing the word foresight, it would then read, "The point is, his link is hardly a "blow for Cornelius and his creationist fans", but rather it reinforces the fact that proteins require ingenuity and skill to design". Lack of evidence for X when you are not testing for X is certainly not evidence against X.

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  178. John,

    Let's look at what you originally wrote…

    The point is, his link is hardly a "blow for Cornelius and his creationist fans", but rather it reinforces the fact that proteins require ingenuity, foresight, and skill to design.

    I'd would happily agree If you had said

    When the researchers designed these proteins, they exhibited ingenuity, foresight, and skill.,

    but we knew that already. This wasn't a conclusion gained by interpreting observations of the experiment. Researchers actually created proteins in a lab as part of the experiment, so their design was directly evident. And the writers of the article were informed of that evidence.

    However, you actually wrote …"rather it reinforces the fact that proteins require ingenuity, foresight, and skill to design."

    Which proteins are you referring to? All proteins? Proteins that were designed? Proteins we know were designed by researchers? You've conveniently omitted this detail. This is the equivocation I'm referring to.

    Again, if the latter, we knew that already. But if you implied the former or its predecessor, there are no direct observations that inform us that proteins found in nature were actually designed. To reach this conclusion you'll need to interpret observations, present arguments, etc. And the link referenced was relevant to the argument / interpretation in Example 1: Evolving a virus in Cornelius' OP.

    Given the above, I'm suggesting your comment is attempting to disingenuously conflate protein origin derived from direct observation and protein origin derived by interpreting observation, which is subject to the problem of induction.

    However, it could be that you think the origins of proteins we observe in nature are somehow immune to the problem of induction. Which is why I asked if you thought there was a solution to the problem in an earlier comment.

    Furthermore, even if we remove "foresight" from your quote I don't' think you agree with this either. Do you think God must be 'clever' or be 'skilled' at creating proteins, since these traits are supposedly *required* to design them? I don't think you do.

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  179. John replied:

    I'm quite happy to agree with you that if the researchers in the article Cornelius cited tried their hands at designing a more stable protein domain, then it would be much more likely to increase infectivity.

    John, I'm referring to the relevance of the link that Pendant quoted and Troy referenced earlier to Cornelius' Example 1: Evolving a virus from the OP.

    Specially you wrote:

    The point is, his link is hardly a "blow for Cornelius and his creationist fans", but rather it reinforces the fact that proteins require ingenuity, foresight, and skill to design.

    My reply contrasts the results of the research in the link to what Cornelius wrote. I'm actually quoting from the first part of his OP : Example 1: Evolving a virus.

    "… to reference Cornelius' first example, the [researchers discovered] artificially designed proteins [which] "showed no similarity to the native sequence" [yet] could replace a protein "which is supposed to have evolved."

    To quote from this section of the OP.

    What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host. Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

    Again, the link is relevant because it suggests proteins which show no similarity to those found in nature could replace proteins that are thought to have evolved.

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  182. -- continued --

    This is a blow to the argument that it's statistically unlikely evolution could find protein Y, which provides functionality X.

    In at least one case (the experiment referenced), we've discovered that proteins other than Y can also be substituted to provide functionality X. Furthermore they can be substituted despite showing no similarity to protein Y. Finally, regarding your attempt to appeal to the intelligence used as part of implementing the experiment, this intelligence was blind to function.

    You might claim that, in the case of human beings, this intelligence was not blind to function. For example, God may have wanted us to have exactly five fingers. As such, he could have somehow miraculously intervened to ensure we ended up with proteins that resulted in exactly five digits (a specific function) rather than proteins which could have naturally produced four, six or some other number of digits.

    However, evolutionary theory doesn't exclude this possibility. Instead, it assumes it's not necessary. And since it's your claim that the intelligence who designed human begins was *not* blind to fitness, you're the one who needs to make the case for any particular concrete function was actually intended by design.

    Do you think God is really concerned with the exact number of digits on our hands? If so, why?

    If not, which parts of human beings *were* designed for specific function and on what basis did you reach this conclusion?

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  184. Scott: "Which proteins are you referring to? All proteins? Proteins that were designed? Proteins we know were designed by researchers? You've conveniently omitted this detail. This is the equivocation I'm referring to."

    I was referring to proteins we know were designed by the researchers. It seems you're finally reading some of what I've been writing. Thank you. And my original comment was in no way equivocation.

    Scott: "Again, if the latter, we knew that already."

    If you knew, then why feign ignorance this long?

