Thursday, December 20, 2012

UCEs: See Something—Say Something

Another Big Failure

Although it may seem that genomes would be made up of genes, in many higher species genes constitute only a small fraction of the DNA. The remainder of the genome is full of various elements and segments, some of which seem to be of little functional importance.

Prediction

Evolution predicts that more distant species should have greater differences in their genomes. After all, species in distant limbs of the evolutionary tree likely have different evolutionary pressures and have been evolving independently for millions of years. This genome difference should be all the more obvious for DNA changes that are functionally unimportant. Such changes can accumulate independently in the different evolutionary lineages, as they go unchecked by evolution’s selection process.

When DNA changes do influence function then the prediction becomes more complicated. These DNA changes may be selected for, or against, depending on how they affect the function, and ultimately the reproductive advantage, of the organism. But for DNA segments that are not functionally constrained, the theory of evolution predicts divergence across different species. Or in other words, for functionally unconstrained DNA, similar sequences should not be found in distant species. The corollary to this prediction is that similar DNA sequences found in distant species must be functionally constrained.

Falsification

This prediction has been falsified in the many examples of functionally-unconstrained, highly similar stretches of DNA that have been discovered in otherwise distant species. For instance, thousands of so-called ultra-conserved elements (UCEs), hundreds of base pairs in length, have been found across a range of species including human, mouse, rat, dog, chicken and fish. Evolutionists were astonished to discover these highly similar DNA sequences in such distant species. In fact, across the different species some of these sequences are 100% identical. Species that are supposed to have been evolving independently for 80 million years were certainly not expected to have identical DNA segments. “I about fell off my chair,” remarked one evolutionist. [1]

Evolutionists assumed such highly preserved sequences must have an important function. But even if true, it would be difficult to see how so little sequence variation could be tolerated. The results were not what evolutionists expected, but this was just the beginning. Subsequent laboratory studies failed to reveal any phenotype effects. A variety of knockout experiments were done to determine the function of these sequences that evolution was supposed to have preserved. But in many of the regions no function could be found. One study knocked out several UCE regions, including a stretch of 731 DNA base pairs that was hypothesized to regulate a crucial gene. Evolutionists expected the knock out to result in lethality or infertility but instead found normal, healthy mice. Months of observation and a battery of tests found no abnormalities or significant differences compared to normal mice. [2] As one of the lead researchers explained:

For us, this was a really surprising result. We fully expected to demonstrate the vital role these ultraconserved elements play by showing what happens when they are missing. Instead, our knockout mice were not only viable and fertile but showed no critical abnormalities in growth, longevity, pathology, or metabolism. [3]

Another study knocked out two massive, highly conserved, DNA regions of 1.5 million and .8 million base pairs in laboratory mice and, again, the results were viable mice, indistinguishable from normal mice in every characteristic they measured, including growth, metabolic functions, longevity and overall development. [4] “We were quite amazed,” explained the lead researcher. [5]

Extensive tests have failed to find a function for many of the UCEs and these results were surprising to evolutionists. Perhaps some mysterious functions will be discovered in the future, but the years of research at this point indicate evolution’s prediction is false. The best information we have to date, and it is extensive, indicate that the genomes of distant species include highly similar and even identical stretches of DNA that otherwise are not functionally constrained.

It is worth noting that problems posed by this evidence will not all disappear even if some mysterious function is discovered in the future. Highly similar sequences in distant species, functional or not, are simply not consistent with evolution. Because such sequences are in distant species, according to evolution such sequences must date back to a very distant ancestor. In other words, these sequences not only must have important function in the extant organisms in which they are found, but they must have evolved early in the history of life, and they must have been important in a very different organism, under very different conditions.

And whatever the mysterious function is, it must be incredibly sensitive to every detail in the DNA sequence. But how could the sequence initially evolve if little or no variation is allowed? Evolution requires a functional pathway to arrive at the sequence in the first place but the highly restricted UCEs would have none. We would have to believe that functionally important stretches of DNA, hundreds of base pairs in length, just happened to form and then were preserved by evolution. The odds against this are astronomical.

Reaction

“It can’t be true” was one evolutionist’s reaction to the UCE findings in recent years. [6] The findings falsify predictions of evolution, but they are true and they have been verified independently. Some evolutionists considered the possibility of sequence armoring. That is, perhaps these highly conserved sequences are a consequence of a strong, local, resistance to mutations at certain locations in the DNA. But it is difficult to imagine how such localized DNA protection could occur, and in any case empirical observations have ruled out this explanation.

