Home » Intelligent Design » Junk DNA: The Real Story

Junk DNA: The Real Story

By now you have probably heard about so-called junk DNA. In recent decades the genomes of a growing number of species have been mapped out. Not surprisingly, scientists did not understand how many of these DNA sequences worked. For instance, repetitive sequences are common, but what do they do? As these data accumulated evolutionists increasingly viewed such sequences as useless junk. Then, years later, various functions began to emerge as our knowledge grew. This junk DNA story is the latest version of what seems like a repeating bad dream that goes like this. Scientists discover something new in biology but don’t understand it. Evolutionists, unaware that they are staring at a design whose complexity dwarfs their puny understanding, decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Later, when the function is eventually uncovered, evolutionists automatically claim the design as an evolutionary achievement. The structure goes from junk to treasure without a second thought.  Read more
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88 Responses to Junk DNA: The Real Story

  1. I have always believed that if design is ultimately responsible for the complexity found in life, then junk DNA does not make any sense at all. The problem I have though is this; Why would the genome of certain onion species be about 5 times bigger than a humans? This presents a real problem for design proponents as finding uses for some previously thought junk DNA sequences is fine, but how many novel functions can you expect to find for something as relativity simple as an onion?

    Evolutionists have made this point many times and readily accept that whilst certain sequences previously thought to be useless might show function, it is unwise to commit to the thesis that all DNA has purpose. This is a serious point. Onions are just one example amongst a vast list of simple organisms that have comparatively large genomes.

    Speaking as a computer scientist, the analogy would be to say that a simple password acceptance routine (the onion) has more lines of code when compared to a full blown operating system (the human). The premise of this problem is that complexity is directly proportional to size of genome. This might not be the case but if it is not then as design proponents what are we suggesting?

  2. aqeels -

    Why should humans be more complex? Humans have the least variability of just about any species on the planet. Plants, on the other hand, have to deal with a huge variety of biochemical situations. The human mind can adapt its environment to what it needs. Plants have no ability to adapt their environment, and therefore have to adapt themselves to whatever environment the find themselves in. Therefore, their biochemistry library (i.e. genome) is much bigger.

    I think your view of life is overly genocentric, and that is why it is causing difficulties.

  3. This OP is again riddled with assertions– none of which are actually supported by any evidence.

    For starters, junk DNA is a colloqial term. If you actually learn about what Cornelius calls ‘junk DNA’ you get much more info about what types there are, where it is found, how it likely came to be, and what its potential function could be.

    Among other things, you learn about the long history of experiments on ‘junk DNA’ by biologists (none of which is an ID proponent).

    What you find is, that in some cases function is found for stretches of this DNA. In very rare cases (like RNAi) completely new functions are found. However, biologists looked for those functions, no matter what the OP says. And the reason they were only found late is not because some biologists decided to go against some form of ‘prevailing dogma’. The function if this DNA has continually be studied.

    And johnnyb’s interjection about genome size would be spot on: If he had any evidence whatsoever that the onion is capable of genomic adaptation due to its ‘junk DNA’ while humans are capable of such adaptations because of their mind.

    A quick google search (e.g. here ) can be extremely informative.

    (It has a link to look at all the research on the onion genome as well. Read it here and compare that to the post by johnnyb.)

  4. 4

    hrun (3):

    This OP is again riddled with assertions– none of which are actually supported by any evidence.

    For starters, junk DNA is a colloqial term. If you actually learn about what Cornelius calls ‘junk DNA’ you get much more info about what types there are, where it is found, how it likely came to be, and what its potential function could be.

    Among other things, you learn about the long history of experiments on ‘junk DNA’ by biologists (none of which is an ID proponent).

    What you find is, that in some cases function is found for stretches of this DNA. In very rare cases (like RNAi) completely new functions are found. However, biologists looked for those functions, no matter what the OP says.

    In fact, the OP doesn’t say otherwise. Did you actually read the OP, or is this just an evolutionary canard?

  5. In fact, the OP doesn’t say otherwise. Did you actually read the OP, or is this just an evolutionary canard?

    You keep forgetting that all those scientists that studied the function of ‘junk DNA’ were actually evolutionists.

    And yet, I did read the OP. For starters, like so many times before, you misrepresent the term ‘junk DNA’.

    And take for example this paragraph:

    Evolutionists, unaware that they are staring at a design whose complexity dwarfs their puny understanding, decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Later, when the function is eventually uncovered, evolutionists automatically claim the design as an evolutionary achievement. The structure goes from junk to treasure without a second thought.

    It’s fiction, until you actually are able to support it with actual facts. That will be very hard for you.

  6. 6

    aqeels:

    I have always believed that if design is ultimately responsible for the complexity found in life, then junk DNA does not make any sense at all.

    I can’t argue with you there. This is a classic metaphysical argument for evolution which is not falsifiable. Evolution must be true.

    The problem I have though is this; Why would the genome of certain onion species be about 5 times bigger than a humans?

    Darwin’s book, and the evolution genre, is full of “Why would’s”. Design is falsified and therefore evolution, in one way or another, must be true. It is a fact and a theory. The fact tells us it is true. The theory tries to explain how in the world the absurdity could actually have happened. And we call this science. :-(

    This presents a real problem for design proponents as finding uses for some previously thought junk DNA sequences is fine, but how many novel functions can you expect to find for something as relativity simple as an onion?

    I have no idea, but I can tell you that even if uses were found for all of it, evolution would not be harmed, for this is just one example of many biological structures that evolutionists mandate must not have been designed. Indeed, in cases where function is found, even there evolutionists don’t give up their contention — they say even if function if found, a designer would not have done it in such a strange way. That’s religion for you.

  7. 7

    hrun:

    You keep forgetting that all those scientists that studied the function of ‘junk DNA’ were actually evolutionists.

    Again, I never said otherwise. Some evolutionists use the strategy of tossing out unfounded criticisms as fast as possible.

  8. Some evolutionists use the strategy of tossing out unfounded criticisms as fast as possible.

    Ahh, now you are at least agreeing that it might be ‘SOME evolutionists’ rather than ‘evolutions’.

    So if you never disputed that evolutionary biologists study and discover function in ‘junk DNA’ then what the point of your statement above? In fact, what is the point of the whole post?

  9. 9

    hrun:

    Ahh, now you are at least agreeing that it might be ‘SOME evolutionists’ rather than ‘evolutions’.

    Ah, you’ve caught me, and now you can see me backpedaling to try to save face from my obvious inaccuracies you have cogently pointed out.

    So if you never disputed that evolutionary biologists study and discover function in ‘junk DNA’ then what the point of your statement above? In fact, what is the point of the whole post?

    Again, you should try reading before criticizing with unfounded preconceptions about what the evolution skeptic must be saying.

  10. Again, you should try reading before criticizing with unfounded preconceptions about what the evolution skeptic must be saying.

    Yes. Thanks. Again, no support. Just the claim that now somebody who actually read the text misunderstood it.

    Rather than criticizing me, you might want to consider that what you wrote is in fact very misleading. And, rather than criticizing me, you might want to take the time to erradicate such misunderstanding.

    Just a thought.

  11. This has got to be one of the most ridiculous things I have ever read.

    Duplications, deletions and insertions of genomes are occurring all the time. Are you saying that every time a duplication/insertion occurs, it has an important function? This is obviously ridiculous and would go against ID concepts about increasing information. Or are all of these changes harmful? Which wouldn’t make sense since plenty of organism are still around with multiple insertions/duplications.
    Or are many of the duplications/insertions functionless. If so…there’s your junk DNA.

  12. 12

    hdx:

    This has got to be one of the most ridiculous things I have ever read.

    Duplications, deletions and insertions of genomes are occurring all the time. Are you saying that every time a duplication/insertion occurs, it has an important function? This is obviously ridiculous

    Responses of evolutionists to criticism of their theory are often a good example of how steeped they are in their own metaphysics. You can point it out to them, but they are unmoved. They automatically read their own metaphysical issues into the criticism, and then criticize you for not adequately handling their metaphysical concerns. These responses we’re seeing here are typical, and they speak volumes about what evolution is all about.

  13. CH these guys are proving your point at every turn in that their metaphysics is driving their science.,,, You must be gently laughing and shaking your head in disbelief as you type responses,

  14. CH these guys are proving your point at every turn in that their metaphysics is driving their science.,,, You must be gently laughing and shaking your head in disbelief as you type responses,

    What do you know about my (or hdx’s) science?

    In any case, how are we proving a point? I am simply trying to discern WHAT exactly CS is trying to claim in his posts about ‘junk DNA’.

    I thought I knew, yet, I was told that I did not read carefully engouh. You, apparently, know as well. Would you like to hazard a guess as to what exactly he is trying to claim about ‘junk DNA’?

  15. hrun, for you to not see how evolutionary thinking has hindered research, for over 30 years, into the apparent “complexity that dwarfs our puny understanding” is the height a metaphysical bias blinding objective judgment on the matter. As well, Evolutionary thinking continues to impede meaningful progress in this area by its continued insistence in misleading the researchers with totally unwarranted conjectures belittling the genome of function. Conjectures that arise from nothing more than a belief that evolution must be true rather than from what the empirical evidence such as ENCODE has suggested.

  16. Dr Hunter,

    Thank you for writing a blog post that I actually come close to agreeing with.

    I strongly agree that all apologetics are religious. I think the “junk DNA as negative apologetic” stance accurately describes the reactions of some people to the Paleyite apologetic “beauty/efficiency/wonder is evidence of God”.

    By itself, junk DNA cannot be used as a blanket apologetic against creation, only against creation by an omni-(scient, potent, benevoloent) deity who thinks like we do. Knock out experiments on the ‘omni’ genes of the deity can lead to junk DNA. A tri-omni deity that thinks like a praying mantis instead of man might create junk DNA. Angra Mainyu might create junk DNA. So we can see that the negative apologetic of junk DNA is quite limited in power.