    Scott: "But if you implied the former or its predecessor, there are no direct observations that inform us that proteins found in nature were actually designed."

    Well I did not directly observe these scientists either, I had to trust a written record of their actions. But their work, if true, does have implications for what was required to generate proteins many times larger and more complicated.

    Scott: "Given the above, I'm suggesting your comment is attempting to disingenuously conflate protein origin derived from direct observation and protein origin derived by interpreting observation, which is subject to the problem of induction."

    I'll try not to use anymore arguments with you that involve induction.

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  186. Scott: "Again, the link is relevant because it suggests proteins which show no similarity to those found in nature could replace proteins that are thought to have evolved."

    I already explained the only reason he brought up similarity was because there was a KNOWN fitness peak within that segment of the gene. He made no claim that other sequences could not arise that would replace the function lost. That is why he also evaluated the rise of infectivity apart from the similarity to the original segment. In the study then cited, this would be comparable to evaluating the fitness level after the cell was resuced.

    The link cited says in effect the same thing as the paper CH cited, when given a large library of sequences, part of a previously knocked out function can sometimes be partially restored. Except in the new link, the proteins were all designed to fold which sort of makes up for an entire gene being knocked out instead of just a segment.

    Scott: "This is a blow to the argument that it's statistically unlikely evolution could find protein Y, which provides functionality X."

    No it is not. It it also not a blow to the argument that it's statistically unlikely evolution could find proteins other than Y to provide functionality X (which is what I think you're getting at). Against neither case does it provide contrary evidence precisely because evolution was not involved. If the researchers concluded that intelligent design was necessary to restrict selection to over a million variants, all of which were designed to fold, this is the opposite of random mutation. When there is the smallest success, it can then hardly be credited to the powers of random mutation.

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  187. Scott: "Furthermore they can be substituted despite showing no similarity to protein Y."

    As I mentioned above, the test showed that none of the 18 variants replaced the function of what was knocked out, so there would no longer be any reason to assume similarity was necessary. Even if it was the same function, it would still not be necessary for them to show similarity, although similarity might strongly imply the same solution was being rediscovered. CH gave other sequences a fair shot by discussing infectivity apart from sequence.

    Scott: "Finally, regarding your attempt to appeal to the intelligence used as part of implementing the experiment, this intelligence was blind to function."

    But it was not blind to creating a library of over a million different folding sequences. I'm certain that if the researchers in the article CH cited had been able to prepare a library of stable domains this size, they would have seen much better results apart from sequence similarity also. Then you could claim victory for evolution there too. Get it?

    Scott: "However, evolutionary theory doesn't exclude this possibility. Instead, it assumes it's not necessary. And since it's your claim that the intelligence who designed human begins was *not* blind to fitness, you're the one who needs to make the case for any particular concrete function was actually intended by design."

    So, unless I go down a list of "particular concrete function"s making a case here and there that they were designed by intent, you will continue to use this study to show the power of evolution? How about we back up the claims about floor wiping, and blows to Cornelius first. If you can concede that this study illustrates more about what design is like than what evolution is like, I will oblige you with more examples of what designers are capable of.

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  188. John wrote:

    I was referring to proteins we know were designed by the researchers. It seems you're finally reading some of what I've been writing. Thank you. And my original comment was in no way equivocation.

    John,

    It was clear you were appealing to the fact that, in designing the experiment, the researchers designed the proteins in question. This was obvious because I've seen this sort of hand waving used by anti-evolutions many times. I'm referring to what appeared to be implied conclusions you drew since your comment seem to group proteins designed by researchers with proteins we find in nature.

    I wrote: "Again, if the latter, we knew that already."

    John wrote: If you knew, then why feign ignorance this long?

    If we knew this already, and your comment was actually limited in scope to proteins we knew were designed by the researchers, then why bring it up in the first place? What's the point in repeating the obvious?

    John wrote: Well I did not directly observe these scientists either, I had to trust a written record of their actions.

    John,

    Scientific theories use the unseen (a posited underlying explanation) to explain the seen (observed phenomena which theory encompasses.) In this context, the researchers having created the proteins in question would still be considered observed phenomena (the seen). However, this is not the case in regards to proteins we observe in nature.

    For example, we would explain researchers designing proteins (the observed phenomena) with the explanations posited by theories of neuroscience, cognitive theory, etc. (the unseen) However, we do not observe non-human designers, let along non-human designers designing proteins. Nor could we observe them if they did so in the past without a time machine, etc. As such, a conclusion that proteins in nature were designed, or had evolved naturally, would be subject to the problem of induction as they would represent an unseen explanation. Empirical observations alone are insufficient to get us there.