Evolutionists have also considered the possibility of functional redundancy. In this case, no deleterious effects are observed in the knockout mice because other DNA regions perform the same function as do the deleted UCE regions. But then this would not explain why the UCE are so highly conserved.

On the other hand, perhaps the deleterious effects of removing an apparently functionless UCE are observed only in subsequent generations. But again, this idea has difficulty explaining why the UCEs are so highly conserved.

Perhaps the most common hypothesis is that many of the UCEs have functions that are difficult to detect. This is certainly possible, but it raises the problem of how evolution could select for such rare sequences and subtle function.

UCEs are another example of how the theory, rather than the evidence, drives evolutionary thought. The DNA must have a function, even though myriad tests have found none. If we cannot detect the function, then there must be a problem with the tests. There must be a function which otherwise is undetectable to us. It is a perfect example of how metaphysical certainty resists falsification as Antony Flew once illustrated in his gardener parable:

Once upon a time two explorers came upon a clearing in the jungle. In the clearing were growing many flowers and many weeds. One explorer says, “Some gardener must tend this plot.” The other disagrees, “There is no gardener.” So they pitch their tents and set a watch. No gardener is ever seen. “But perhaps he is an invisible gardener.” So they set up a barbed-wire fence. They electrify it. They patrol with bloodhounds. (For they remember how H. G. Well’s The Invisible Man could be both smelt and touched though he could not be seen.) But no shrieks ever suggest that some intruder has received a shock. No movements of the wire ever betray an invisible climber. The bloodhounds never give cry. Yet still the Believer is not convinced. “But there is a gardener, invisible, intangible, insensible, to electric shocks, a gardener who has no scent and makes no sound, a gardener who comes secretly to look after the garden which he loves.” At last the Sceptic despairs, “But what remains of your original assertion? Just how does what you call an invisible, intangible, eternally elusive gardener differ from an imaginary gardener or even from no gardener at all?”

For evolutionists evidence such as the UCEs cannot pose a problem for the theory. There must be an explanation. And as in Flew's parable, sometimes evolutionists have creative explanations for why the evidence does not seem to reveal their gardener.

References

1. Karen Lurie, “Junk DNA,” ScienCentral July 20, 2004.

2. N Ahituv, Y Zhu, A Visel, A Holt, V Afzal, LA Pennacchio, EM Rubin, “Deletion of ultraconserved elements yields viable mice,” PLoS Biol 5 (2007): e234.

3. DOE/Lawrence Berkeley National Laboratory, “Mice thrive missing ancient DNA sequences,” ScienceDaily 6 September 2007.

4. M. A. Nobrega, Y. Zhu, I. Plajzer-Frick, V. Afzal, E. M. Rubin, “Megabase deletions of gene deserts result in viable mice,” Nature 431 (2004): 988-993.

5. S. Pagán Westphal, “Life goes on without ‘vital’ DNA,” New Scientist June 3, 2004.

6. E. Pennisi, “Disposable DNA puzzles researchers,” Science 304 (2004): 1590-1591.

43 comments:

  1. CH, you're really getting forgetful (or lazy) in your old age.

    You already presented this canard and we already went over your butchering of the paper about the knockout mice back in April 2012, remember?

    I guess Creationists only have so many lies to tell about science before they have to start repeating themselves.

    ReplyDelete
    Replies
    1. Hmmmm, most recent reference almost 6 years old. That is a bit suspicious, isn't it?

      But I guess a man of Dr Hunter's integrity must have made a thorough investigation of more recent literature.

      That's it. Evolution is dead.

      Delete
  2. UCA is not dead if, by dead, you mean proved absolutely impossible. Remember, UCA doesn't even rule out intelligent manipulation of genomes. It only requires that each organism (except possibly the universal common ancestor) arose genealogically from an ancestor.

    But this article does demonstrate the great difficulty of explaining the UCE's naturalistically and evolutionarily. On the other hand, common design works just fine if they are redundant and well-protected by some kind of DNA protection and/or repair process. Apart from the latter, I'm as awed as the UCA'ists are.

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  3. Liar for Jesus Jeff

    But this article does demonstrate the great difficulty of explaining the UCE's naturalistically and evolutionarily. On the other hand, common design works just fine if they are redundant and well-protected by some kind of DNA protection and/or repair process.


    We know LJFF. Saying "POOF GAWDDIDIT" explains 100% of all observable phenomena. Pity that it's scientifically impotent, unfalsifiable, and intellectually dishonest as an explanation.

