Saturday, May 1, 2010

Playing With Truth

I used to believe facts and figures counted. I thought that objective, obvious evidence would carry the day. But evolutionists have long since dispelled such silly notions for me. In one public debate with a professor, I read through a dozen or so objective, scientific failures of evolution. With a wave of the hand the professor easily dismissed the entire list. “Those,” he assured the audience, “are all fallacies.” It later became obvious he hadn’t the foggiest idea of what he was talking about.

Scientists have a duty to represent accurately what they know, and what they don’t know, to the public. They should not oversell their favorite ideas or undersell ideas they oppose. Those ideas probably don’t seem too controversial but a debate can take on a life of its own. In the heat of battle truth is the first casualty. Now new research confirms Aeschylus’ age old observation. The research concludes that it is right to overstate the validity of Darwin’s theory to ensure success in public debate. The ends justify the means.

But arch evolutionist PZ Myers objects as he rehearses the familiar “evolution is a fact” refrain. Echoing Joseph Le Conte who found that evolution is not merely as certain as gravity, “Nay, it is far more certain,” Myers explains that evolutionists’ high claims are entirely warranted:

The evidence for evolution really is overwhelmingly in its favor. It isn’t proven in a mathematical sense, there is no illusion that we have accounted for every single possible mechanism, and there is still active exploration of all the details, but there is no doubt anywhere sensible that evolution, that populations change over time driven by natural processes, and that all life on earth shares a common ancestry, is a fact, amply confirmed and tested.

That would be a difficult claim to defend. In fact, given the current state of science it would be impossible to defend as evolution’s predictions seem to be continually turning out to be false. For instance, the reconciliation of the molecular and the visible, morphological, features has been a major problem in trying to resolve the evolutionary tree. The molecular and morphological features often indicate “strikingly different” evolutionary trees that cannot be explained as due to different methods being used.

The growing gap between molecular analyses and the fossil record, concluded one researcher, “is astounding.” Instead of a single evolutionary tree emerging from the data, there is a wealth of competing evolutionary trees. And often what evolutionists conclude is downright strange. Over time insects must have evolved wings, then lost them in the evolutionary process only then later yet again to evolve them (or less parsimoniously, the wings could have disappeared over and over throughout the tree). Or again, bats must have independently evolved, in separate lineages, the same intricate echolocation capability.

As one researcher put it, “Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.” These are not minor statistical variations and the general failure to converge on a single topology has some researchers calling for a relaxation from “tree-thinking.”

A relaxation from tree-thinking? And this is but a sampling of the many falsified predictions of evolution. There are many more where these came from as evolutionists are constantly surprised. You can see 14 fundamental predictions that were falsified here. Predictions which evolutionists are absolutely sure of are routinely found to be false. “I about fell off my chair” is the typical refrain of evolutionists.

We can argue about the epistemological standing of evolution, but a scientific fact it is not. But for Myers it’s all so simple:

We tend to assume the creationists can’t really be that stupid, and figure they must have some legitimate complaint about some aspect of evolution with which we can sympathize. They don’t. They really are that nuts.

Truth is the first casualty.

40 comments:

  1. 'I used to believe facts and figures counted' - then I found god.
    So then I started writing all these articles which pretend to be about science but in reality are all about promoting creationism. Oh, I pretend I'm raising the possibility of ID as evolution can't explain everything, even though it has about a trillion times as much evidence as creationism does; but the truth is we all know that ID is just creationism with a mask.

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  2. Cornelius -

    "I used to believe facts and figures counted."

    Facts such as:

    - The theory of evolution is a THEORY; a scientific hypothesis which has passed a certain standard fo evidence.

    - ID or Creationism is not, by any standard, a scientific theory since it makes no testable predictions and invokes supernatural agents.

    - There is no evidence for a God or supernatural designer.

    - Invoking a God or supernatural designer to explain observations is profoundly unscientific.

    - The theory of evolution is simply a naturalistic theory which explains the evidence (or, at the very least, much of it) inkoving only natural forces. It is NOT a default option for the assumnption that Creationism is impossible ('It couldn't have been God, therefore it must be evolution').

