Friday, November 11, 2016

Here’s That Study That Found Pseudo-Pseudogenes

Evolution is Getting Demolished

It is one of the strongest arguments for evolution: dysteleology, the apparent lack of design in the biological world. And the most obvious and compelling examples of such dysteleology are in the genome. And the most celebrated examples of dysteleology in the genome are the pseudogenes—genes which are broken. They are the long since abandoned junk of the genome. And the most obvious example of such brokenness is a stop codon that has accidentally arisen somewhere in the middle of the gene. These so-called premature termination codons (PTCs) halt the production of proteins in mid-stream. And the most abundant source of pseudogenes is the olfactory receptor families—genes involved in detecting odors. All those pseudogenes are a sure sign that no designer worth his salt would have constructed such a world. Evolution must be true, as evolutionists from Charles Darwin to Jerry Coyne have proclaimed. There’s only one problem—such examples of junk always turn out to be false.

At evolution’s foundation is the claim of lack of function, and that is a terrible argument. First of all, it is metaphysical rather than scientific. It is not a positivist argument—evolutionists have no idea how genes, or anything else for that matter—actually evolved. The argument is that such nonfunctional structures would never have been designed or created. That conclusion does not come from science, and cannot be tested by science. It is a religious argument.

But in addition to the metaphysics, showing that a structure has no function makes no sense to begin with. For one would have to watch the structure, in the organism, for the entire life of the organism. And one would have to be able to measure function—all possible functions. Needless to say, no evolutionist has ever done that.

But it gets worse.

Not only is the dysteleology argument religious and nonsensical, it is also false. At least in the cases that have been investigated. Over and over, the long lists evolutionists make of nonfunctional structures just get shorter and shorter.

That brings us to pseudogenes.

For sometime it has been known that not all pseudogenes are pseudogenes. That is, not all pseudogenes are junk. Some pseudogenes have been found to be performing useful functions. But typically these are onesies, twosies.

Now, a new study has found something more interesting—a PTC in an olfactory receptor pseudogene that, in certain contexts, is not actually a termination codon after all. The gene has a stop codon, and yet the gene is successfully used to create a protein. The translation process somehow can read-through what normally would be a stop codon. The paper suggests this is accomplished with a near-cognate tRNA, which inserts an amino acid rather than causing a halt:

We suggest that read-through is due to PTC recognition by a near-cognate tRNA that allows insertion of an amino acid instead of translation termination.

What appeared to be a pseudogenes is actually functional. It is a pseudo pseudogene.

Furthermore, and importantly, this is not an isolated case. They found other examples, and conclude this could be a “widespread phenomenon.”

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. … We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such “pseudo-pseudogenes” could represent a widespread phenomenon.

Widespread phenomenon? This adds yet more support to the Project Encode suggestion, which evolutionists immediately pushed back on, that most of the genome is functional rather than junk as evolutionists had insisted (for example, see here, here, and here).

Pseudogenes comprise only a small fraction of the genome, but they have served as the poster child of junk DNA, and proof of evolution.

Instead, once again history appears to be reliable guide as pseudogenes appear to be going down the same path as those other supposedly “nonfunctional” structures. Instead of nonfunctional, pseudogenes are beginning to look like they may have a rather sophisticated function that was not apparent to evolutionists.

Of course function is often not apparent to evolutionists because they view biology as an accident. Organisms are built on a vast number of chance events so of course they will be found to be full of mistakes.

But in its inexorable march of progress, science always seems to find function. Evolution seeks lack of function, which makes no sense, and science just keeps on finding more function. Evolution and science, it seems, are in an eternal conflict.

Don’t expect contriteness anytime soon though. For evolutionists, the finding of function was never a problem. It simply is an example of evolution finding function for what was nonfunctional. The junk was repaired and took on some new function. In fact, it remains powerful evidence for evolution because it is obviously so quirky. When the supposedly “backward” retina of the mammalian eye was found to be incredibly sophisticated, evolutionists didn’t miss a beat. After all, it was still a kludge of a design. As Richard Dawkins put it, “it is the principle of the thing that would offend any tidy-minded engineer!”

So it really doesn’t matter how much function is found, and how optimal a design is. For man has found nature to be wanting, and so it must have formed by chance. This, in a nutshell, is Epicureanism.

Religion drives science, and it matters.

45 comments:

  1. Wow, you've disproven evolution yet again. That's gotta be at least 100 times. Funny thing then not a single researcher in the scientific community pays any attention to your Nobel worthy revelations. Any idea why that is?