    I don’t know the intertwined history of evolution and religion well enough to know when was the first use as an apologetic device of Ohno’s back-of-the-envelope calculation that a large part of the human genome was not under any strong selection pressure. However, it should be clear that such use is an ‘exaptation’ of a legitimate scientific question – if Ohno’s assumptions are accurate, how do we account for all that DNA?

    Finding function for a very small amount of repeated sequences (according to the paper you reference, those REs just 5′-ward or embedded in the 3′ UTR of a protein coding gene) is to some the tip of the iceberg of junk DNA function. To others it the tip of the icecube. As long as there is new science emerging from this area, some on each side will appropriate the result for polemic use.

  17. hrun, for you to not see how evolutionary thinking has hindered research, for over 30 years, into the apparent “complexity that dwarfs our puny understanding” is the height a metaphysical bias blinding objective judgment on the matter.

    Okay. Included in this accusation is a clear statement: “Evolutionary thinking has hindered research for over 30 years.”

    See, I thought that this was one of the points CH was making.

    Now, is there any factual support for this?

    Another clear statement is: “As well, Evolutionary thinking continues to impede meaningful progress in this area by its continued insistence in misleading the researchers with totally unwarranted conjectures belittling the genome of function.”

    Again, do you have factual support, or does this remain an assertion?

    Finally, embedded in this “Conjectures that arise from nothing more than a belief that evolution must be true rather than from what the empirical evidence such as ENCODE has suggested.” is the assertion that empirical evidence of ENCODE runs counter to ‘a belief that evoluion is true’. Again, a bold statement without any factual support.

    Okay, here we have three assertions without any support. Since you made them, and not CH, I ask you: Support them with facts.

  18. hrun:
    1:
    Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional.

    The slow, painful death of junk DNA:
    Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function; it is something that is required by evolution. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work….Junk DNA is a necessary mathematical extrapolation… Without Junk DNA, evolution runs into insurmountable mathematical difficulties.(on top of already insurmountable mathematical difficulties) http://creation.com/junk-dna-slow-death

    Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, “they are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”

    2.
    The Unseen Genome, Gems Among the Junk:
    “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003) http://www.evolutionnews.org/

    3.

    Concluding statement of the ENCODE study:
    “we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more ‘neutral’ view of many of the functions conferred by the genome.” http://www.genome.gov/Pages/Re.....e05874.pdf

    A ‘scientific revolution’ is taking place, as researchers explore the genomic jungle:
    “The science of life is undergoing changes so jolting that even its top researchers are feeling something akin to shell-shock. Just four years after scientists finished mapping the human genome – the full sequence of 3 billion DNA “letters” folded within every cell – they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.”
    http://www.boston.com/news/glo.....ed/?page=1

    you want to know what is really funny hrun? Genetic Reductionism is falsified in the first place!

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    http://www.metacafe.com/watch/4187488

    DNA: The Alphabet of Life – David Klinghoffer
    Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell’s building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn’t there. Instead, “It is as if the ‘idea’ of the fly (or any other organism) must somehow permeate the genome that gives rise to it.”

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

    “There is now considerable evidence that genes alone do not control development. For example when an egg’s genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.”
    The Design of Life – William Dembski, Jonathan Wells Pg. 50

  19. Mr BA^77,

    The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.”
    The Design of Life – William Dembski, Jonathan Wells Pg. 50

    If you want to see how a discussion of Wells’ position turned out, just hit that link and check the comments from 198 onwards. The Cliff Notes (TM) version is:

    Rabbit egg + human DNA,
    combined in a particular way
    = human stem cells,
    the contradiction of Wells,
    and the limerick of Nakashima!

  20. Nak, and just why should I ever trust anything you say? especially since you have twisted evidence countless times before? Am I suppose to just forgive and forget all the times you have tried to deceive people on UD with your extremely biased, “slight of hand”, presentation of evidence??

  21. Nak, I read through that link and you provided no peer review, the basic Jest is Joseph paitently tried to correct you, you did not listen, Joseph left (apparently tired of talking to the deaf) then you went on for a few more post with nothing relevant to say nor evidence presented. Then you thumped your chest and declared victory as if that is how truth is found in science. It would be funny but it is too sad for me to muster a laugh. I believe the one line out of the whole exchange sums it up, and is the most truthful, is this quote by Joseph in 273:

    “IOW you have proven your dishonesty beyond any reasonable doubt.”

    Here is another video for you to ignore the implications of Nak;

    Fearfully and Wonderfully Made – Glimpses At Development In The Womb
    http://www.metacafe.com/watch/4249713

  22. Mr BA^77,

    Nak, and just why should I ever trust anything you say?

    The point of linking to the original thread was that I don’t expect you to take my word for it. I’m helping you and anyone else interested in following up on the discussion go look, read and decide for themselves. Comment 198 in that thread cites a peer reviewed scientific research paper on interspecies nuclear transfer. Wells is wrong.

  23. Nakashima-san,
    bornagain 77 isn’t interested in evidence, and certainly not evidence from the peer-reviewed scientific literature. Bits and pieces copied willy nilly from various creationist and ID videos, plus selected quote-mines lifted from various creationist and ID quote-mine lists, strung together in an incoherent and meaningless sequence, then paste-bombed into threads so long that even the most committed ID partisan can barely wade through them – yes, by all means, but actual scientific research reports complete with references cited? Don’t be ridiculous…

    BTW, I have always liked Barry Commoner’s response to the question of whether he was “born again” (when running for president on the Citizens’ Party ticket back in 1980):

    “I was born 63 years ago in Brooklyn, New York, and I don’t intend to repeat the process.” [ http://news.google.com/newspap.....53,5380977 ]

    Commoner was running against Ronald Reagan, Jimmy Carter, and John Anderson, all three of whom had stated that they were “born again Christians”.

  24. A recent finding of “junk” DNA function involves repetitive elements which have been found to be active in certain tissues. The researchers concluded that this activity “has a key influence” on the overall activity of the mammalian genome. As one evolutionist admitted, “As a class [repetitive elements] are not just a junk DNA. They’re not just parasites, but they can shape the architecture of the genome.”

    So does this mean gene duplications increase information?

  25. McNeill, taking cheap shots? What’s the deal? Are you angry at me for publicly calling your bluff on your umpteen variations of deception? Hey don’t get mad at me! Just falsify Abel’s null hypothesis with any one of the numerous variations (besides point mutations) you have listed? If you want to get mad, get mad, but at least rightly place your anger, and get mad at yourself for lying to yourself and others with no empirical evidence to back yourself up.

    Hmm Nak, seems that the peer review evidence you alluded to was refuted by, of all people Voice coil in 221

    As of the 2006 review cited above there were five instances of interspecies nuclear transfer resulting in live births (read, “fully developed”). All such cross species transfers occurred within the same genus. All resulted in animals of the species donating the nuclei. Therefore these within genus differences are determined by DNA.
    http://www.uncommondescent.com.....ent-342112

    Which for me, clearly indicates that the body plans are strictly constricted to a morphological pattern, whereas the DNA provides the parts necessary for the body plan, with the Gaur example you merely provided more building material for the “cow’ to build the body plan with since you reached up higher on the originally created kind of the cow that had been diversified from in the first place

    And since it is in fact the major body plans of phyla that appear abruptly in the Cambrian, with lack of transitions, I believe the onus is on you to show morphological novelty from overriding body plans rather than just solidifying the already established point that body plans are not encoded in DNA..

    Now Nak if you do decide to provide relevant peer-review that does show body plans are decided by DNA I wi8ll gladly look at it to show you where your flaws in thinking are. Deal?

  26. 26

    Allen_MacNeill,

    BTW, I have always liked Barry Commoner’s response to the question of whether he was “born again” (when running for president on the Citizens’ Party ticket back in 1980):

    “I was born 63 years ago in Brooklyn, New York, and I don’t intend to repeat the process.”

    That’s just a silly misunderstanding of what it means to be “born again.” Do you normally like silly misunderstandings?

  27. BA77:Now Nak if you do decide to provide relevant peer-review that does show body plans are decided by DNA I wi8ll gladly look at it to show you where your flaws in thinking are. Deal?

    I’m not Nakishima nor do I intend to speak for him but here is one of many references in relation to DNA and body plans.

    Studies of DNA damage and cell death in embryonic limb buds induced by teratogenic exposure to cyclophosphamide

    Dr. Jeanne M. Manson *, Linda Papa, Marian L. Miller, Christine Boyd
    Department of Environmental Health, University of Cincinnati, Cincinnati

    *Correspondence to Jeanne M. Manson, Associate Professor of Environmental Health, University of Cincinnati, 3223 Eden Avenue, Cincinnati, OH 45267

    Keywords
    teratogen • cyclophosphamide • limb buds • DNA damage • cell death

    Abstract
    Many teratologic investigations have shown that certain types of chemical insults to the embryo (those altering replication, transcription, and translation) can cause excessive cell death in tissues destined to become malformed. Chemical carcinogens also induce cell death in target tissues, but the critical event is believed to be heritable alteration in the DNA of surviving cells. In the present study, an attempt was made to study the interaction between cell death and DNA damage in the initiation of birth defects. The pattern of DNA damage induced by cyclophosphamide was examined at time intervals before, during, and after the necrotic episode in mouse embryo limb buds. The alkaline elution assay was used to measure alkali-labile sites in single-strand DNA due to its adaptability to small tissue samples.
    An ip dose of 20 mg/kg of cyclophosphamide induced forelimb malformations in 85% of surviving mouse fetuses and 30% embryolethality when administered at 9 am on Day 11. As early as 5 hr after exposure, a slight excess of necrosis was observed in treated limbs by light microscopy, while at 24 hr, massive necrosis was evident. By 48 and 72 hr, excess necrosis was not observed in treated limbs. When alkaline elution analysis was conducted at prenecrotic (1-, and 5-hr), necrotic (24-hr), and postnecrotic (48-, and 72-hr) intervals, a trend toward increasing DNA damage in treated limbs with time was observed. The greatest differences in elution values occurred during the postnecrotic period. Although mean retention values were not significantly different, significantly increased variance was obtained in retention values of treated limbs at all time intervals other than 1 hr. This may reflect the actual in vivo situation where relatively few cells within a heterogeneous population of cells carry sublethal DNA damage into the postnecrotic period. These results suggest that not all limb bud cells affected by teratogenic exposure to cyclophosphamide die, but that some persist to the postnecrotic period carrying heritable alterations in their DNA.