    - The theory of evoultion will remain the best explanation of the available evidence until another theory comes along which better accounts for the evidence: that is, accounts for all the evidence the theory of evolution accounts for, and more besides.

    Facts like that, you mean?

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  3. Dr. Hunter again confuses science in progress with failed science. I don't see a single paper in here that supports evolution has 'failed' in this, or any respect.

    There are two primary ways molecular phylogenies go wrong:

    1) Not enough data. Too few sequences lead to errors. It is hard to make a nested hierarchy, when most of the branches don't have data!!!

    2) Horizontal gene transfer.

    Taking the first (too little data):
    The Nature paper referenced is published in 2000. The Human genome project is completed in 2003, with many others later.

    Lockhart and Cameron's paper in Trends in Ecology & Evolution 2001 is essentially begging for multiple bee genomes to be sequenced:

    "Additional molecular sequences might help to identify hidden biases in the current data, test the strength of support for unrooted
    data partitions, and confirm the position of the root. The potential value of additional sequence data is indicated from the conservative substitution patterns observed in the protein genes studied to date. These data show low amounts of contradictory signal in
    distance Hadamard spectra (Fig. 4). Thus, efforts to obtain complete mitochondrial genome and nuclear sequences seem very worthwhile."

    Summary: We don't have enough data. Where enough data is present, phylogeny is clearer (low contradictory signal!). Please get more data for us, or fund our sequencing project!

    Even Woese's proposal is based on rDNA sequences-not whole genome comparisons available today.

    The second, horizontal gene transfer is most problematic in prokaryotes. Even the evolutionary biologist Wolse, who you cite in this post, describes in that paper two phases of evolution-
    one early phase dominated by horizontal (bacteria) followed by vertical evolution (animals, plants, etc.), which shows clear phylogeny and nested hierarchy.

    For HGT, I'd look at some recent references. More data, better technique rescues phylogeny even in bacteria, and can actually track the HGT events.

    En route to a genome-based classification of Archaea and Bacteria?
    Syst Appl Microbiol. 2010 Apr 19.

    "...However, recent studies indicate that the species tree and the hierarchical classification based on it are still meaningful concepts, and that state-of-the-art phylogenetic inference methods are able to provide reliable estimates of the species tree to the benefit of taxonomy. Conversely, we suspect that the current lack of completely sequenced genomes for many of the major lineages of prokaryotes and for most type strains is a major obstacle in progress towards a genome-based classification of microorganisms. We conclude that phylogeny-driven microbial genome sequencing projects such as the Genomic Encyclopaedia of Archaea and Bacteria (GEBA) project are likely to rectify this situation."

    What is missing from Dr. Hunter's analysis is that the majority of the time, the molecular data is very nice, forms beautiful phylogenies, and matches the fossil data. Where they don't, important re-analysis has been conducted.

    On a side note, having single word, or single line quotes, divorced from context, with no reference to the subject of the study, or the conclusions of the scientist is dangerously close to BornAgain style quote mining. This seems especially true, when most articles are stuck behind a pay-wall. Selective usage at best-you get a link that most readers won't and can't verify.

    Ironic for an article that leads off "Scientists have a duty to represent accurately what they know, and what they don’t know, to the public. They should not oversell their favorite ideas or undersell ideas they oppose."

    Why don't you take a single article--with complete genome sequences--describe the methods, results, and conclusions, and describe how the authors think it disproves molecular phylogeny or evolution.

    That would be an evidence-based debate. This is nonsense, a bunch of one-liners for your faithful.

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  4. Dave said...
    "... - then I found god.
    So then I started writing all these articles which pretend to be about science but in reality are all about promoting creationism. Oh, I pretend I'm raising the possibility of ID as evolution can't explain everything, even though it has about a trillion times as much evidence as creationism does; but the truth is we all know that ID is just creationism with a mask."

    Bare and futile assertions like this have been iterated ad nauseum by dolts of your shoe sized IQ for years.

    No one is impressed by your useless comment.

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  5. Ritch:

    "Facts such as:
    - The theory of evolution is a THEORY; a scientific hypothesis which has passed a certain standard fo evidence"

    Really?