    ReplyDelete
    Replies
    1. And thorton knows quite a bit about scientifically impotent, unfalsifiable and intellectually dishonest theses- see the ToE

      Delete
  4. Oh, now I see, moron. I'm glad you finally articulated such a clear argument for positing kazillions of ad-hoc hypotheses unnecessarily!!!

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    Replies
    1. Go ahead Liar for Jesus Jeff. Describe for us what predictions the "POOF GAWDDIDIT" hypothesis. makes. Explain for us what would falsify the "POOF GAWDDIDIT" hypothesis.

      Delete
    2. Demonstrating that blind and undirected processes can doit would falsify God

      Delete
    3. I wouldn't say anything can falsify benevolent/competent teleology, because without that we have no non-arbitrary epistemology as far as I can tell. But yes, Moronton, a naturalistic theory that predicted the relevant phenotypes at the relevant times when applied to relevant initial conditions WOULD render UCA the better, because more parsimonious, hypothesis.

      As for the naive falsificationism you believe in, Moronton, there's nothing that could falsify UCA by it EITHER. Parsimony is the only hypothesis rejection criteria that is applicable to either SA or UCA (unless someone can think of a falsifiable implication of UCA--and they haven't yet).

      Delete
  5. Chubby Joe G

    Demonstrating that blind and undirected processes can doit would falsify God


    How would you conclusively demonstrate that GAWD was not directing the processes and just making them look like they were blind and undirected?

    "POOF GAWDDIDIT" isn't falsifiable, makes no predictions, isn't science.

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    1. LoL! Your position doesn't make any predictions, tardface. It can't even be tested.

      Delete
    2. Chubby Joe G

      EVOLUTION HAS NO EVIDENCE!!!!


      Chorus #2765 of the Fatboy Sonata

      Delete
    3. little-dickhead thorton spewing its lies again.

      EVOLUTION HAS PLENTY OF EVIDENCE. UNGUIDED EVOLUTION IS TOTALLY UNSUPPORTED AND UNSUPPARTABLE.

      And it is very telling that said little dickhead cannot provide a testable hypothesis, predictions nor positive evidence for unguided evolution.

      Delete
    4. Chubby Joe G

      EVOLUTION HAS NO EVIDENCE!!!!


      Hey Fatboy, Lenski's E coli experiment started off with 12 identical colonies all cloned from the same organism, yet after 30,000 generations it ended up with 12 demonstrably different colonies each with its own unique genetic mutations and psychological features. If evolution is Intelligently Guided why didn't all 12 colonies end up the same?

      What is the physical mechanism by which your Magic Designer does the guiding? Your standard cowardly evasion of "genetic algorithms" won't cut it Chubs. Give us a physical mechanism for how genetic material is manipulated.

      Delete
    5. If evolution is Intelligently Guided why didn't all 12 colonies end up the same?

      I have alreday been over that with you. It's like this- tghey weren't all trying to solve teh same problem and then there is more than one way to solve any one problem.

      With Dawkin's "weasel" every time you run it it takes a different path to the solution.


      What is the physical mechanism by which your Magic Designer does the guiding?

      Built-in responses to environmental cues start the mutation process until the solution is found. Just as I have been telling you.

      That said if your position had some positive evidence you would just present it. But you are too much of an ignorant coward to even provide a testable hypothesis for unguided evolution.

      Delete
    6. Chubby Joe G

      I have alreday been over that with you. It's like this- tghey weren't all trying to solve teh same problem and then there is more than one way to solve any one problem.


      What different "problems" were each colony trying to solve Chubs? Please be specific and provide your supporting evidence.

      With Dawkin's "weasel" every time you run it it takes a different path to the solution.

      What was the correct "solution" to the E coli experiment, and why did all 12 colonies end up with different "solutions"?

      Built-in responses to environmental cues start the mutation process until the solution is found.

      What is the physical mechanism for how these supposedly built in mechanisms are consciously guided? Where is this pre-specified "solution" kept?

      You keep waving those fat hands Chubs but you Creationists never provide any answers.

      Delete
    7. What different "problems" were each colony trying to solve

      There was more than one selection pressure. And more than one way to survive.

      What was the correct "solution" to the E coli experiment, and why did all 12 colonies end up with different "solutions"?

      The solution is to adapt to survive. And tehre is more than one way to do that, obvioulsy.

      Built-in responses to environmental cues start the mutation process until the solution is found.

      What is the physical mechanism for how these supposedly built in mechanisms are consciously guided?