    I’m looking forward to yoru commentary! Hopefully there will be no videos.

  28. Yes, especially when they’re jokes, not misunderstandings. Barry Commoner knew exactly what it meant to be “born again”, and so do I. He was making a joke, specifically about the apparent necessity to profess being a “born again” Christian when running for president (in 1980, anyway). But, as I said (in a comment that apparently has not made it through moderation), it’s hard to make jokes that are understood by the ideologically committed…

  29. MacNeil, “it’s hard to make jokes that are understood by the ideologically committed.”

    Would the “ideologically committed” be some sort of “religious” person who refused to change their beliefs even though all evidence they cling to melts away as knowledge increases?

    And MacNeill just whom do you think fits that personification?

  30. re acipenser: your kidding right? you cite a study of intentionally damaged DNA (they subtracted information for building parts of body plans) and then they observe various stages of malformed Body Plans??? Though their may be a nugget to glean somewhere in it, I really fail to see how this is relevant in any way to bolstering Nak’s falsified claim that body plans derive from DNA?

  31. BA77:re acipenser: your kidding right? you cite a study of intentionally damaged DNA (they subtracted information for building parts of body plans) and then they observe various stages of malformed Body Plans??? Though their may be a nugget to glean somewhere in it, I really fail to see how this is relevant in any way to bolstering Nak’s falsified claim that body plans derive from DNA?,

    The scientists who conducted this experiment did not subtract anything but to test their hypothesis that genotoxic agents, i.e., those that alter the DNA of an organism, cause malformations during development. In short pertubations of the DNA result in altered/malformed body plans that which you claimed was not possible.

    Perhaps you aren’t familiar with teratogenises and how DNA is involved in formation of body plans.

  32. 32

    Allen_MacNeill,

    But, as I said (in a comment that apparently has not made it through moderation), it’s hard to make jokes that are understood by the ideologically committed…

    We’re all ideologically committed, even if the ideology is one of keeping all ideologies provisionally, that idea cannot be provisional if all other ideas will continue to be. Besides, I thought the joke was silly, and such silliness doesn’t strike me as funny, but rather a way to be passive aggressive against being born-again, a central tenet of Christianity, of which passive aggressiveness is exactly how you strike me. Not everything is permissible because it appears as a joke, or comes as a punchline, for this kind of satire is really passive aggressiveness, and I find that silly and inappropriate, and I won’t tolerate it. Are we clear?

  33. To add to #31 if the DNA is not altered then normal body-plan devlopment proceeds normally.

    In the real world 3-5% of human births result in defects many of which are attributable to altered DNA either via a heritable problem or DNA damage during some stage in development. DNA alteration at differing stages cause different types of malformation.

  34. Yes, Clive, perfectly clear.

    As to being “born again” being a central tenet of Christianity, I don’t remember it being taught to me in the 12+ years I was in Sunday school (Homer Congregational Church, Homer, NY), nor in my confirmation classes, nor did it come up during the 10+ years that I served on the board of directors of Cornell United Religious Work, nor have I heard it mentioned in 30+ years of attending the Ithaca Friends Meeting. But I suppose by your definition none of those organizations are genuinely Christian.

    On the other hand, I have often heard the phrase used as a rhetorical weapon, intended by those brandishing it to denigrate exclude people who did not immediately profess to having experienced it. Would that be the kind of “born again” you don’t want me to make jokes about, Clive?

  35. To return to the topic under discussion in this thread, having been a very small part of the scientific community that has investigated the various functions of DNA and how it regulates the assembly and operation of living organisms, I don’t recall every having someone tell me that “junk DNA” didn’t have any function. On the contrary, what nearly everybody has said about DNA from the very beginning is that we don’t yet know a lot about how DNA does what it does. Being in a general state of ignorance about how DNA sequences become manifested in the structure and function of living organisms, the safest position to take (that is, “safest” in terms of not deluding oneself) is to assume nothing a priori, and then to modify one’s model(s) as new information becomes available.

    This means that the so-called “junk DNA” should not be assumed to have a function until such function(s) can be empirically verified. To some this may appear to be a position in which researchers are asserting that “junk DNA” has no function. However, a much more accurate depiction of their position would be that no function for DNA should be assumed until it has been verified.

    Personally, I think the term “junk DNA” was an extremely unfortunate choice of words. “Non-coding DNA” would have been much more descriptive, more precise, and would not carry along any metaphysical baggage.

    In this context, I find it interesting that many of the people now actively investigating the functions of non-coding DNA do not (or at least no longer) refer to it as “junk DNA”. No, that designation seems to come primarily from anti-evolutionists, who brandish it as a straw-man in rhetorical debates.

    For confirmation or falsification of my impressions, I think it would be educational if those who disagree with my assessment would post examples from the recent peer-reviewed literature in which researchers investigating gene expression have consistently used the term “junk DNA” in the way it has been used in this thread.

  36. This article really points out one of the fundamental sceintific distinctions between the ID and Neo Darwinist paradigrms.

    The essential issue has to do with sceintific progress- which comes by the enhancement of discovery and understanding. When Darwinists find a section of code that looks somewhat organized but cannot immediately find any function exact for it- by the virtue of their own investigative philosophy they are content with assuming that no such function exists at all- and hence the fruit of that conclusion is a SCIENCE STOPPER. On the other hand ID looks specifically for the hallmarks of design- which implies purposiveness- and so assumes at the onset that some functionality probably does exist- so long as the SC of the subject being investigated warrants it- leads to a more aggressive and in depth scientific pursuit of the nature of the phenomena- like likes of code in the genome.

    So obviously – as was the case with some of the greatest of minds like Newton- an ID perspective is a heuristically fruitful scientific position. And this is why it SHOULD be taught in schools- public and private alike- as it is not a religious doctrine at all- but a scientifically sound secular paradigm which has been proven to support the production of excellent scientific fruits.

  37. Based on Frost122585′s assertion in comment #36, one should therefore expect that, since the overwhelming majority of geneticists are “Darwinists”, they should have long ago stopped investigating the functions of non-coding DNA, and therefore ID scientists must have made the vast majority (indeed, virtually all) of the discoveries about the biological functions of non-coding DNA since 1972 (the publication date of Ohno’s paper, in which the term “junk DNA” was first used). Is this the case, Frost 122585?

  38. If so, please post citations to the primary literature in which ID scientists have discovered the functions of non-coding DNA that were ignored by “Darwinist” geneticists and developmental biologists. Also, it would help to show the ratio of original research papers, to verify that the overwhelming majority of the discoveries in the field of non-coding DNA function can be attributed to scientists committed to ID, and that the paltry few so-called “discoveries” made by committed “Darwinist” geneticists have been on a steady downhill decline since 1972.

  39. And, while you’re at it, please post direct citations to the recent primary literature in which “Darwinist” geneticists have asserted that non-coding DNA regions not only don’t have any discernible biological functions, but can’t have such functions, and should therefore not be investigated.

  40. Allen at 37,

    You claim is bunk. I said that ID is more scientifically fruitful because it leads people to EXPECT that functions may exist and hence that would encourage them to spend more time and energy looking them- and not that Darwinists would not find any at all. It is often the case in science that one branch helps another unintentionally. Such is the case where the development of space exploration technology is copted and used in other fields.

    But the point is that if more people are taught about the scientific usefulness of the design inference then there will be a more open minded pursuit of the nature and origin of phenomena from the perspectives of functionality and purposefulness.

    Now take Newton for example- he discovered many useful mathematical and scientific things concerning nature which one can easily see came from his belief that there must have been rationality in God’s design- that is, that the teleology of the world was so obvious (as you even seem to admit at some level) that it only makes sense that there is a rational way of explaining it because rationality (or intelligence) is behind the essence and nature of a design inference. You can also say the opposite is generally true- that where rationality ceases to exist so do intelligence.

    And Allen I have never said that ALL Darwinist biologists claim that functionality cannot exist regarding a specific presupposed junk DNA sequence etc- I have merely pointed out that the two paradigms of ID and neo Darwinism conflict on their inferences and operations- and that indeed ID is a much better paradigm when it comes to exploring the nature and origin of phenomena- because if the rigorous standards of an ID inference are met then an more intense and thorough investigation is warranted- and if those design criteria are not met then there is less waste of time trying to find more complex and convoluted explanations for things that are “probably” the result of simple predictable or chance based processes.

  41. SO the simple point here is that Darwinism does not DEMAND an understanding of the functionality of coding in DNA that looks designed – and that if no functionality is manifestly obvious then there is no reason to suppose that such functionality need exist. Where as ID implies at the get go that there probably IS a functionality and that it is fruitful to vigorously investigate and pursue what that is until it is properly understood.

    And this fundamental difference is obvious. IF you do not presuppose that Atlantis exists then why would you waste you time and energy looking for it? If you did not think that there should exist cures for diseases in the rain forests then why would you waste you time and money and risk you life looking for them? Many people still might go out in pursuit of these efforts but not as many as those who do think that such exploration are “probably” worth pursuing. And in the case with Newton his pursuit of science in light of ID like theological beliefs was obsessive to the result of his life’s work being possible unmatched by that of any other intellectual. Would he have put so much time into discovering the plan of the creator if he did not believe that a creator surely exist by the manifest beauty of the creation?

    Since Newton wrote more on theology than math and physics I certainly doubt it.

  42. Allen MacNeill,

    On the other hand, I have often heard the phrase used as a rhetorical weapon, intended by those brandishing it to denigrate exclude people who did not immediately profess to having experienced it. Would that be the kind of “born again” you don’t want me to make jokes about, Clive?