    This is the distinction I'm attempting to convey.

    John wrote: But their work, if true, does have implications for what was required to generate proteins many times larger and more complicated.

    So exactly what are these implications? Again, even if we remove "foresight" from your quote, does this mean God must be clever or skillful since theses properties are necessary for designing proteins? Or was this specifically directed at finite human designers?

    Again, if the latter, this is rather non-controversial, which seems to suggest this another example of the typical hand waving we see here all the time.

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  189. John wrote:

    I already explained the only reason he brought up similarity was because there was a KNOWN fitness peak within that segment of the gene.

    John,

    Here's the problem. As I mentioned earlier, Cornelius often posts articles that imply experiments have unintended goals or he treats evolutionary predictions as if they were empirical mandates of realty. He then appeals to the fact that these supposed goals, outcomes or predictions did not come to pass, which supposedly indicates evolution is bad science.

    Again, I'll refer to Example 1: Evolving a Virus. Here's the setup.

    In this study evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

    Now, compare this with the abstract. Would you say this is an accurate representation? For example, were the researchers trying to reconstruct the entire virus? No, they were exploring the fitness landscapes of the g3p minor coat protein. Did they "simply" the process? No, they were focused in on a particular gene because it was critical in the effectively of the virus. I could go on, but the fact that even Cornelius felt it was necessary to create an entirely separate post on this same paper reflects the disconnect.

    Then, as usual, he points out how everything failed to turn out as expected. Even this "simplified" experiment failed miserably to meet it's supposed goals. What were those silly evolutionists thinking?

    What they discovered was that the evolutionary process could produce only tiny levels of functionality (in this case the virus’ ability to infect a host). Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

    […]

    The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult.

    […]

    The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

    If the flaws in the arguments presented are not obvious to you, then It's unclear if further discussion would be fruitful. We can say the same regarding the relevance of the paper Troy posted. In fact, it's unclear that Cornelius would have written his follow up article, as it appears to be a direct response to Troy's comment. Again, this sort of presentation is par for the course here.

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  190. -- Continued --

    However, you seem to be referring to the actual work in the paper Cornelius linked to, rather than the misrepresentation found in the OP.

    Troy's paper is also relevant here because it describes the use of directed evolution to explore fitness space. How is that relevant? To quote the paper: "Proteins can be tuned to adapt to new functions or environments via simple adaptive walks involving small numbers of mutations."

    We may not knot be able to predict which functions or environments these proteins will be suited for, but we've been able to use trial and error to create organism suited for specific goals not found in nature. Are these modified organisms as efficient at achieving these goals as organisms found in in nature? Given the above it seems unlikely. However, evolutionary theory does not suggest particular fitness or efficiency in nature was specified.

    Also "Directed evolution has also shown how mutations that are functionally neutral can set the stage for further adaptation." I could elaborate on this, but I think the relevance is obvious.

    Now, If I understand you correctly, you're suggesting that God could have created and exploited this same process in creating the biological complexity we observe.

    Sure he could. Evolution doesn't suggest that he couldn't. But, scientific theories do not merely represent logical possibilities; they represent explanations about observed phenomena.

    What is the underlying explanation as to why God, or any other designer, would create this specific process then manipulate it in this specific way to achieve the specific biological complexity we observe?

    ID fails to present any explanation. "That's just what the designer must have wanted"

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  191. John wrote:

    But it was not blind to creating a library of over a million different folding sequences.

    What you've described is an empirical observation of phenomena: one or more researchers designed sequences so they would fold into proteins as part of the experiment. What you need to do next is explain how you can reach the specific conclusion implied in the OP (Evolutionary theory isn't overwhelming collaborated by evidence or falsified by observations of proteins in nature) based on this observation.

    However, it seems that the majority of the arguments so far depend on implicit assumptions that everything was designed. which is not an assumption of evolutionary theory. This is also despite the fact that Cornelius supposedly is neutral and claims to present no solution of his own.

    So, unless I go down a list of "particular concrete function"s making a case here and there that they were designed by intent, you will continue to use this study to show the power of evolution?

    Please see my previous comment. The fact that "Proteins can be tuned to adapt to new functions or environments via simple adaptive walks involving small numbers of mutations." is an incredibly useful feature of biology. Evolutionary theory, is an explanation that includes this observation, among others.