    ReplyDelete
    Replies
    1. Always glad to see the vacuous comments from evolutionists.

      Delete
    2. Seriously, it's no exaggeration to say you've disproven evolution as many times as Behe, Meyer, Axe and Gauger put together. Still the DI hardly ever mentions your name. It's just not fair!

      Delete
    3. Funny that not a single researcher in the scientific community can tell us how to test the claims of evolutionism.

      Delete
    4. They have been tested hundreds of time. And passed the test. Maybe you should concentrate on suing the government over teaching evolution in schools. Baby steps Joe, baby steps.

      Delete
    5. William:
      They have been tested hundreds of time.

      That is your opinion and only an opinion. Too bad you cannot find any support for it. Baby, steps, William, baby steps.

      There isn't anything in peer-review that demonstrates natural selection and drift can produce ATP synthase, bacterial flagella, cilia, neurons, etc. And no one knows how to test the claim. Obviously William doesn't know or he would have said how or at least provided some references.

      Delete
    6. Btw, welcome back to DG Joe. I am sure that you will add the same level of commentary that was so welcomed by Mapou.

      Delete
    7. William, my discourse, unlike yours, is honest and supported. Now how about those references or admit that you were bluffing, ie being dishonest.

      Delete
    8. Yippee! It's everyone's favorite YEC Joe G, still wading in the shallow end of the gene pool and making turnips seem intelligent by comparison! :D

      Delete
    9. Unlike Ghostrider's my family tree has branches. Ghostrider likes to keep it all in the family

      Delete
    10. Joe: "There isn't anything in peer-review that demonstrates natural selection and drift can produce ATP synthase, bacterial flagella, cilia, neurons, etc."

      I am not going to do all of the work for you Joe. Just do a search for mutations, natural selection, drift, HGT, protein folding, etc., etc., etc.,

      "And no one knows how to test the claim."

      Again, stop being so lazy and do a little of your own work. Or, better yet, propose some mechanism, and ways to test the proposal, that ID can do any of this in biology. When you have done that, you will have no problem getting it published in peer-reviewed journals. They are always looking for well structured hypothesis with cleverly designed testing approaches and results.

      Delete
    11. William your bluff is duly noted. I did all that work and that is why I am confident in what I said is true.

      As for testing the design inference that has already been published by several people.

      And as for peer-review there isn't anything there that supports natural selection's ability to produce complex functionality.

      So please stop bluffing, admit that you don't know jack about the subject and you are just a blind parrot willingly accepting the word of others.

      Why did the evos at the Dover trial have to lie and bluff as opposed to just presenting the alleged evidence that you think exists?

      Delete
    12. A few years ago Dr Behe had a peer-reviewed article that was a review of peer-reviewed articles. In it he described the complete lack of peer-review supporting the claim that natural selection and drift can produce complex protein machinery. What he did find is many articles on mutations leading to a loss of function.

      But I am sure you will continue to try to bluff your way through this discussion. Too bad that just exposes you as someone too lazy to actually do the work and find out for itself.

      Delete
    13. could you please provide a link to it? Thank you.

      Delete
    14. LoL! Do your own work-

      "Experimental Evolution, Loss-of-Function Mutations and 'The First Rule of Adaptive Evolution',", Quarterly Review of Biology 2010

      Delete
    15. Hmm, apparently it has been cited 39 times since 2010. My first publication, admittedly a piece of crap scientifically, was cited more often than that.

      Delete
    16. Wow, you are quite the piece of work. Regardless of how often it has been cited the point stands-> you are a bluffing loser who is too lazy to do the work.

      Delete
    17. Actually, the number of times your papers have been cited is a better indication of the veracity of your work than the number of papers you have published. Everyone who has done any real science knows this. And the fact that the Behe paper you referenced has had fewer citations than the piece of crap paper I wrote in 1985 "speaks volumes" (to quote one of the prominent ID proponents).

      Feel free to reference any of the hundreds of published peer reviewed papers by ID scientists. You must have many. Or Louis. Or Mullings. Or Murray. Or Behe or Axe. Or Cornelius. Or Cunningham. Or Torley. Or Mung. Or Arrington. Or Egnor.

      Amongst this sheer mass of brain-trust, the library of peer reviewed papers must be owerwhelming.



      Delete
    18. There isn't anything published in peer-review that supports evolutionism, William. Stop with your delusions already.

      ATP synthase is elucidated in peer-review and everything written supports the design inference.