    I don’t like it as a rhetorical weapon either. But that wasn’t your intended target, it was passive aggressive disdain for the idea in general or at the commenter in particular, or so it appeared, and I don’t want to see it.

  43. Mr BA^77,

    Now Nak if you do decide to provide relevant peer-review that does show body plans are decided by DNA I wi8ll gladly look at it to show you where your flaws in thinking are.

    Why make yourself the poster child of closemindedness?

  44. Mr Frost,

    On the other hand ID looks specifically for the hallmarks of design- which implies purposiveness- and so assumes at the onset that some functionality probably does exist- so long as the SC of the subject being investigated warrants it- leads to a more aggressive and in depth scientific pursuit of the nature of the phenomena- like likes of code in the genome.

    So, what is the SC threshold for investigating something? Can you give me an example of one stretch of junk DNA whose SC measures above that threshold, and another that measures below it? You’re making a prediction that scientific investigation of the first will be more fruitful than scientific investigation of the second, correct?

  45. Nak,

    I could just respond to your post by saying something like “don’t be the poster child for the close minded” but I don’t think that would be an adequate response- so I wont.

    The threshold of what is or is not junk DNA may differ from one opinion to another- and junk DNA can indeed exist where there is natural deterioration of an aboriginal design that is somehow conferred and passed down generations- but the point is that when you site an example of junk DNA which calls into question the overall design of an ID inferred subject- this is when ID will go further and try to show and prove why there is the functionality predicted by the design inference- and it is through this extra step and effort that ID makes a unique contribution due to it’s unique operation.

    And the threshold of design is always when something cannot be reduced to randomness and necessity- or laws and chance– due to it’s overwhelming complexity and functional specificity.

    I cannot give you an exact example of where some junk DNA is inferred to probably be useful and later proven as such- but I will admit that trying to differentiate between what is aboriginal to the design and what is degraded and indeed junk is one of the toughest challenges for ID.

    So not all junk DNA need be eliminated for ID to be correct in its theory- but the balance between the two needs to support the necessity of a design inference. Or to quote Richard Dawkins- “biologists can accept a certain amount of chance in their explanations of origins – but not too much”

    Which too on the other hand cuts both ways.

  46. 46

    CH I wonder if the Darwinists are right. What little junk DNA there is probably arose through evolutionary processes. This of course says nothing about whether or not there was a designer or even what kind of designer he was, since the original design may have been perfect but degraded since then.

  47. A recent finding of “junk” DNA function involves repetitive elements which have been found to be active in certain tissues. The researchers concluded that this activity “has a key influence” on the overall activity of the mammalian genome. As one evolutionist admitted, “As a class [repetitive elements] are not just a junk DNA. They’re not just parasites, but they can shape the architecture of the genome.”

    So does this mean gene duplications increase information?

  48. Mr Frost,

    I suppose one of the reasons I’m not a poster child for close mindedness is that I take your position seriously and want to understand it better.

    And the threshold of design is always when something cannot be reduced to randomness and necessity- or laws and chance– due to it’s overwhelming complexity and functional specificity.

    Yes, but can you associate that idea with a way to put a numeric measurement to it, and do you have examples of those numeric measurements for sample sequences?

    It seems to me that triplet repeats, SINEs, SINEs degraded by point mutations, etc. would all fall squarely into the “can be produced by law and chance” category. If so, I don’t see why any ID supporter such as yourself would have difficulty with them being called junk.

  49. re: acipenser 33

    And if the parts supplier did not provide all the parts necessary for a “planned” machine at a robotic factory would not the general sequence of the malformed assembly of the machine that resulted from the robot because of insufficient parts, who is following a overriding architectural plan, look exactly as the patterns of malformed development you cite?
    To falsify the growing body of evidence that Body Plans do not reside in DNA, you must demonstrate morphological novelty for body plans arising from changes in the DNA. But alas something tells me you are going to fail.

    AMBER: THE LOOKING GLASS INTO THE PAST:
    Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.
    http://bcb705.blogspot.com/200.....st_23.html

  50. Nak, It is funny that a fellow evolutionist would provide the references to defeat your supposed falsification of body plans by showing that all “successful” live births are “within kinds”, thus the evidence that clearly showed you to be drastically overstating your position for DNA reductionism (materialism) is from your own camp! Yet in the glorious display of “open mindedness” and fair play, which you undoubtedly display in admitting that you are wrong in your claims for novel body plan morphogenesis arising from DNA, you turn around and claim I am the one who is a “poster child for close mindedness”.

    You know what is funny Nak? I DON”T NEED evolution to be true, because I am perfectly fine with the concept of God creating through evolutionary processes if He so desired. But you Nak ABSOLUTELY NEED evolution to be true or else you entire atheistic worldview collapses. So please tell me Nak which of us is more apt to be fair minded with the evidence and which of is more likely to be “a poster child for close mindedness”? I think the way in which you responded to the falsification of your position on this very thread is clear indication of who the poster child is.

  51. BA77:And if the parts supplier did not provide all the parts necessary for a “planned” machine at a robotic factory would not the general sequence of the malformed assembly of the machine that resulted from the robot because of insufficient parts, who is following a overriding architectural plan, look exactly as the patterns of malformed development you cite?
    To falsify the growing body of evidence that Body Plans do not reside in DNA, you must demonstrate morphological novelty for body plans arising from changes in the DNA. But alas something tells me you are going to fail.

    Alas the failure of the Body Plans aren’t coded in the DNA hypothesis fails miserably. Falsified by the data that clearly demonstrates that DNA pertubation/alteration results in malformed body plans. Specific alterations related to the timing of development of the body plan produces specific effects on the body plan. If the DNA were not responsible for the body plan then pertubation of the DNA should not produce any alterations of the body plan…..alas the data does not support such a conclusion and clearly points to the role of DNA in the body plan.

    The data is clear and the citation is far from being an isolated incidence. In fact there are entire journals dedicated to such research and the evidence points to one conclusions: DNA alterations affect body plan development. If DNA does not contain the ‘body plan’ what rational can be brought to explain the data…..hopefully no videos and/or blog citations will be presented in leui of data to support your hypothesis.

  52. Hmm acispenser,,, seems that someone forgot to inform the humble fruit fly of your “clear” findings verifying DNA reductionism;

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    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

    Hopeful monsters,’ transposons, and the Metazoan radiation:
    Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable “hopeful monsters” render these explanations untenable.
    Paleobiologists Douglas Erwin and James Valentine

  53. BA77:Hmm acispenser,,, seems that someone forgot to inform the humble fruit fly of your “clear” findings verifying DNA reductionism;

    As was feared the appearence of the blog post and youtube in leui of data but let’s take a look at what was posted:

    Similar mutations in other genes also produce various anatomical deformations

    yes, mutations in the genome influence the body plan…..supports the DNA:body plan hypothesis it appears.

    and…

    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

    clearly this is something we know is not true or seen as evidenced by the previous post in BA77′s link.

    and..

    Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile;

    3-5% of malformations in human births can hardly be considered rare but again the concept of DNA mutations and the resultatnt morphological effects are clearly presented supporting yet agian the tenent that DNA pertubations are associated with altered body plans.

    Thank you for posting the creationist support of the DNA:body plan linkage now do you have any actual data that supports the notion of a lack of relationship between DNA and morphology?

  54. acispenser,,, you don’t seem to grasp the whole concept of establishing scientific credibility.

    The question is to validate the assertion that DNA mutations “PRODUCE” novel morphological features. I clearly pointed out that this minor requirement for scientific validity has not been met. You point to mutation studies to DNA that “PREVENT” body plans from fully developing due to lack of the proper supply of proteins from the DNA, and then you say this conclusively proves that DNA has the overriding architectural plans for Body Plans within itself. Your logic is non-sequitur. i.e. it does not follow that you have conclusively made your point that you would like to make. All you have done is show that you can’t build a house without all the proper building materials. Which is a point I totally agree with in the first place. Now if you want to conclusively make your point, just turn a fruit fly into a butterfly, or anything else, by mutations to DNA.

  55. BA77:acispenser,,, you don’t seem to grasp the whole concept of establishing scientific credibility.

    You reached this conclusion how? Is it because I chose to cite the published literature rather than a youtube or blog post.

    but let’s look at what assertion was on the table:

    BA77:Now Nak if you do decide to provide relevant peer-review that does show body plans are decided by DNA I wi8ll gladly look at it to show you where your flaws in thinking are. Deal?

    now the goalpost have shifted which is no suprise to me but now the original assertion has been shifted to this:

    BA77:Now if you want to conclusively make your point, just turn a fruit fly into a butterfly, or anything else, by mutations to DNA

    The original assertion was that DNA does not decide body plans as you stated. The citation I presented directly refutes your notion as does the three links you provided in #52. Now you can continue to shift the goalpost as your position erodes but doing that does not change the data whatsoever.

    If the DNA does not contain the overriding architectural plan then you need to present an alternate interpretation of the data or accept that DNA mutations alter the architecture of the body plan. Your own citations do not support your assertions. In fact they demonstrate that mutations in DNA can and do result in novel morphological changes, i.e., four wings instead of two is quite a novel development.

    I anxiously await the next setting up of the goalpost and hope that they will remain in this field of play and not be shifted to another field altogether…but we will see how that goes.

  56. acispenser,,, hmmm, you get four wings instead of two wings on the fruit fly(the second set of wings lack flight muscles by the way so it is a detrimental mutation to the HOX gene) , identical wings on the fruit fly that were already present in the beginning of the experiment,,, and then all of the sudden this means that morphological novelty is a slam dunk for Neo-Darwinism and you are now free to extrapolate that bacteria can become elephants, penguins and aardvarks given a few billion more mutations and a few billion years to play with.

    WOW how in the world did I miss it. Thank you so much acispenser for setting me straight, and letting me see how blind I was and how I was grossly moving goalposts around to a different field on a entirely different planet.

    Must of been a flashback to the sixties to think otherwise.