      What is the physical mechanism for how computer programs are consciously guided?

      Where is this pre-specified "solution" kept?

      What pre-specified solutions? Weasel doesn't have any pre-specified solutions. Just a target- all solutions are different.

      Delete
    8. That said if your position had some positive evidence you would just present it. But you are too much of an ignorant coward to even provide a testable hypothesis for unguided evolution.

      IOW thorTARD doesn't have a viable alternative to Intelligent Design.

      Delete
    9. Chubby Joe G

      There was more than one selection pressure. And more than one way to survive.

      The solution is to adapt to survive. And tehre is more than one way to do that, obvioulsy.


      So there isn't any pre-set solution, just selection pressure to survive. Congratulations Chubs, you've just described exactly evolution through random genetic variation.

      T: "What is the physical mechanism for how these supposedly built in mechanisms are consciously guided?"

      What is the physical mechanism for how computer programs are consciously guided?


      Cowardly evasion noted. In computers the physical mechanism is the transistor voltages and states which implement the Boolean logic. How does your Magic Designer physically manipulate the DNA and/or the environment to get the "guided" results it wants Chubs? If the solutions are random then they're not guided.

      Keep squirming fatboy, you're so fun to watch.

      Delete
    10. you've just described exactly evolution through random genetic variation.

      And just how did you or anyone determine all genetic changes are random/ chance/ happenstance events?

      In computers the physical mechanism is the transistor voltages and states which implement the Boolean logic.

      In living organism the physical mechanism is the DNA and states which implement the genetic code.

      IOW there would be any number of targets to choose from. And directed mutations to get to them.

      If the solutions are random then they're not guided.

      And how can you determine they are random/ chance/ happenstance events?

      Please do tell, we have only been waiting for over 150 years.


      Delete
    11. Chubby Joke G

      And just how did you or anyone determine all genetic changes are random/ chance/ happenstance events?


      No one can prove that Chubs. We empirically observe that the changes are random WRT reproductive fitness, and there's zero evidence of any conscious guiding.

      If you want to claim there is outside conscious guidance you need to provide evidence for it fatboy. That's what you IDiot Creationists can't do.

      In living organism the physical mechanism is the DNA and states which implement the genetic code.

      That's not a mechanism for how an outside agency consciously manipulates the DNA to get the desired results Chubs. Try again you fat failure.

      Delete
    12. And just how did you or anyone determine all genetic changes are random/ chance/ happenstance events?

      No one can prove that

      Well THAT is the claim that needs to be supported.

      We empirically observe that the changes are random WRT reproductive fitness,

      No, dumbass. According to MAYR the mutations are random as in chance/ happenstance events, period.

      Random wrt fitness is cowardly bullshit.

      and there's zero evidence of any conscious guiding.

      Yeah and there's no evidence for conscious guiding of a computer program either.

      If you want to claim there is outside conscious guidance you need to provide evidence for it

      No outside guidance required, moron. However you need to provide evidence that all genetic changes are random/ chance/ happenstance events, and you can't.

      That's not a mechanism for how an outside agency consciously manipulates the DNA to get the desired results

      No one cares about your strawman, assface.

      Delete
    13. Cowardly thorton sock puppet, closet YEC-

      Mommy, Joe keeps exposing my cowardice and ignorance. Please protect me!

      Delete
  6. We often read of evolutionists "falling off their chair". It seems to be a high job related risk factor.

    ReplyDelete
  7. The trouble for neo-Darwinism with finding the alternative splicing patterns to be 'species specific' is because random changes in regulatory 'coding patterns' are going to be far more sensitive and detrimental to 'random' changes than random mutations to the genes of an organism are. Richard Dawkins elaborates on why the genetic code is intolerant to random change here:

    Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011
    Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal:
    "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10)
    OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code).
    Simple counting question: does "one or two" equal 23? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.
    http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html

    “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
    Donald E. Johnson – Bioinformatics: The Information in Life

    Shannon Information - Channel Capacity - Perry Marshall - video
    http://www.metacafe.com/watch/5457552/

    "A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107."
    (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

    "Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source -- from a mind or personal agent." (Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

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  8. For us, this was a really surprising result. We fully expected to demonstrate the vital role these ultraconserved elements play by showing what happens when they are missing. Instead, our knockout mice were not only viable and fertile but showed no critical abnormalities in growth, longevity, pathology, or metabolism. [3]

    It is important to understand that this expectation, and subsequent surprise, were a consequence of evolutionary theory. For instance, merely looking at the DNA of a particular species would have led to no such expectation. It was the finding of this DNA in multiple species and, importantly, its evolutionary interpretation, that led to this interpretation.