      How many citations does the alleged theory of evolution have? What articles cited it?

      Delete
    19. Actually, the number of times your papers have been cited is a better indication of the veracity of your work than the number of papers you have published.

      Hearsay. It was a REVIEW paper. It was not any original work. And being a REVIEW paper it would be selectively cited.

      Everyone who has done any real science knows this.

      More hearsay and not even an argument.

      Feel free to reference any of the hundreds of published peer reviewed papers by ID scientists.

      Feel free to reference ONE paper that demonstrates natural selection and drift can produce any functional protein complex. Let's see this "real science" you mentioned. Or admit tat you are a bluffing loser as you have more than enough time to ante up and you have failed to do so.

      Delete
    20. "Hearsay. It was a REVIEW paper. It was not any original work. And being a REVIEW paper it would be selectively cited."

      So, it wasn't a peer reviewed science paper worthy of scrutiny as real science papers are. Thank you for admitting this.

      Delete
    21. LoL! You are obviously a moron. If it is in peer-review it went through scrutiny.

      However your side doesn't have any peer-review papers supporting its claims. Loser.

      Delete
    22. William runs away after his bluffs have been called.

      How typical...

      Delete
    23. No Joe. I'm still here. I will respond to your questions and challenges when they are valid questions and challenges that can't be found by a 30 second google search.

      Delete
    24. LoL! And more bluffs from the master.

      Why is it that the evos at Dover had to lie and bluff their way through the trial when a 30 second google search would have done?

      What, exactly, should I search for that the leading evos didn't know to search for?

      Thank you for proving that you are a self-deluded loser.

      Delete
    25. "
      Why is it that the evos at Dover had to lie and bluff their way through the trial when a 30 second google search would have done?"


      Sorry Joe. I'm Canadian. Dover wasn't even a blip in our news cycle. When it was mentioned, it was just to shake our heads over the fact that the courts would even pretend to take the creationists seriously.

      While you guys were banning stem cell research over religious grounds, we were advancing medicine. While you guys were denying evolution, real scientists were using the idea to advance medical research.

      But feel free to deny your own senses (although you have repeatedly demonstrated that you have no sense).

      Delete
    26. And more substance-free drivel from William the bluffer. Whatever, it is clear that you have nothing but your lies and nonsense.

      What "evolution" were we denying? ID is not anti-evolution. What medical research was advanced by evolution? Enough of your lies and bluffs. Ante up or shut up.

      Feel free to keep up your self-delusion (although you have shown no signs of doing so).

      Delete
    27. When it was mentioned, it was just to shake our heads over the fact that the courts would even pretend to take the creationists seriously.

      ID isn't creation and that is why we don't take you seriously. Besides if you side actually had something then ID is a non-starter. So one has to wonder why does anyone take your position seriously?

      While you guys were banning stem cell research over religious grounds, we were advancing medicine.

      False. We have advanced said research to the point we know embryonic stem cells are not always needed, if at all.

      While you guys were denying evolution, real scientists were using the idea to advance medical research.

      No one goes into medical research saying "Natural selection and drift can produce complex protein machinery over trillions and trillions of generations, we just know it. And because of that this is how we proceed.

      But feel free to continue with your willful ignorance and cowardly bluffing.

      Delete
    28. "ID isn't creation ..."

      So, design isn't an act of creation? That may come as a surprise to architects, engineers and artists.

      "Besides if you side actually had something then ID is a non-starter."

      When ID starts something, like actual science, get back to me.

      "No one goes into medical research saying "Natural selection and drift can produce complex protein machinery..."

      Then feel free to stop a course of antibiotics the moment you start feeling better. Or accept a transfusion or a transplant from anyone. Or take a drug that was tested on starfish rather than mammals.

      Delete
    29. So, design isn't an act of creation?

      Creationists rely on the Bible whereas ID does not

      When ID starts something, like actual science, get back to me.

      LoL! ID has more science going for it than your position does. ID at least makes testable claims. We don't have to bluff.

      Then feel free to stop a course of antibiotics the moment you start feeling better.

      You are one sad person as antibiotics has nothing to do with the lie that Natural selection and drift can produce complex protein machinery

      Or accept a transfusion or a transplant from anyone. Or take a drug that was tested on starfish rather than mammals.

      Thankfully none of that has anything to do with the lie that natural selection can produce complex protein systems.

      Just how stupid and desperate are you?

      Delete
    30. "Creationists rely on the Bible whereas ID does not."