  57. Acipenser, you know I really appreciate you setting me free from my creationist ways by showing me that fruit fly thing. You know the whole I was created by almighty God thing was just so stifling, It is just so much more exciting to realize my great-great grandpappy was a mud puddle and that I to shal be a mud puddle once again (and my mom use to get mad because I played in mud puddles) But as you know Acipenser, I am a newbie to these heathen ways of yours so you are going to have to walk me through a few things for a few days so I don’t relapse into praising almighty God for creating heaven, earth and life. Now I know that whole Body Plan thing is settled now with the whole four-winged fruit thing fly. Though I do have some nagging doubts with the Cortical Inheritance issue to Body Plans, yet I might be able to overcome those doubts with my new blind faith in mud puddles. Yet there is another issue, besides Body Plans, that I don’t think my new heathen faith is quite ready to handle. Doggone it acipenser its those nagging functional proteins. I just can’t seem to believe they are accidental. Though you hate videos bear with to see what I mean:

    Evolution vs. Functional Proteins – Doug Axe – Video
    http://www.metacafe.com/watch/4018222

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723

    Now Jack Szostak tried to get that number for functional proteins down to 1 in a trillion (1 in a trillion ain’t a miracle is it?), yet these guys come along and go and upset that 1 in a trillion apple cart:

    A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells
    Excerpt: “Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division.”
    http://www.plosone.org/article.....ne.0007385

    But I was thinking hey anything can happen once, you know once you got a functional protein all you got to is switch some amino acids around,, right,, and ba da boom ba da bing you got yourself elephants, aardvarks and penguins. But what do you know Acipenser, this Behe guy comes along and turns that apple cart over:

    Dollo’s law, the symmetry of time, and the edge of evolution – Michael Behe – Oct 2009
    Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,,
    A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses. http://www.evolutionnews.org/2.....f_tim.html

    Severe Limits to Darwinian Evolution: – Michael Behe – Oct. 2009
    Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2......html#more

    So as you can see Acispenser I am in real deep kimshe as far as my beliefs and may relapse to, I don’t even want to say the word, Creationism ,,, I know this sunday I should go to worship in a mud puddle as my newfound heathen instincts are telling me, but I am just terrified I don’t have the strength to do that and I may falter go to church instead. Any thing you can do to help me in this moment of crisis would be appreciated.

  58. Mr BA^77,

    I’m not sure why I should feel refuted, or why you are hung up on live birth. The paper I referenced listed the tests which showed that the resulting stem cells were human, not rabbit. Wells, whom you are trying to defend here, does not demand live birth.

    Here’s a fun reference about teosinte and a morhoplogical change related to DNA change. It seems the change from annual to woody perennial is moderately common.

  59. Nakashima et al. It is amusing to see your arguments re BODY plans involve CELLS and not BODIES.
    Methinks you protest too much.

  60. Dang it Nak the parental corn lineage (teosinte) ain’t gone to help me overcome those dang nagging doubts about functional proteins I was asking acispenser about.

    To top it all off Nak shoot now you done gone and opened up my doubts about the ability of evolution to account for novel Body Plans all over again, since I know there is a fairly large amount of variation in the parental stock of many “kinds” of plants:

    Evolution? – Mustard Plant – The Deception Of Unlimited Variation – video
    http://www.metacafe.com/watch/4113898

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

    The reduced genetic variability brought about by “natural selection” in major food crops, such as corn, is a major concern facing scientists today since the much larger genetic variability, which is found in the parent species of corn, maize, gives greater protection from a disease wiping out the entire crop of corn.

    Genetic diversity and selection in the maize starch pathway:
    The tremendous diversity of maize and teosinte has been the raw genetic material for the radical transformation of maize into the world’s highest yielding grain crop. http://www.pubmedcentral.nih.g.....tid=130568

    “Supergerms are not supergerms any more than hybrid corn is supercorn—today’s hybrid corns are so delicate that they can’t even sprout unless they are planted underground. They can’t even grow effectively unless the ground is weeded. They can’t even reproduce unless technicians at seed-houses mate them artificially and with great effort.” http://www.answersingenesis.or.....rgerms.asp

    Geez Nak why did you have to go and bring that up,,, Now that whole Genetic Entropy thing is also crushing my new found heathen faith, besides the extreme rarity of functional proteins. You really ain’t helping acispenser convert me to a chance worshipping, mud puddle wallowing, heathen are you. You best just let him talk me through this shaky period of my conversion process til I can stand on my own two hairless ape atheistic legs and shake my fist at the sky at the deity I no longer believe in.

  61. re#18:

    Allen_MacNeill has actually answered most of these points. But in order to be specific. You have failed to provide specific support:

    - for research that was actually hindered
    - for evolutions insistence to mislead researchers
    - for evolution to have totally unwarranted conjectures
    - for evolution to belittle a genome of function
    - for ENCODE to run counter to empirical evidence

    You have, yet again, posted a lot of opinion (from you and other folks). But alas, no evidence. In fact, there might actually be evidence, but nobody would know about it, since nobody seems to be willing to post it.

  62. [...]hence the fruit of that conclusion is [that Neo Darwinist paradigrms are (sic)] a SCIENCE STOPPER.

    Ah… another clear statement. Yet, the evidence actually runs counter to this claim. ID proponents continually purport that Neo Darwinist paradigms are domninant in universtiy research, yet, it is just that (being indoctrinated with Neo Darwinist paradigms) that continued to do science on ‘junk DNA’ and found some function. Research (under the indoctrination of Neo Darwinist paradigms) continues.

    So your assertions is clearly false. Science was not stopped.

  63. Far from it. In fact, if we broaden our perspective it is hard to think of any improvement in our understanding of the world or any refinement or new development in our technology which is not founded on methodologically natural, materialistic science. Restrictive or not, it works.

  64. Mr Mad doc,

    Nakashima et al. It is amusing to see your arguments re BODY plans involve CELLS and not BODIES.

    Well, that is what bodies are made out of! ;)

  65. hrun,
    since it is a established fact that evolution is completely false from first principles of science, (Dembski, Marks, Abel, Behe, Sanford, Second Law) i.e. basically falsification boils down to no demonstration of any information generation from material processes whatsoever, (a fact which you will vehemently attack but alas you cannot produce any empirical evidence to the contrary), and yet in spite of this glaring lack of evidence and the apparent “information complexity in DNA that dwarfs our puny understanding”,, leading evolutionists continue to refuse to admit to any such weaknesses whatsoever. Furthermore leading evolutionists such as Ayala, even as of last week, continue to insist that vast swaths of the DNA is functionless junk. Yet you, in your smug defiance of reason and common sense, insist that this is insistence is somehow not a science stopper, and to make it all the more ludicrous you ask for peer review, instead of opinions, that says it is a science stopper. plus you twist the last line of the ENCODE study to say that it did not directly state to take a neutral view of Junk DNA. Please tell me Hrun why leading evolutionists payed no attention to the premier study on the function DNA and that they continue to insist that the majority of DNA is junk? Have they lost their minds? I can think of no other reason! It would be absolutely funny for me save for the fact that you guys actually think you are the “rational” ones, as well as the mortifying fact that you “scientists” are feeding this relentless stream of garbage to our children in public schools.,,, I have a surprise for you hrun,,, Here is a peer review paper that shows Junk DNA to be a science stopper, but alas, you will ignore it as you do everything else:

    On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. Richard Sternberg
    Excerpt: the case is made for viewing REs as integrally functional components of chromosomes, genomes, and cells. It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.
    http://www.ncbi.nlm.nih.gov/pubmed/12547679

    here is a cool article detailing how Francis Collins is leading biological science down the wrong track:

    Weird Science – Casey Luskin
    Excerpt: Sternberg strikingly concluded that “the selfish DNA narrative and allied frameworks must join the other ‘icons’ of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature.” Sternberg, along with leading geneticist James Shapiro, elsewhere predicted that “one day, we will think of what used to be called ‘junk DNA’ as a critical component of truly ‘expert’ cellular control regimes.”,,,, Time and again, ID proponents have discovered that what Darwinists dismiss as defective actually has purpose and function,
    http://www.salvomag.com/new/ar.....luskin.php

  66. since it is a established fact that evolution is completely false from first principles of science

    I guess that says it all. Taking that into account, everything you say makes perfect sense.

    a fact which you will vehemently attack but alas you cannot produce any empirical evidence to the contrary

    You define information, I will provide empirical evidence. It’s as simple as that. However, without that you will simply claim that either no REAL information was created or the only a SMALL amount of information was created (and neither should count).

    and yet in spite of this glaring lack of evidence and the apparent

    What lack of evidence? There is plenty of evidence for novel mutations creating novel functions.

    Furthermore leading evolutionists such as Ayala, even as of last week, continue to insist that vast swaths of the DNA is functionless junk.

    Of course. They are right. Vast swaths of DNA most likely is functionless junk. Have you forgotten the example about the three types of onion again?

    Yet you, in your smug defiance of reason and common sense, insist that this is insistence is somehow not a science stopper, and to make it all the more ludicrous you ask for peer review, instead of opinions, that says it is a science stopper.

    Yes, it is me who defies both reason and common sense. And I am smug to boot. Yet, you have failed to support your assertion that evolution is a science stopper. The data: science goes on all the time, science is done by evolutionists, science occurs in those indoctrination palaces of evolution, science gets published in evolution journals, and so forth. So, sadly, against all evidence, you have failed to give any positive evidence of your assertion.

    plus you twist the last line of the ENCODE study to say that it did not directly state to take a neutral view of Junk DNA.

    How exactly did I twist the words of ENCODE? Did ENCODE actually claim that it runs counter to the belief that evolution is true? Of course not. You simply made that up and then posted it as fact.

    Please tell me Hrun why leading evolutionists payed no attention to the premier study on the function DNA and that they continue to insist that the majority of DNA is junk?

    Which leading evoluionists payed no attention to the premier study on the function of DNA. Yet another assertion without proof. And, quite possibly, the reason why they do assert that lots of DNA doesn’t have a function is because it doesn’t? Remember the three onions again.