    ReplyDelete
  9. How many times can the evidence continue to contradict their expectations/predictions before the public wakes up and realizes they are being sold an evolutionary fairytale, not a scientific 'fact'???

    If the theory of evolution were a horse, they would have shot it long ago.

    ReplyDelete
  10. NV,

    "If the theory of evolution were a horse, they would have shot it long ago."

    Some people just get very attached to a lame horse. They can't imagine living without it.

    In this case it would require a complete overhaul of their world view. Such a prospect is truly horrifying to many.

    ReplyDelete
  11. Nic

    In this case it would require a complete overhaul of their world view. Such a prospect is truly horrifying to many.


    Feel free to offer another hypothesis for the history and processes of life on Earth, one that explains ALL the empirical evidence in a better more consilient manner, makes better predictions, gives better specific details about mechanisms. Be sure your hypothesis is falsifiable too.

    Door's only been open to you Creationist "scientists" for 150 years now but no one's stepped up yet.

    How about it Nic? You game to be the first to offer something better?

    ReplyDelete
    Replies
    1. LoL! Unguided evolution can't even muster a testable hypothesis. IOW thorton is lying, agaian.

      Delete
    2. Liar for Jesus Jeff

      Moronton, there is NO single hypothesis that explains all of the empirical evidence. Much less is there one such single hypothesis that is falsifiable.


      LOL! So you can't offer a single alternate hypothesis. All you can do is scream the Creationist mantra about how ToE got it all wrong.

      That's why you and the rest of your Creationist idiots will always be a meaningless clown circus to real science LFJJ.

      Delete
    3. thorton,

      Shut up- you can't offer a testable hypothesis for us to offer an alternative to.

      Delete
    4. Cowardly thorton sock puppet, closet YEC-

      Mommy, Joe keeps exposing my cowardice and ignorance. Please protect me!

      Delete
    5. Chubby Joe G

      I have provided plenty of positive evidence for ID. Others have also.


      Hey Chubs, could you please list some of the colleges and universities that offer courses in this positive evidence? Which classes should I take to learn all about the iron-clad case for Intelligent Design Creationism?

      Put the Cheesy Poofs down and speak up Chubs, I can't hear you.

      Delete
    6. LoL! Please list ONE college or universitiy that can provide a testable hypothesis along with positive evidence for unguided evolution.

      Which classes do they offer that tells us how many mutations it takes or how many generations it takes to construct new complex protein machinery, new body plans and new body parts?

      Which classes offer anything beyond equivocation and attacking strawmen?

      Delete
    7. Fatboy, you forgot to list the schools that teach the positive evidence for Intelligent Design Creationism.

      Oh wait, how about this one?

      Ringling Bros. and Barnum & Bailey Clown College

      I bet you're a proud alumnus!

      Delete
    8. Umm, every college and university that teaches physics, chemistry, cosmology and biology teaches the positive evidence for Intelligent Design.

      Every one, without exception.

      Go figure...

      Delete
    9. Thorton,

      "Feel free to offer another hypothesis for the history and processes of life on Earth, one that explains ALL the empirical evidence in a better more consilient manner,..."

      Do you seriously believe evolution explains ALL the empirical evidence? If so, you are truly delusional. Evolution can't even provide a remotely plausible explanation for the origin of life. Until it can do that all else is simply presumptive conjecture.

      Delete
  12. Fatboy Joke Gallien

    Umm, every college and university that teaches physics, chemistry, cosmology and biology teaches the positive evidence for Intelligent Design


    Fatboy, if you're going to lie don't make it so over the top.

    Go ahead and post a course syllabus that mentions evidence for Intelligent Design Creationism.

    C'mon fatty put up the data.


    ReplyDelete
    Replies
    1. Every physics course that discusses the laws of nature. Every biology course that discusses biology- all of them present evidence for Intelligent Design.

      Go ahead and post a course syllabus that mentions evidence for the blind watchmaker.

      C'mon momma's boy put up the data.





      Delete
    2. This comment has been removed by the author.

      Delete
    3. Oops! No courses mentioning Intelligent Design Creation from Chubs!

      Maybe your new sockpuppet can post some fatty, because you sure can't.

      Delete
    4. Oops no courses mentioning the blind watchmaker from thorton, the momma's boy.

      Maybe some other evoTARD sock puppet will post some, momma's boy, because you sure can't

      Delete