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  192. Scott: "If we knew this already, and your comment was actually limited in scope to proteins we knew were designed by the researchers, then why bring it up in the first place? What's the point in repeating the obvious?"

    My comment was not limited in scope to those in the study troy cited. My comment was short because it was obvious. The problem was that what was obvious was not taken into account when it was claimed this was a blow to CH.

    Scott: "This is the distinction I'm attempting to convey."

    Yes, I understand you have a dim view of inductive reasoning. It's odd that you wrote all that, since you still seem to be using inductive reasoning yourself.

    Scott: "So exactly what are these implications?"

    Do you really care? It involves inductive reasoning. Let me know if you change your mind on that, and I'll let you know what the implications are.

    Scott: "Again, if the latter, this is rather non-controversial, which seems to suggest this another example of the typical hand waving we see here all the time."

    Hehe, "rather non-controversial"... hedging your bets to the end eh?. But yes, by using inductive reasoning, it would seem that God must be clever and skillful. As for this being "typical hand waving", perhaps your problems using inductive reasoning are manifesting themselves here also.

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  193. Scott: "Here's the problem. As I mentioned earlier, Cornelius often posts articles that imply experiments have unintended goals or he treats evolutionary predictions as if they were empirical mandates of realty. He then appeals to the fact that these supposed goals, outcomes or predictions did not come to pass, which supposedly indicates evolution is bad science."

    You have quite a problem then apparently. I hear this objection alot, "Experiment X was carried out to disover whether Y or not Y, but opponent is unfairly drawing conclusion A from the data".

    Scott: "Now, compare this with the abstract. Would you say this is an accurate representation? For example, were the researchers trying to reconstruct the entire virus? No, they were exploring the fitness landscapes of the g3p minor coat protein."

    Again, I just care about the data. I care about what they did, not what they were trying to do or hoped to do. The authors brought up the comparison to wild type fitness, the required library to obtain it, and similarity to the original sequence. Abstracts are written after the fact, and one can often tell from the language employed whether a researcher was hoping for more or just "exploring". I don't really care.

    Scott: "Did they "simply" the process? No, they were focused in on a particular gene because it was critical in the effectively of the virus."

    Who cares why? You guys are arguing over weasle words that don't affect the data. Go ahead and cut out his motive mongering and insert the authors claims of "exploring". It doesn't change what happened.

    Scott: "Then, as usual, he points out how everything failed to turn out as expected. Even this "simplified" experiment failed miserably to meet it's supposed goals. What were those silly evolutionists thinking?"

    I hereby give you permission to draw your own conclusions from the data, for example; "what ought we to expect to evolve given the library size, number of generations, number of bases randomized, selection pressure, etc." Only sheep care about what the authors might or might not want to show. As I said, I don't really care about what CH said they expected. I'm talking to you to see what YOU expected.

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  194. Scott: "If the flaws in the arguments presented are not obvious to you, then It's unclear if further discussion would be fruitful. We can say the same regarding the relevance of the paper Troy posted."

    Seeing as you can't coherently point any out yourself, I tend to agree. What you posted above that was the same thing the authors said themselves, just with CH's characterizations. The data is the same.

    Scott: "However, you seem to be referring to the actual work in the paper Cornelius linked to, rather than the misrepresentation found in the OP."

    Finally, I'm almost tempted to go back and redact, but pfff too late now.

    Scott: "I could elaborate on this, but I think the relevance is obvious."

    I can't believe your parroting abstracts to me as if they are data. Yay, a neutral mutation could happen and then non-neutral mutations can happen after that! WOW!! DEEP DOOD! The stage is totally set! They use that jargon so people will think they are smart when they understand something simple.

    Scott: "Now, If I understand you correctly, you're suggesting that God could have created and exploited this same process in creating the biological complexity we observe."

    Setting aside you're track record of understanding me, no, I never suggested that. I don't see why he couldn't have, but I don't think he did.

    Scott: "Sure he could. Evolution doesn't suggest that he couldn't. But, scientific theories do not merely represent logical possibilities; they represent explanations about observed phenomena."

    ... that are a collection of logical possibilities.

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  195. Scott: "What is the underlying explanation as to why God, or any other designer, would create this specific process then manipulate it in this specific way to achieve the specific biological complexity we observe?"

    Again, I don't think he did. If you are a theistic evolutionist, that is your burden to explain. I don't see the need to believe in two sets of miracles. But as you said, science is about more than what, it's about why! Now who's asking teleological questions? BANG! that's why :D

    Scott: "ID fails to present any explanation. "That's just what the designer must have wanted"

    This must be the survivor because it survived!