    Have they lost their minds? I can think of no other reason!

    They have not lost their minds. That you can’t think of another reason is no surprise to anybody.

    It would be absolutely funny for me save for the fact that you guys actually think you are the “rational” ones, as well as the mortifying fact that you “scientists” are feeding this relentless stream of garbage to our children in public schools.

    You forget that it is also the ‘scientists’ that find functional gems in areas of mainly functionless DNA. For example, check out the Nylonase. Perfect example. And so pertinent to ID as well. Oddly enough… found by evolutionists. They just continue doing science and finding new functions, no matter what you assert.

    I have a surprise for you hrun,,, Here is a peer review paper that shows Junk DNA to be a science stopper, but alas, you will ignore it as you do everything else:

    Where does it show that there is any stopping of science. I just don’t see the supporting data to your claim.

    Yes, if you take the term ‘junk DNA’ and say that it is all functionless, then indeed, nobody should look at it. Gladly, only people like you claim that to be the case. It might be educational for you to actually attend a bio course.

  67. hrun, since you will allude to the complexity found in life processes instead of purely material processes, here is what you need to falsify to prove evolution correct:

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.metacafe.com/watch/3995236

    Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
    http://www.metacafe.com/watch/3995248

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

    The “fitness test” must be passed by the sub-species against the parent species. If the fitness test is shown to be passed then the new molecular function, which provides the more robust survivability for the sub-species, must be calculated to its additional Functional Information Bits (Fits) it gained in the beneficial adaptation, and then be found to be greater than 140 Fits. 140 Fits is what has now been generously set by Kirk Durston as the maximum limit of Functional Information which can reasonably be expected to be generated by the natural processes of the universe over the entire age of the universe (The actual limit is most likely to be around 40 Fits)(Of note: I have not seen any evidence to suggest that purely material processes can exceed the much more constrained “2 protein-protein binding site” limit, for functional information generation, found by Michael Behe in his book “The Edge Of Evolution”). This fitness test, and calculation, must be done to rigorously establish that the principle of Conservation of Information has been violated.

    Is that clear enough for you hrun?

    further note:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    http://mdpi.com/1422-0067/10/1/247/ag

  68. Nylonase is your “evidence hrun?

    Some materialists believe they have conclusive proof for evolution because bacteria can quickly adapt to detoxify new man-made materials, such as nylon, even though it is, once again, just a minor variation within kind, i.e. though the bacteria adapt they still do not demonstrate a gain in fitness over the parent strain once the nylon is consumed (Genetic Entropy). I’m not nearly as impressed with their “stunning” proof as they think I should be. In fact recent research has shown the correct explanation for the nylon-eating enzyme, produced on the plasmids, seems to be a special mechanism which recombines parts of the genes in the plasmids in a way that is non-random. This is shown by the absence of stop codons, which would be generated if the variation were truly random. The non-randomness and “clockwork” repeatability of the adaptation clearly indicates a designed mechanism that fits perfectly within the limited “variation within kind” model of Theism, and stays well within the principle of Genetic Entropy since the parent strain is still more fit for survival once the nylon is consumed from the environment. (Answers In Genesis)

    Nylon Degradation – Analysis of Genetic Entropy
    Excerpt: At the phenotypic level, the appearance of nylon degrading bacteria would seem to involve “evolution” of new enzymes and transport systems. However, further molecular analysis of the bacterial transformation reveals mutations resulting in degeneration of pre-existing systems.
    http://www.answersingenesis.or.....n-bacteria

    Why Scientists Should NOT Dismiss Intelligent Design – William Dembski
    Excerpt: “the nylonase enzyme seems “pre-designed” in the sense that the original DNA sequence was preadapted for frame-shift mutations to occur without destroying the protein-coding potential of the original gene. Indeed, this protein sequence seems designed to be specifically adaptable to novel functions.” http://www.uncommondescent.com.....nt-design/

  69. hrun I couldn’t help notice that you tacked evolutionary onto scientists in your reference to the discovery of the nylonase adaptation. Are they scientists first or are they evolutionists first? Since I can’t separate your rhetoric from rational thought, would you please provide their diplomas in molecular biology and point out where it says “evolutionary” on then. i.e.

    “Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming’s discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No.
    Philip S. Skell – Professor at Pennsylvania State University.
    http://www.discovery.org/scrip.....38;id=2816

    Science Owes Nothing To Darwinian Evolution – Jonathan Wells – video
    http://www.metacafe.com/watch/.....han_wells/

  70. Just to illustrate to everybody the type of reasoning you use:

    First you write:

    evolution is completely false from first principles of science, [...] demonstration of any information generation from material processes whatsoever

    I show that in fact there is empirical evidence to show that information can be generated by material processes. As an example, take Nylonase. Since I am aware of your type of reasoning I write the following:

    you will simply claim that either no REAL information was created or the only a SMALL amount of information was created

    Then, predictably, you write:

    Some materialists believe they have conclusive proof for evolution because bacteria can quickly adapt to detoxify new man-made materials, such as nylon, even though it is, once again, just a minor variation within kind.

    To summarize the exchange:
    You claim there is no evidence of information being produced. I show there is just that type of evidence. You claim, oh no, that’s not what I meant. I meant MORE information than that.

    (then you go on to tack on many quotations yet again that are absolutely not pertinent to anything)

  71. hrun I couldn’t help notice that you tacked evolutionary onto scientists in your reference to the discovery of the nylonase adaptation.

    I was echoing YOUR charge, namely that universities and thus science are FULL of people who believe evolution to be true– thus the evolutionary. You can remove it if you like.

  72. hrun0815, you must prove that information is generated by purely natural processes; you cannot use the degradation of preexisting information that was already in the genome as proof of the generation of new information. That is why I specifically cited this test:

    Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
    http://www.metacafe.com/watch/3995248

    as well as citing this article:

    Nylon Degradation – Analysis of Genetic Entropy
    Excerpt: At the phenotypic level, the appearance of nylon degrading bacteria would seem to involve “evolution” of new enzymes and transport systems. However, further molecular analysis of the bacterial transformation reveals mutations resulting in degeneration of pre-existing systems.
    http://www.answersingenesis.or.....n-bacteria

    You see hrun, once you remove the nylon from the environment the “parent” bacteria will ALWAYS be more fit for survival and the “improved” nylon bacteria will ALWAYS eventually die away. Why is this always the case? If functionality (i.e. functional information) “was generated” by purely material processes, then why have you not cited thousands of articles demonstrating the generation of such functional complexity/information. Can you not provide even one example of increased functionality that will pass the fitness test? Since not (and it is NOT), Why don’t you find it even a little suspect that bacteria are suppose to turn into elephants, aardvarks and penguins. Please tell me why.

    further notes:

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    and this:

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart,(thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s “genetic drift” theory requires.)
    http://www.sciencemag.org/cgi/...../5213/1060

    30-Million-Year Sleep: Germ Is Declared Alive
    http://query.nytimes.com/gst/f.....gewanted=2

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

  73. hrun0815, you must prove that information is generated by purely natural processes; you cannot use the degradation of preexisting information that was already in the genome as proof of the generation of new information.

    First of all, we have yet another case of changing goalposts. If you read your previous post you will see that you agree that this is a purely natural process. You only complain about the amount of information generated.

    Second, in your previous post you also agree with the fact that information is generated in the Nylonase case. There is no mention of ‘degradation of preexisting information’.

    Third, I specifically asked for a definition of information, so you can’t hide behind the ‘degradation of preexisting information’.

    Fourth, it is clear to everybody that this is NOT a case of information degradation. Neither Nylon nor Nylonase existed earlier: both are recent inventions, so the creation of Nylonase can not ce degradation of preexisting information.

    I find this exchange (while tedious for me) highly informative for everybody around. It very well exemplifies one of the most common discussion techniques used here and elsewhere.

  74. one, I asked for a demonstration of generation of functional information, you did not provide one.

    two I never agreed that nylonase generated is a demonstration of the generation of functional information over and above what was already present.

    three I gave you Szostak’s paper on the definition of functional information.

    four you cannot extrapolate that the bacteria “invented” the ability to digest nylon without demonstrating a gain of functional information by passing the fitness test over the parent strain.

    I couldn’t agree with your concluding comment more.

    In further note it should be clearly pointed out that bacteria have been “detoxifying” the earth of toxic materials for billions of years. This terra-forming ability of bacteria is a very ID friendly fact and is very antagonistic to your atheism.

    further notes:

    Interestingly, while the photo-synthetic bacteria were reducing greenhouse gases and producing oxygen, and metal, and minerals, which would all be of benefit to modern man, “sulfate-reducing” bacteria were also producing their own natural resources which would be very useful to modern man. Sulfate-reducing bacteria helped prepare the earth for advanced life by detoxifying the primeval earth and oceans of poisonous levels of heavy metals while depositing them as relatively inert metal ores. Metal ores which are very useful for modern man, as well as fairly easy for man to extract today (mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper to name a few). To this day, sulfate-reducing bacteria maintain an essential minimal level of these heavy metals in the ecosystem which are high enough so as to be available to the biological systems of the higher life forms that need them yet low enough so as not to be poisonous to those very same higher life forms. These following studies show this “latent” ability of SRB’s to detoxify the earth of poisonous levels of heavy metals:

    Bacterial Heavy Metal Detoxification and Resistance Systems:
    Excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.
    http://www.springerlink.com/co.....04577v8t3/
    http://www.int-res.com/article.....26p203.pdf

    The role of bacteria in hydrogeochemistry, metal cycling and ore deposit formation:
    Textures of sulfide minerals formed by SRB (sulfate-reducing bacteria) during bioremediation (most notably pyrite and sphalerite) have textures reminiscent of those in certain sediment-hosted ores, supporting the concept that SRB may have been directly involved in forming ore minerals. http://www.goldschmidt2009.org...../A1161.pdf

    Transitional Metals And Cytochrome C oxidase – Michael Denton – Nature’s Destiny
    http://books.google.com/books?.....3&lpg

    As well, geological processes helped detoxify the earth of dangerous levels of metal:

    The Concentration of Metals for Humanity’s Benefit:
    Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth’s crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth’s crust strongly suggests supernatural design.
    http://www.reasons.org/TheConc.....tysBenefit

    And on top of the fact that poisonous heavy metals on the primordial earth were brought into “life-enabling” balance by complex biogeochemical processes, there was also an explosion of minerals on earth which were a result of that first life, as well as being a result of each subsequent “Big Bang” of life there afterwards.