    Theory:
    "An extremely well-substantiated explanation of some aspects of the natural world that incorporates facts, laws, predictions, and tested hypotheses." www.nmsr.org/wrkshp9.htm

    "a well-substantiated explanation of some aspect of the natural world; an organized system of accepted knowledge that applies in a variety of circumstances to explain a specific set of phenomena;" http://wordnet.princeton.edu/perl/webwn?s=theory

    Now compare to:

    "The history of organic life is undemonstrable; we cannot prove a whole lot in evolutionary biology, and our findings will always be hypothesis. There is one true evolutionary history of life, and whether we will actually ever know it is not likely. Most importantly, we have to think about questioning underlying assumptions, whether we are dealing with molecules or anything else." Jeffrey H. Schwartz, Professor of Biological Anthropology, University of Pittsburgh, February 9, 2007

    Sorry Ritch but once again you lose.

    "- ID or Creationism is not, by any standard, a scientific theory since it makes no testable predictions and invokes supernatural agents."

    1) ID is not creationism.

    Creationism is, by definition, based on the bible or the Coran or ....

    ID is based on design detection techniques used in many scientific domains. If ID is not science then neither are any of those others.

    ID doesn't necessarily invoke the supernatural.

    Even Panspermia (atheists Francis Crick, Hoyle etc.) is an ID compatible hypothesis.

    2) You refuse to acknowledge the predictions made by ID - that's because your mind is still on hold. And THAT's because you don't want there to be anything other than that which your own pathetic little reasoning process can feel secure with.

    "- There is no evidence for a God or supernatural designer."

    ROTFL

    You wish -denial of evidence does not = no evidence- but I seem to remember easily demonstrating how hapless your logic on that one is.

    "- Invoking a God or supernatural designer to explain observations is profoundly unscientific."

    See above - you're obviously very wrong.

    Yet, Your asinine theory invokes an unknown and unknowable first life form. Pure presumption.
    And thus to quote you it is "profoundly unscientific."

    Then it invokes mutations + selection to account for all 13 million life forms on earth - without the slightest grain of empirical evidence.

    ID does not invoke gods - only intelligence and thus looking at the obvious design in DNA etc, some unfathomably deep intellect of some loving entity.

    The most obvious is no doubt some God, but many others invoke aliens. Again, Crick, Hoyle et al.

    "...a naturalistic theory which explains the evidence (or, at the very least, much of it) inkoving only natural forces."

    It also invokes impossible luck - you conveniently forgot that part.

    Darwinian evol. invokes materialism - a religious assumption.

    Darwin was himself a hypocritical materialist seeking to rid science of God.

    "Facts like that, you mean?"
    Indeed.

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  6. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1/BIO-C.2010.1

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  7. Hitch, those who pervert the truth in a bare and futile attempt to support anti-evolutionary assertions impress no-one with an IQ above their shoe size when they make useless comments based upon creationism.
    'Evolutionary theory' is the same as 'germ theory', classed as a theory but supported beyond doubt by the weight of evidence.
    Your use of selective descriptors adds no value to your argument.

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  8. And now, can we talk about the science please? Thank goodness RobertC drops in to straighten stuff out. Dr. Cornelius dumped a bunch of references on us, some behind pay-walls. We have to pick his references apart one by one.

    The refs never say what Dr. Cornelius says they say. RobertC addressed a couple of Cornelius' refs above, I'll address this one.

    === Dr. Cornelius: ===
    For instance, the reconciliation of the molecular and the visible, morphological, features has been a major problem in trying to resolve the evolutionary tree.
    =====

    Here, "major problem" links to a paper which I know because creationists quote-mine it all the time. In it, Trisha Gura first says there's a big confict between those who build phylogenetic trees using fossils and those built with DNA. However, the specific example he/she explores in more detail (whale evolution) shows a small discrepancy that is resolvable, and it appears, already resolved, actually a triumph for Darwin's theory of universal descent.