    Scott: "What you need to do next is explain how you can reach the specific conclusion implied in the OP (Evolutionary theory isn't overwhelming collaborated by evidence or falsified by observations of proteins in nature) based on this observation."

    WOW, thanks alot! First down and a million yards to go huh? I guess since the evidence is overwhelming (except for here) it will just take me an overwhelming amount of time to debunk all the story telling that gets rewritten after every new finding "sheds light" on how evolution works. And all that, "based on this observation"? Well, I will clearly fail since I now have only one bullet, and you still have an "overwhelming" number of bullets.

    Scott: "However, it seems that the majority of the arguments so far depend on implicit assumptions that everything was designed. which is not an assumption of evolutionary theory."

    I would use the phrase "depend on the observation that many proteins appear exquisitely designed".

    Scott: "The fact that "Proteins can be tuned to adapt to new functions or environments via simple adaptive walks involving small numbers of mutations." is an incredibly useful feature of biology. Evolutionary theory, is an explanation that includes this observation, among others."

    So do ID and creation, they just try to include more observations.

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  196. John wrote:

    My comment was not limited in scope to those in the study troy cited. My comment was short because it was obvious.

    So then what is the scope limited to? We still don't know because it's *not* obvious. Proteins created researchers as a whole? Proteins created by human beings?

    The problem was that what was obvious was not taken into account when it was claimed this was a blow to CH.

    Until we determine what the scope of your comment is, it's unclear how we can take it into account.

    I wrote: Scott: "This is the distinction I'm attempting to convey."

    John wrote: Yes, I understand you have a dim view of inductive reasoning. It's odd that you wrote all that, since you still seem to be using inductive reasoning yourself.

    Pointing out that you're disingenuously conflating apples with oranges doesn't mean that I have a "dim view" of either apples or oranges.

    Of course, you probably already knew that since I wrote:

    I'm referring to what appeared to be implied conclusions you drew since your comment [seemed] to group proteins designed by researchers with proteins we find in nature.

    and…

    As such, a conclusion that proteins in nature were designed, or had evolved naturally, would be subject to the problem of induction as they would represent an unseen explanation.

    I wrote: "So exactly what are these implications?"

    John wrote: Do you really care? It involves inductive reasoning. Let me know if you change your mind on that, and I'll let you know what the implications are.

    Again, pointing out that someone's math doesn't seem to add up isn't the same as having a "dim view" of mathematics.

    John wrote: But yes, by using inductive reasoning, it would seem that God must be clever and skillful.

    So, unless God was clever and skillful, he couldn't have designed proteins? As a theist, do you real think this?

    God might *be* clever, but the last time I checked, God doesn't need to be either clever or skillful to do anything since he's supposedly an omniscient and omnipotent being. That's like saying God had to come up with some "clever" way to "search" through the sequence space and needed the skill to actually perform that search. Again, this doesn't seem to add up.

    Of course, if you're referring to human beings, again, that's rather non-controversial.

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  197. John wrote:

    You have quite a problem then apparently. I hear this objection alot, "Experiment X was carried out to disover whether Y or not Y, but opponent is unfairly drawing conclusion A from the data".

    No, It's Cornelius' problem since he's the one depending on a misrepresentation of the researchers' goal to reach his conclusion. The fact that the researchers didn't end up evolving the exact original same virus is a straw man of evolutionary theory.

    Again, I just care about the data.

    So I understand you correctly, you don't care about Cornelius' inductive reasoning derived from the research, you just care about the phenomena observed during the research? But this puts us back to square one since empirical observations alone are insufficient in regards to the origin of proteins we find in nature.

    Only sheep care about what the authors might or might not want to show.

    It would seem we're in agreement here since I was pointing out how Cornelius' argument is appealing to what the authors supposedly wanted to show, but didn't actually occur. It's a bad argument.

    I'm talking to you to see what YOU expected.

    What did I think the researchers expected? But we've already agreed this is a bad argument? Or perhaps you mean, what did I think the researchers would observe when they ran their experiments? Or what do I think the impactions of the observations are?

    I wrote: "If the flaws in the arguments presented are not obvious to you..

    Seeing as you can't coherently point any out yourself..

    I've already pointed out several problems with the argument Cornelius presented. Furthermore, it seems you do think this is obvious since you don't care about what he wrote and that his argument, in part, depends on "about what the authors might or might not want to show."

    Finally, I'm almost tempted to go back and redact, but pfff too late now.