    The Creation of Minerals:
    Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization. http://www.reasons.org/The-Creation-of-Minerals

    To put it mildly, this minimization of poisonous elements, and “explosion” of useful minerals, is strong evidence for Intelligently Designed terra-forming of the earth that “just so happens” to be of great benefit to modern man.

    Man has only recently caught on to harnessing the ancient detoxification ability of bacteria to cleanup his accidental toxic spills, as well as his toxic waste, from industry:

    What is Bioremediation? – video
    http://www.youtube.com/watch?v=pSpjRPWYJPg

    Clearly many, if not all, of these metal ores and minerals laid down by these sulfate-reducing bacteria, as well as laid down by the biogeochemistry of more complex life, as well as laid down by finely-tuned geological conditions throughout the early history of the earth, have many unique properties which are crucial for technologically advanced life, and are thus indispensable to man’s rise above the stone age to the advanced “space-age” technology of modern civilization.

    Metallurgy
    http://en.wikipedia.org/wiki/Metallurgy

    Inventions: Elements and Compounds – video
    http://videos.howstuffworks.co.....-video.htm

    Bombardment Makes Civilization Possible
    What is the common thread among the following items: pacemakers, spark plugs, fountain pens and compass bearings? Give up? All of them currently use (or used in early versions) the two densest elements, osmium and iridium. These two elements play important roles in technological advancements. However, if certain special events hadn’t occurred early in Earth’s history, no osmium or iridium would exist near the planet’s surface. http://www.reasons.org/Bombard.....onPossible

    further note:

    Engineering and Science Magazine – Caltech – March 2010
    Excerpt: “Without these microbes, the planet would run out of biologically available nitrogen in less than a month,” Realizations like this are stimulating a flourishing field of “geobiology” – the study of relationships between life and the earth. One member of the Caltech team commented, “If all bacteria and archaea just stopped functioning, life on Earth would come to an abrupt halt.” Microbes are key players in earth’s nutrient cycles. Dr. Orphan added, “…every fifth breath you take, thank a microbe.”
    http://www.creationsafaris.com.....#20100316a

  75. one, I asked for a demonstration of generation of functional information, you did not provide one.

    two I never agreed that nylonase generated is a demonstration of the generation of functional information over and above what was already present.

    three I gave you Szostak’s paper on the definition of functional information.

    four you cannot extrapolate that the bacteria “invented” the ability to digest nylon without demonstrating a gain of functional information by passing the fitness test over the parent strain.

    I couldn’t agree with your concluding comment more.

    In further note it should be clearly pointed out that bacteria have been “detoxifying” the earth of toxic materials for billions of years. This terra-forming ability of bacteria is a very ID friendly fact and is very antagonistic to your atheism.

    further notes:

    Interestingly, while the photo-synthetic bacteria were reducing greenhouse gases and producing oxygen, and metal, and minerals, which would all be of benefit to modern man, “sulfate-reducing” bacteria were also producing their own natural resources which would be very useful to modern man. Sulfate-reducing bacteria helped prepare the earth for advanced life by detoxifying the primeval earth and oceans of poisonous levels of heavy metals while depositing them as relatively inert metal ores. Metal ores which are very useful for modern man, as well as fairly easy for man to extract today (mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper to name a few). To this day, sulfate-reducing bacteria maintain an essential minimal level of these heavy metals in the ecosystem which are high enough so as to be available to the biological systems of the higher life forms that need them yet low enough so as not to be poisonous to those very same higher life forms. These following studies show this “latent” ability of SRB’s to detoxify the earth of poisonous levels of heavy metals:

    Bacterial Heavy Metal Detoxification and Resistance Systems:
    Excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.
    http://www.springerlink.com/co.....04577v8t3/
    http://www.int-res.com/article.....26p203.pdf

    The role of bacteria in hydrogeochemistry, metal cycling and ore deposit formation:
    Textures of sulfide minerals formed by SRB (sulfate-reducing bacteria) during bioremediation (most notably pyrite and sphalerite) have textures reminiscent of those in certain sediment-hosted ores, supporting the concept that SRB may have been directly involved in forming ore minerals. http://www.goldschmidt2009.org...../A1161.pdf

    Transitional Metals And Cytochrome C oxidase – Michael Denton – Nature’s Destiny
    http://books.google.com/books?.....3&lpg

    As well, geological processes helped detoxify the earth of dangerous levels of metal:

    The Concentration of Metals for Humanity’s Benefit:
    Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth’s crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth’s crust strongly suggests supernatural design.
    http://www.reasons.org/TheConc.....tysBenefit

    And on top of the fact that poisonous heavy metals on the primordial earth were brought into “life-enabling” balance by complex biogeochemical processes, there was also an explosion of minerals on earth which were a result of that first life, as well as being a result of each subsequent “Big Bang” of life there afterwards.

    The Creation of Minerals:
    Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization. http://www.reasons.org/The-Creation-of-Minerals

    To put it mildly, this minimization of poisonous elements, and “explosion” of useful minerals, is strong evidence for Intelligently Designed terra-forming of the earth that “just so happens” to be of great benefit to modern man.

  76. further notes hrun:

    Man has only recently caught on to harnessing the ancient detoxification ability of bacteria to cleanup his accidental toxic spills, as well as his toxic waste, from industry:

    What is Bioremediation? – video
    http://www.youtube.com/watch?v=pSpjRPWYJPg

    Clearly many, if not all, of these metal ores and minerals laid down by these sulfate-reducing bacteria, as well as laid down by the biogeochemistry of more complex life, as well as laid down by finely-tuned geological conditions throughout the early history of the earth, have many unique properties which are crucial for technologically advanced life, and are thus indispensable to man’s rise above the stone age to the advanced “space-age” technology of modern civilization.

    Metallurgy
    http://en.wikipedia.org/wiki/Metallurgy

    Inventions: Elements and Compounds – video
    http://videos.howstuffworks.co.....-video.htm

    Bombardment Makes Civilization Possible
    What is the common thread among the following items: pacemakers, spark plugs, fountain pens and compass bearings? Give up? All of them currently use (or used in early versions) the two densest elements, osmium and iridium. These two elements play important roles in technological advancements. However, if certain special events hadn’t occurred early in Earth’s history, no osmium or iridium would exist near the planet’s surface. http://www.reasons.org/Bombard.....onPossible

    further note:

    Engineering and Science Magazine – Caltech – March 2010
    Excerpt: “Without these microbes, the planet would run out of biologically available nitrogen in less than a month,” Realizations like this are stimulating a flourishing field of “geobiology” – the study of relationships between life and the earth. One member of the Caltech team commented, “If all bacteria and archaea just stopped functioning, life on Earth would come to an abrupt halt.” Microbes are key players in earth’s nutrient cycles. Dr. Orphan added, “…every fifth breath you take, thank a microbe.”
    http://www.creationsafaris.com.....#20100316a

  77. one, I asked for a demonstration of generation of functional information, you did not provide one.

    Again, this is the perfect example of how people like you argue.

    What you actually said was: “falsification boils down to no demonstration of any information generation from material processes whatsoever”. Nowhere do you talk about ‘functional’ information.

    Yet again you shifted the goalposts to weasel out.

    In addition, clearly the enzyme of Nylonase is functional. Since neither the enzyme nor the DNA to encode the enzyme was there before, the mutation producing both is a mutation that increases functional information. Yet again, you will attempt to weasel out of that as well (while yet again failing to provide any usable definition of information).

  78. Shifting the goalpost??? now that is funny that you would accuse me of that when in fact, Isn’t the number “goal” of evolution to conclusively and scientifically demonstrate a gain in functional complexity? And you do indeed claim to have evolved complexity with nylonase (as in you mean the gaining of greater complexity than the complexity that was present before) yet when I clearly lay out the evidence (fitness test and definition of functional information threshold) of why your example falls short of such a conclusive demonstration of “evolution”, you tell me I am the one shifting goalpost! hrun I NEVER ONCE claimed that variation within a kind was impossible! In fact I expect there to be limited variations within “kinds”, I only claimed that all such variations within a “kind” will be found to fall under the principle of Genetic Entropy, and will thus be found to stay within the firmly established overriding principles of science found in the Second Law of Thermodynamics (Sewelle) and Conservation Of Information (COI) as elucidated by Dembski and Marks

    i.e. hrun please tell me exactly why the nylonase failing the fitness test should be considered anything other that a very interesting variation within a “kind” that stays well within those known overriding principles of science.

    Evolution’s great claims of mud turning into men demands rigorous proof. Why do you not demand such proof yourself?

  79. hrun, you accused me of providing no definition of information again even though I provided it? If you don’t like the rigorous definition of information I supplied I suggest you take it up with Nobel Prize winner Jack Szostak who co-authored the paper:

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – video
    http://www.metacafe.com/watch/3995236

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: “Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.”

    further note:

    Assessing the NCSE’s Citation Bluffs on the Evolution of New Genetic Information – Feb. 2010
    http://www.evolutionnews.org/2.....ion_b.html

    How to Play the Gene Evolution Game – Casey Luskin – Feb. 2010
    http://www.evolutionnews.org/2.....ution.html

    It should be noted that evolutionists like to play head games with Claude Shannon’s broad definition of information since “non-functional” information bits may be considered information in his broad definition, yet when looked at carefully, Shannon’s work actually fully supports Intelligent Design as is illustrated in the following video and article:

    DNA and The Genetic Code Pt 3 – Perry Marshall – video
    http://www.youtube.com/watch?v=FtMQUFOwEFo

    Skeptic’s Objection to Information Theory #1:
    “DNA is Not a Code”
    http://cosmicfingerprints.com/dnanotcode.htm

  80. Yes, again, now you are talking about FUNCTIONAL information. And you did not define information in the first place. You simply quoted a paper that had a definition of information. It is not at all apparent, that that was specifically what you were talking about.