    On whale evolution, Gura writes: "systematists [using bones] have long classified even-toed hoofed mammals, called artiodactyls, as a group, or ‘clade’, that could be further broken into four extant subclades — camels and llamas; cattle and deer; pigs and peccaries; and hippopotamuses [sic]... The teeth of ancient cetaceans [whales/dolphins] look almost identical to those from an extinct group called the mesonychids. So morphologists [using bones] have classified the cetaceans and mesonychids together as a sister group to the Artiodactyla. But that view came under fire when molecular evidence entered the arena... [DNA researchers] focused on the DNA carried in cellular organelles called mitochondria, which placed cetaceans in the middle of the Artiodactyla. Other teams, studying a range of different genes and proteins, singled out hippos as more closely related to whales than to any other artiodactyl, be it a cow, camel or pig."

    Right away, this is a tiny discrepancy, the disagreement being whether whales are artiodactyls, related to hippos, or whether whales (together with mesonychids) are in a clade that is a sister group to artiodactyls. Oh, Darwinism's finished!

    No, it's not, this is a small discrepancy, already resolved. The answer is, as Gura writes, DNA analysis using retrotransponons, specifically SINEs, show the whales are indeed very closely related to hippos. "After comparing the SINEs found at seven locations in the genome for artiodactyls and whales, the Japanese researchers again concluded that hippos are more like whales than other members of the Artiodactyla."

    Darwin wins. Confirmation of universal common descent.

    As for Dr. Cornelius' other refs, RobertC and I will have to pick through them one by one.

    Tell me, Dr. Cornelius, since you cited this paper, what is your explanation for the distribution of SINE retrotransposons (which are nonfunctional)?

    Do you, Cornelius, have another explanation for the retrotransposon data, beside common descent of whales and hippos? Yes or no. Yes or no. Don't evade. Yes or no. Yes or no. Yes or no.

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  9. Artiodactyls? Mesonychids? If they can't make up their minds between those,they might as well concede that whales are fish with independent mammal characteristics. It's just as reasonable, really.

    In seriousness, I'm pretty sure that the "problems" of phylogeny are only such insofar as they stick out in an otherwise consistent system. Does the crazy orbit of Mercury mean Newton and Laplace's should be discarded? Come on.

    I used to believe facts and figures counted. I thought that objective, obvious evidence would carry the day.

    I'm trying to remember, Dr. Hunter… how old do you believe the Earth is? What about the Universe — is it much older? And one small other question: Are humans reproductively descended from distant non-human primates?

    Does the "obvious evidence" disagree or agree with the scientific consensus on those questions?

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  10. word missing fix:

    mean Newton and Laplace's *models*

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  11. This comment has been removed by the author.

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  12. Ah Hitch, you brighten my day. You really do.

    Firsty, you quote Jeffrey H. Schwartz, another biologist who is certainly no friend to ID. He (like the VAST majority of people with credentials in biology) accepts evolution. This alone should be a warning sign that he is not making the point that you apparently think he is making.

    As for the quote itself, well, what he says is quite true. But it is the problem with studying the HISTORY of anything - recent human events, ancient human events, or indeed the natural world. PROOF is always going to be lacking because the events themselves are in the past. How can you prove events long gone? All you can do is gather evidence and form testable hypotheses which account for the evidence.

    The THEORY of evolution does that. And it has been extensively tested. Again, the clue is in the title - THEORY = a hypothesis which has passed a standard of evidence. So no, I do not 'lose' on this one.


    ID is not creationism.


    I never said they were the same (though I believe them to be extremely close in principle). But ID is still not a scientific theory.


    ID doesn't necessarily invoke the supernatural.
    Even Panspermia (atheists Francis Crick, Hoyle etc.) is an ID compatible hypothesis.


    Really? So we can claim the very first life form on Earth came from another planet (via a meteor, let's say) and then gave rise to the whole diversity of life we see today through the process of evolution? That is an ID - compatible theory? That strikes me as odd since an actual intelligent designer is conspicuously missing.

    Panspermia is an alternative to abiogenesis, not evolution. Evolution is only concerned with how life DEVELOPS, not how it began.


    You refuse to acknowledge the predictions made by ID - that's because your mind is still on hold.


    Present me with some predictions ID makes.


    You wish -denial of evidence does not = no evidence


    Again, present me with solid, empirical evidence for God. The onus is on you to do so. And believe me, an absolute cache of fame and riches awaits anyone who is able to do so.