    It's not as if I posted this group of comments over a series of hours or days. They were composed offline and all posted within 10 minutes. You could have easily read each of them in full, then responded.

    I wrote: "I could elaborate on this, but I think the relevance is obvious."

    I can't believe your parroting abstracts to me as if they are data.

    It is data. Directed evolution has also shown how mutations that are functionally neutral can set the stage for further adaptation. Did you note the word "Directed"? Furthermore, I think it obvious that it's revenant because this is part of the explanation that evolutionary theory uses to explain biological complexity. Concluding something is relevant to evolutionary theory is not the same as concluding evolutionary theory is true.

    I wrote: "Now, If I understand you correctly, you're suggesting that God could have created and exploited this same process in creating the biological complexity we observe."

    Setting aside you're track record of understanding me, no, I never suggested that. I don't see why he couldn't have, but I don't think he did.

    So you're denying that biological complexity has evolved over time?

    I don't see the need to believe in two sets of miracles.

    Why this set of miracles rather than some other set of miracles? That's the set you happen to prefer?

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  198. I wrote Scott: "What is the underlying explanation as to why God, or any other designer, would create this specific process then manipulate it in this specific way to achieve the specific biological complexity we observe?"

    Again, I don't think he did. If you are a theistic evolutionist, that is your burden to explain. If you are a theistic evolutionist, that is your burden to explain.

    But as creationist, I take it, you don't have any burden?

    On one hand, we know this process exists, we know it's interacting with our environment over time and we know it can be directed to design organisms. These are all empirical observations (the seen.) On the other hand, you claim the (unseen) explanation for biological complexity we observe, which would include this process, is God. As such, it's your burden to explain how this phenomena fits in with your claims.

    For example, Even if only has a negative effect, it would seem that God must, at a minimum, miraculously manipulate this process so just the right species go extinct when he wants them to, while others do not.

    So, regardless if your'e a creationist or an IDist, what is this explanation?

    I would use the phrase "depend on the observation that many proteins appear exquisitely designed".

    I would use the phrase, "depends on naive empiricism."

    So do ID and creation, they just try to include more observations.

    Please see above. Feel free to enlighten us with how these observations are explained by creationism. Here's a hint. "That's just what the designer must have wanted." isn't an explanation.

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  199. Scott: "Until we determine what the scope of your comment is, it's unclear how we can take it into account."

    The scope of designed proteins refers to proteins that are designed, whether we observed them being designed or not. These are not the first proteins designed by humans. So if you doubt the ones we find in nature were designed, if you like, you can imagine only the proteins you personally know to be designed are being referred to and it won't change the point of my statement. That point is that you cannot appeal to designed proteins as evidence that it is not necessary for proteins to be designed for them to arrive at a different solution. Hopefully this restatement will finally clear it all up.

    Scott: "Pointing out that you're disingenuously conflating apples with oranges doesn't mean that I have a "dim view" of either apples or oranges."

    As I said, I'm not equivocating if proteins in nature are designed, nor do you need to use inductive reasoning to arrive at the conclusion that they were to understand the point of my comment. My comment was not adduced as evidence of design in nature, but to indicate the reliance on design in an argument purporting to dispense with needing it. For you to claim you cannot comprehend my statement due to ontological barriers is what is disingenuous.

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  200. Scott: "God might *be* clever, but the last time I checked, God doesn't need to be either clever or skillful to do anything since he's supposedly an omniscient and omnipotent being. That's like saying God had to come up with some "clever" way to "search" through the sequence space and needed the skill to actually perform that search. Again, this doesn't seem to add up."

    So he has infinite cleverness and skill.

    Scott: "No, It's Cornelius' problem since he's the one depending on a misrepresentation of the researchers' goal to reach his conclusion."

    I reached his conclusions without assuming anything about the researchers goals. But the methods are there to read. The conclusions can be reached without direct knowlege of the researchers hopes and dreams.

    Scott: "The fact that the researchers didn't end up evolving the exact original same virus is a straw man of evolutionary theory."

    You are absolutely correct. Which is probably why CH's statement, "Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved" dwelled on this trivial point about 1/4 as long as the researchers did themselves.

    Me: "Again, I just care about the data."

    Scott: "So I understand you correctly, you don't care about Cornelius' inductive reasoning derived from the research, you just care about the phenomena observed during the research?"

    No, if you go back, in context you will realize I said, I didn't care how CH characterized the researcher's hopes and dreams. Conclusions similar to his can be drawn minus certainty of the researcher's thought life.

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