    By the way, you also said that in this case you were using ‘genetic entropy’ as a measure to see if information was generated. We can now safely throw that statement out on the trash heap?

    In either case, can you convincingly show that application of Szostak’s definition of functional information to the Nylonase example leads to no functional information being generated. NO! Of course you can’t! If you could you would have already done so AND it is clear that the definition by Szostak actually vehemently disagrees with your assertion.

    But, as always, this type of tactic employed by you is par for the course.

    Here is my challenge:

    You claim that in the case of Nylonase no functional information was added. In addition, you base your claim on Szostak’s usage of the term.

    Prove to me and everybody around by applying Szostak’s definition to the Nylonase example that in this particular case no new information was added.

    My first prediction is: You would fail if you were to attempt to address the challenge. My second prediction is: You will not even attempt to take up the challenge. My third prediction is: You will attempt to weasel out of taking up the challenge (probably by yet again by moving the goal posts, attempting to redefine the terms used in your previous posts and finally by quoting a whole lot of stuff that only has tangential meaning to this post).

  81. hrun you state;

    Prove to me and everybody around by applying Szostak’s definition to the Nylonase example that in this particular case no new information was added.

    simple,

    when the nylon is removed from the environment the parent strain will be more fit, thus more functional, than the Nylon strain. Thus you have not demonstrate a gain of functional complexity that was not already present, (i.e. the bacteria are engineered to automatically detoxify the environment of toxins hrun) I resent you claiming I have not been clear in this matter and regard your method of twisting the facts to suit your own purpose to be absurd. My patience is gone with you so go ahead and thump your chest that you have “demonstrated evolution” in the next few threads but I will not waste my time with such insanity with you any more.

  82. Re #80: You quoted Szostak as saying that “we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex.”

    How in the world do you believe that you actually applied the Szostak definition to Nylonase?

    What is I(Ex) of the Nylonase system? What if F(Ex) of the Nylonase system? It is clear to everybody (except for maybe you) that you have not applied the definition you provided. It is simply another attempt to weasel out of the challenge.

    Just admit that you are unable to apply the Szostak definition to the system of Nylonase.

    You indeed look like you pretended to address the challenge. But you failed. You have in fact NOT utilized the definition given by Szostak. Instead, you simply made yet another definition up out of thin air and that way attempted to weasel out of the challenge.

    Here, I make it real simple for you: According to Szostak the definition of ‘functional information’ for an experimental system is ‘I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex’ Apply this definition you claim is the one you use to the Nylonase system. In other words: What is F(Nylonase) and what is I(Nylonase)?

  83. bornagain77, I trust that you are working on applying the definition of functional information by Szostak to the Nylonase example. Alternatively, I trust that you are crafting a post apologizing and finally retraction your baseless assertions.

    Once this assertion is FINALLY dealt with, we could move on to your next, if you like. I simply would like to make this as obvious as possible to anybody following this thread.

  84. bornagain77 @ 75:

    “To put it mildly, this minimization of poisonous elements, and “explosion” of useful minerals, is strong evidence for Intelligently Designed terra-forming of the earth that “just so happens” to be of great benefit to modern man.”

    It sounds like you are suggesting that the Intelligent Designer used bacteria to “terraform” the earth in preparation for/the benefit of human life. Would you care to speculate on how long this process took?

  85. Muramasa, well, surprisingly, there actually is evidence for terraforming in the some of the oldest sedimentary rocks on earth:

    The following video is good for seeing just how far back the red banded iron formations really go (3.8 billion years ago). But be warned, Dr. Newman operates from a materialistic worldview and makes many unwarranted allusions of the “magical” power of evolution to produce photosynthetic bacteria. Although to be fair, she does readily acknowledge the staggering level of complexity being dealt with in photosynthesis, as well as admitting that no one really knows how photosynthesis “evolved”.

    Exploring the deep connection between bacteria and rocks – Dianne Newman – MIT lecture video
    http://mitworld.mit.edu/video/496

    These following articles explore some of the other complex geochemical processes that are also involved in the forming of the red banded iron, and other precious ore, formations.

    Banded Rocks Reveal Early Earth Conditions, Changes
    Excerpt: Called banded iron formations or BIFs, these ancient rocks formed between 3.8 and 1.7 billion years ago at what was then the bottom of the ocean. The stripes represent alternating layers of silica-rich chert and iron-rich minerals like hematite and magnetite. First mined as a major iron source for modern industrialization, BIFs are also a rich source of information about the geochemical conditions that existed on Earth when the rocks were made. http://www.sciencedaily.com/re.....184428.htm

    Rich Ore Deposits Linked to Ancient Atmosphere – Nov. 2009
    Excerpt: Much of our planet’s mineral wealth was deposited billions of years ago when Earth’s chemical cycles were different from today’s.
    http://www.sciencedaily.com/re.....193640.htm

    as well there is somewhat of a connecting line with oxygen that we can make to terraforming:

    New Wrinkle In Ancient Ocean Chemistry – Oct. 2009
    Excerpt: “Our data point to oxygen-producing photosynthesis long before concentrations of oxygen in the atmosphere were even a tiny fraction of what they are today, suggesting that oxygen-consuming chemical reactions were offsetting much of the production,”
    http://www.sciencedaily.com/re.....141217.htm

    The Life and Death of Oxygen – 2008
    Excerpt: “The balance between burial of organic matter and its oxidation appears to have been tightly controlled over the past 500 million years.” “The presence of O2 in the atmosphere requires an imbalance between oxygenic photosynthesis and aerobic respiration on time scales of millions of years hence, to generate an oxidized atmosphere, more organic matter must be buried (by tectonic activity) than respired.” – Paul Falkowski
    http://www.creationsafaris.com.....#20081024a

    The Story of O2 – Falkowski – 2008
    How did biological, geochemical, and geophysical processes produce an atmosphere that allowed complex animal life;
    http://www.sciencemag.org/cgi/.....2/5901/540

    The geologic record shows a 10% oxygen level at the time of the Cambrian explosion of higher life-forms in the fossil record some 540 million years ago. The geologic record also shows a strange and very quick rise from the 17% oxygen level, of 50 million years ago, to a 23% oxygen level 40 million years ago (Falkowski 2005, 2008). This strange rise in oxygen levels corresponds exactly to the abrupt appearance of large mammals in the fossil record who depend on those high oxygen levels. Interestingly, for the last 10 million years the oxygen percentage has been holding steady around 21%. 21% happens to be a “very comfortable” percentage for humans to exist. If the oxygen level was only a few percentage lower, large mammals would become severely hampered in their ability to metabolize energy; if only a few percentage higher, there would be uncontrollable outbreaks of fire across the land (Denton; Nature’s Destiny).

    I believe this area is a rich area of “ID” research that has just barely been started to be explored.

  86. Hmm, now I feel ignored by bornagain77. Is that how you treat all your assertions. Once they get actually challenged, you go and simply ignore the challenges– so presumably you can continue making the very same assertions?

    Well, that is one I will have to add to the standard playbook. The result, is however the same. Assert something without support. Get called out. Either waffle or ignore, but never admit that the original assertion was just that (without factual support).

    It is the perfect way how you can maintain your worldview so that it jibes with what you believe and to prevent that pesky facts get in the way.

  87. Muramas,

    I just remebered that this “terraforming” of the earth to make it fit for humans is an area that Dr. Hugh Ross has done fairly extensive work.

    Probability For Life On Earth – List of Parameters, References, and Math – Hugh Ross
    http://www.reasons.org/probabi.....h-apr-2004
    http://www.johnankerberg.com/A.....304RFT.pdf

    In this latest video of Dr. Ross he references far more parameters, necessary for human life, than what is listed in the references I cited, I believe he and his team have the probability up over 1 in 10^1000 now:

    Hugh Ross – Evidence For Intelligent Design Is Everywhere – video
    http://www.metacafe.com/watch/4347236

    I will dig around a little and see if I can find a updated list.

  88. Muramasa,

    I found the reference:

    Does the Probability for ETI = 1?
    Excerpt; On the Reasons To Believe website we document that the probability a randomly selected planet would possess all the characteristics intelligent life requires is less than 10-304. A recent update that will be published with my next book, Hidden Purposes: Why the Universe Is the Way It Is, puts that probability at 10-1054.
    http://www.reasons.org/does-probability-eti-1

    A few more interesting probability numbers from the site for you math hounds:

    In the book I wrote with Fuz Rana, Origins of Life, we describe a calculation performed by biophysicist Harold Morowitz in which he showed that if one were to break all the chemical bonds in an E. coli bacterium, the probability that it would reassemble under ideal natural conditions (in which no foreign elements or chemicals would invade and in which none of the necessary elements or chemicals would leave) would be no greater than 10-100,000,000,000.

    In another book I wrote with Fuz, Who Was Adam?, we describe calculations done by evolutionary biologist Francisco Ayala and by astrophysicists John Barrow, Brandon Carter, and Frank Tipler for the probability that a bacterium would evolve under ideal natural conditions—given the presumption that the mechanisms for natural biological evolution are both effective and rapid. They determine that probability to be no more than 10-24,000,000.

    The bottom line is that rather than the probability for extraterrestrial intelligent life being 1 as Aczel claims, very conservatively from a naturalistic perspective it is much less than 10500 + 22 -1054 -100,000,000,000 -24,000,000. That is, it is less than 10-100,024,000,532. In longhand notation it would be 0.00 … 001 with 100,024,000,531 zeros between the decimal point and the 1. That longhand notation of the probability would fill over 20,000 complete Bibles. In other words, the probability is as close to zero as any scientifically determined probability has ever been.

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