    "Your asinine theory invokes an unknown and unknowable first life form. Pure presumption."

    This first life form is deduced through logical extrapolation. Furthermore, there is nothing supernatural about such an organism. It would still be subject to natural laws like every other living creature.


    Then it invokes mutations + selection to account for all 13 million life forms on earth - without the slightest grain of empirical evidence.


    See your own remarks about 'denial of evidence does not equal no evidence'. Such evidence is found in abundance. Lenski's bacteria study is the one I seem to cite the most. But that's because it is such a neat demonstration of random mutation and natural selection.


    ID does not invoke gods - only intelligence


    ...and beings capable of HAVING such intelligence. You cannot have intelligence with no mind to have it in.


    It also invokes impossible luck - you conveniently forgot that part.


    It does not. If you think otherwise, I suspect you are falling foul of the lottery fallacy.


    Darwinian evol. invokes materialism - a religious assumption.


    Darwinian evolution makes the same materialistic and metaphysical assumption as ALL scientific theories do - that miracles simply do not happen. Any hypothesis which does not make that assumption is simply not science.

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  13. Aren't hippos closer to pigs morphologically than to whales or other artiodactyls?

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  14. And to the best of my knowledge, Lenski's bacteria did not evolve into a new species, even after thousands of generations.

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  15. Lenoxus:


    ===
    In seriousness, I'm pretty sure that the "problems" of phylogeny are only such insofar as they stick out in an otherwise consistent system. Does the crazy orbit of Mercury mean Newton and Laplace's should be discarded? Come on.
    ===

    Yes, and while we're at it, why should that retrograde motion be a falsified prediction of geocentrism anyway?


    ===
    Does the "obvious evidence" disagree or agree with the scientific consensus on those questions?
    ===

    I think the evidence is more important than the crowd.

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  16. "Yes, and while we're at it, why should that retrograde motion be a falsified prediction of geocentrism anyway?"

    Are you arguing for geocentrism now? Totally consused on this point.

    "I think the evidence is more important than the crowd."

    What evidence? Your links and one liners?

    Faith is not evidence based, after all, is it?

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  17. Thanks Dr. Hunter for all your work.

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  18. natschuster -


    Aren't hippos closer to pigs morphologically than to whales or other artiodactyls?


    Actually no. All cetaceans (whales, dolphins and porpoises, basically) are descendants of land-living mammals of the Artiodactyl order. So cestaceans are 'nested within' the Artiodactyl order, perhaps I should say... And they are more closely related to hippos than either are to pigs.


    And to the best of my knowledge, Lenski's bacteria did not evolve into a new species, even after thousands of generations.


    I suspect you miss the point of the experiment. All twelve strains of the same bacteria developed - that is to say, evolved. They all showed the same measured progression through random mutatuion and natural selcetion. Which was the original point of the experiment.

    At that stage they could well have stopped the experiment and declared a sucess and a beautiful demonstration of evolution in action. Then however, the freak result occurred - one sample turned into a completely new strain. It was not the original intended result, and Lenski's experiment would have been a beautiful demonstration of evolution without it. But for Lenski it was just the icing on the cake.

    Saying this new strain was not a new 'species' is misleading. The initial split which is at the base of all cases of speciation had been made - and under the microscope too. The only compontent necessary to turn this new strain into a new species is time - time for it to genetically drift far enough away from the original E.Coli bacteria to call it a new species.

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  19. Lenski's e-coli - Analysis of Genetic Entropy
    Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment.
    http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria

    Upon closer inspection, it seems Lenski's "cuddled" E. coli are actually headed for "genetic meltdown" instead of evolving into something better.

    New Work by Richard Lenski:
    Excerpt: Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal.
    http://www.evolutionnews.org/2009/10/new_work_by_richard_lenski.html

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  20. Multiple Mutations Needed for E. Coli - Michael Behe
    Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell.
    http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O

    The Sheer Lack Of Evidence For Macro Evolution - William Lane Craig - video
    http://www.metacafe.com/watch/4023134

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  21. I was always under the impression that hippos and pigs were considered more closely related to each other than to other artiodactyls because of the details of their anatomy.

    And maybe Lenski's bacteria will not contimue to evolve into a new species. Maybe "evolution" beyond limited change is not possible because it requires too many changes to complex systems, or it might take too long.

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  22. Lenski's e-coli actually helps falsify evolution:

    Problems of the RNA World - Origin Of Life - Lenski's e-coli - Dr. Fazale Rana
    http://www.metacafe.com/watch/4564682

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  23. bornagain77: Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment.

    Adaptation means adapting to the local environment the organism finds itself in. Of course. That's what we expect.

    bornagain77: Upon closer inspection, it seems Lenski's "cuddled" E. coli are actually headed for "genetic meltdown" instead of evolving into something better.

    Well, no. They continue to become better adapted to their environment. What's interesting is that the mutation rate increased once they reached the local fitness peak.

    Behe: If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell.

    We don't expect to see the same amount of evolution in a twenty year experiment with laboratory populations as we would billions of years of evolution in oceans and continents full of bacteria — especially as we are starting with highly derived organisms. What we do see is consistent with expectations, but the details concerning the relationship between adaptive and neutral evolution and rates of mutations are highly interesting to researchers. It may even help with understanding cancer, which occurs when cells mutate and evolve within a single organism.

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  24. Zacherial, the point is that you cannot extrapolate from an experiment that is losing functional information to proof that material processes generate functional information. That you would overlook this glaring deficiency of evolution time and again highlight that religion drives your science and it matters:

    Before you quote Nylonase, read this:

    A Creationist Perspective of Beneficial Mutations in Bacteria
    Excerpt: reduced specificity of a pre-existing enzyme is biochemically degenerative to the enzyme,77, 78 even if it provides a presumed phenotypic benefit. The “beneficial” phenotype of nylon degradation requires the a priori existence of the enzyme and its specificity. Its degeneration is not a mechanism that accounts for the origin of either the enzyme or its specificity.
    http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria

    Plus the fact that once Nylon is removed from the environment the parent strain is "more fit" for survival.

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  25. "We don't expect to see the same amount of evolution in a twenty year experiment with laboratory populations as we would billions of years of evolution in oceans and continents full of bacteria — especially as we are starting with highly derived organisms"

    The time doesn´t matter, it is question of number of generations, based on this experiment how many generation you need for a fish became a anfibian?

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  26. "Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. "

    Because they've been selected at 37C for so many generations.

    "Plus the fact that once Nylon is removed from the environment the parent strain is "more fit" for survival. "

    The infinitely regressive creationist position:

    If a fish develops lungs, it is 'devolution' because it no longer has gills. Now it has to breath air.

    Evolution doesn't act fitness in all environments. It increases fitness in the environment the organism lives in. In that respect, you are less evolved than a fish for life under water.

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  27. I understand that the new nylon eating enzyme is smaller and less efficient than the old enzyme. This means that there was a loss of struture and imformation. I don't know if it is possible to prove from here that a gain in information or function is possible via a random process.

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  28. "Playing with Truth" should be the title of Cornelius' blog.

    As I expected, Dr. Cornelius evades straight questions. Evasion is his entire strategy.

    Do you, Cornelius, have another explanation for the retrotransposon [SINE] data, beside common descent of whales and hippos? The data in the very paper that Cornelius himself cited in support of his hypothesis.

    Do you, Cornelius, have another explanation for the retrotransposon [SINE] data, beside common descent of whales and hippos? Yes or no. Yes or no. Don't evade. Yes or no. Yes or no. YES OR NO YES OR NO YES OR NO YES OR NO.

    If Cornelius doesn't answer, common descent of whales and hippos is proven.

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  29. bornagain77: the point is that you cannot extrapolate from an experiment that is losing functional information to proof that material processes generate functional information.

    That wasn't the point you raised. You pointed to a trade-off that increases fitness for the local environment by sacrificing fitness for an environment the organism is not exposed to. That's what we mean by adaptation.

    bornagain77: Plus the fact that once Nylon is removed from the environment the parent strain is "more fit" for survival.

    Organisms adapt to their environments, not to your arbitrary standards. In any case, nylonase is a novel, complex enzyme, so apparently such an occurrence is possible.

    Blas: The time doesn´t matter, it is question of number of generations, based on this experiment how many generation you need for a fish became a anfibian?

    Generations, population and size of genomes do matter. When starting with a highly derived organism with a small, highly optimized genome, there are fewer available pathways.

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  30. == BornAgain77 wrote: ==
    the point is that you cannot extrapolate from an experiment that is losing functional information to proof that material processes generate functional information.
    ====

    BornAgain (and his creationist sources) make the assertion that Lenski's and the nylonase experiments involve "losing information", which is a bare assertion supported by no facts, no experiments, and no equations. A lot of creationists have joined together in the massive gang rape of information theory, alleging that they have some kind of way of computing how much information there is in a cell. Bull. No creationist has any equation for measuring the information there is in a cell, consequently they cannot assert that information has gone up, down, or sideways in any experiment.

    BornAgain77 cites a paper posted at Answers in Genesis(!!!) called "Lenski's e-coli - Analysis of Genetic Entropy". There is no such thing as genetic entropy; no creationist has any equation for measuring "genetic entropy", which is as imaginary as "vital force" was in the 19th. century.

    Behe: "If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell."

    Funny! The same Behe wrote a whole book in which he alleged that "irreducible complexity" was the distinguishing feature of living systems--and this IC could not evolve!

    And yet IC has appeared in newly evolved biochemical functions that involve multiple interacting enzymes. The three-enzyme system for degrading the man-made pollutant PCP (pentachlorophenol) which did not exist in nature until recently. The seven-enzyme pathway to degrade 2,4 dinitrotoluene (a man-made explosive).

    Add to that new enzymes for nylonase, for degradation of PET (plastic), BG Hall's new beta-galactosidase, atrazine chlorohydrolase, and DNT degradation.

    AIG: "Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C... Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment."

    Irrelevant. They're measuring fitness in an environment that is not the natural environment of Lenski's strain. Fitness in a non-natural environment is not a measure of information. Humans are less "fit" than fish at 100 feet below the ocean, this does not mean that the human body has less "information" than a fish's body.

    Behe: "(2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. ... It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit..."

    This is Michael Behe writing "it seems likely"? On what does he base that inference? This is the same Behe who said the blood clotting cascade in land vertebrates was irreducible... already known to be reducible when he wrote that... AND he said that no protein in HIV had ever evolved a new protein binding site, ERV called him out on that one... AND on and on...

    The functions listed above-- nylonase, citrate uptake, PCP degradation etc.-- are all novel functions. Whether they have more "information" or not, we cannot say until you specify which equation you're using for "information," which the rapists of information theory never do. But if you measure complexity by the number of biochemical functions, these are all novel functions and thus, gains in complexity.

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  31. But a lot of these things involve a loss of stucture, function or effciency, if not information. They involve tradeoffs. I'm not sure toy can prove froom them that you can gain something from a random change.

    And Behe said that only part of the vertebrate blood clotting system is ID, not the whole thing. That's the only part he discussed in his book.

    And he also said that the bacteria already had the enzyme for digesting citrate. It just needed help getting it into the cell.

    And the chlorate digetive system in bacteria involved the development of one new enzyme. The two others in the system already existed.

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  32. And Behe adresses the HIv binding site issue here:

    http://www.amazon.com/gp/blog/post/PLNK2LJVF3SRXVK9O

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  33. And it looks like none actually saw the new binding site appear. They assume it appeared when HIV made the jump from apes to humans. Which is also an assumption.

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  34. natschuster - "But a lot of these things involve a loss of stucture, function or effciency, if not information."

    In the enzymes I cited, the biochemical functions were new. Novel. They are gain of function mutations. They all processed man-made chemicals that did not exist in nature. I left out evolution of antibiotic resistance from the examples above.

    If the biochemical function is new, how can it have "reduced efficiency" compared to the efficiency that existed before? Before, there was no function of this type, hence no efficiency could be defined for the start state.

    You also mention "loss of structure", but I am unaware of that happening. If you wish to define information= size of protein, then any mutation which makes a BIGGER protein is a gain of information. And there are many such mutations, gene fusion etc.

    natschuster: "And Behe said that only part of the vertebrate blood clotting system is ID, not the whole thing. That's the only part he discussed in his book."

    I'm afraid you're wrong on this point-- Casey Luskin of the ID has recently pushed this false history re: Behe's book. Luskin incorrectly wrote that "Behe specifically stated that his argument for irreducible complexity only pertained to irreducible complexity “beyond the fork” where the intrinsic and extrinsic blood-clotting cascades converge."

    To back this up, Luskin cited PAGE 86 of Behe's book, in which Behe does say that. BUT THEN ON PAGE 87, one page later, Behe expanded his definition and asserted that the whole blood clotting cascade was IC! Luskin missed this!

    Behe actually wrote (p.87) regarding the whole clotting cascade: "Because of the nature of a cascade, a new protein would immediately have to be regulated. From the beginning, a new step in the cascade would require both a proenzyme and also an activating enzyme... Since each step necessarily requires several parts, not only is the entire blood-clotting system irreducibly complex, but so is each step in the pathway."

    If you're curious, this error and Luskin's many other errors re: Behe's book are detailed at this Panda's Thumb post; skip down to heading "How many parts in the irreducible system, really?"

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  35. I understand the nylonase is smaller and less efficient than the original enzyme. So there was a loss of effciency.

    Now, some cases of antibiotic resistance are epigenetic. And in some cases the antibiotic resistant strain, when put in an evironment without the antibiotic, does not do well in competion with the original strain.

    On page 86 Behe said that he was discussing only the part below the fork, becasue that was what was well know. But since the part above the fork must have different proteins working together, it must be ID as well. He was talking hypothetically.

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  36. natschuster -


    I understand the nylonase is smaller and less efficient than the original enzyme. So there was a loss of effciency.


    To some degree yes, but this is no surprise under the theory of evolution. Some functionality will be reduced. This is because the bacteria were in an artificial environment - a sterile lab. Functional complexity is necessary in the wild because the bacteria needs to deal with a variety of environments, hazzards, etc. But in a single, controlled environment such finctional complexity is a waste, an extravagance, a disadvantage, and is thus pruned by natural selection.

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  37. But can you prove from nylonase that increasing functional complexity is even possible via a random process?

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  38. natschuster -

    NO, it is not true that the efficiency of the nylonase enzyme decreased. False. The enzyme did not act on nylon before, it did not degrade nylon before. Therefore, its efficiency pre-mutation was ZERO. You could wait 10 million years and it would not degrade one nylon molecule. Post-mutation, its efficiency was positive. Positive numbers are all higher than zero. Enzyme efficiency increased.
    If you want plenty more detail, read this TalkOrigins post on nylonase which points out the many grievous errors in Answers in Genesis' horrible description of nylonase enzymes.

    I think your misunderstanding is regarding the nature of catalytic efficiency. Enzymes (but not nylonase) frequently interact with more than one molecule, they are bifunctional or multifunctional. This is called promiscuity. So catalytic efficiency is not one number defined for an enzyme, it's defined for one function of the enzyme, that is, one type of interaction between the enzyme and just one of its substrates. If it interacts with, say, three subtrates, then it has three efficiencies, and so on.

    In the particular case of the nylonase, pre-mutation the most poweful nylonase enzyme (nylB) was a non-active repetitive element. It has no activity on nylon or anything else; its efficiency was zero.

    natschuster: "can you prove from nylonase that increasing functional complexity is even possible via a random process?"

    Depends how you define "functional complexity." If you define it as the number of regulated biochemical activities, then nylonase, and the other novel enzymes I listed in a prev. post (all of which act on man-made chemicals; none of those I listed act on antibiotics) are all increases in the number of regulated biochemical activities, and thus, all are gains in complexity by this definition.

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  39. According to this (yes a creationist website, but they do provide the sources)


    http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria#fnMark_1_76_1

    nylonase is more of a general purpose enzyme. It lost some efficiency when it acquired the ability to disgest nylon and some similar molecules. There was a loss of some specific function.

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  40. This is interesting:

    http://telic-meme.blogspot.com/2007/11/nylon-bug.html

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