      Who said anything about creationists. You really have to pay attention.

      "You are one sad person as antibiotics has nothing to do with the lie that Natural selection and drift can produce complex protein machinery."

      Calling proteins "machinery" doesn't give credence to the argument that they are designed. Please try harder. Besides, doctors encourage people to take their full course of antibiotics because knowledge of evolution, and experience, has shown that not doing so can result in antibiotic resistance developing. Intelligent people call that process "evolution".

      "Thankfully none of that has anything to do with the lie that natural selection can produce complex protein systems."

      Then feel free to take drugs that have only been tested on starfish. I won't stop you.

      "Just how stupid and desperate are you?"

      You must be clairovoyant. I was just going to ask you that very same question.

      Delete
    31. William:
      Who said anything about creationists.

      You did, moron. Try to follow what you spew

      Calling proteins "machinery" doesn't give credence to the argument that they are designed.

      You are dense as I did not call proteins machinery. A bacterial flagella is though.

      Besides, doctors encourage people to take their full course of antibiotics because knowledge of evolution

      You are deluded as tat has NOTHING to do with natural selection or unguided evolution.

      Then feel free to take drugs that have only been tested on starfish.

      That doesn't follow from what I said. You must be a moron.

      Thank you for proving that you are stupid and desperate.

      Delete
    32. Anyone can do a google search and see that "protein machinery" is an actual term used by biologists to describe things like ATP synthase and other systems that require multiple proteins to come together to form the function.

      This is something that natural selection is supposed to be capable to dong yet no one knows how to even test such a thing. And it has never been observed.

      And no, there isn't anything from any search engine that demonstrates otherwise.

      Delete
  2. "Evolution seeks lack of function, which makes no sense, and science just keeps on finding more function. Evolution and science, it seems, are in an eternal conflict."

    Dr. Hunter,
    Thanks for publishing the science as it confirms common sense and reasonable inference and exposes the "science falsely so called ".

    ReplyDelete
  3. Your argument, in a nutshell, is that evolution predicts junk DNA and the fact that some junk DNA has been found to have function is evidence against evolution. That would be a nice argument if evolution actually predicts junk DNA.

    Junk DNA was originally thought to be a problem for evolutionary theory because it was thought that selection would weed it out. Some theories were even proposed that the junk DNA was needed for structural integrity of the cell.

    But much of the arguments over junk DNA have been centred around human DNA. Late felt due to religious beliefs that god would never produce a human with 90% of its DNA serving no function. There are examples of genomes from different species in which the level of known functional DNA range from far less than the 10% seen for humans to almost 100%.

    Even if new function were to be found in the human DNA at the same rate as it is being found over the last few years (or even at an increased rate), a highly unlikely scenario, this would still require centuries to even approach 20% functionality.

    ReplyDelete
    Replies
    1. You're not grasping the distinction between prediction and confirmation.

      Delete
    2. No. you were grasping when you inferred that junk DNA was a fundamental aspect of evolution.

      Delete
    3. Your argument, in a nutshell, is that evolution predicts junk DNA

      No, that's not the argument.

      Delete
    4. "No, that's not the argument."

      Idiots are so fond of telling those who disagree with them what they really think and believe in, I thought I would give it a try.

      Delete
    5. Cornelius, could you please change Idiots to IDists in my comment. Spell-check made the change. I realize that IDiots is often a term used to label ID proponents but I do not like name calling.

      Thank you

      Delete
    6. WS:

      I'm afraid Google/Blogger does not allow comment editing like that. You're followup will have to do.

      Delete
    7. Cornelius, that is fine. Thank you for the effort. I just hate to be viewed as someone who resorts to cheap insults rather than presenting an argument. Otherwise, I would be no better than Joe. Oops, was that a cheap insult?:)

      Delete
    8. You aren't better than me, William- well you are better than me at bluffing, lying and avoiding the real issues- but that is about it

      Delete
  4. William Spearshake

    Idiots are so fond of telling those who disagree with them what they really think and believe in, I thought I would give it a try.


    Heh. #MindOfACreationist. :)

    ReplyDelete
  5. From a 'design' perspective, the finding of a PTC in a portion of a sequence would not be evidence of "junk DNA," but of some possible function.

    We're now discovering something about this function. Over at Evolution and News, they also have a story about this same paper, and they interpret the PTC as an "if, and only if," logic segment in the overall protein sequence.

    Well, that's how code designer's think, don't they? As you say, Cornelius, science keeps finding function, and the more powerfully technical it becomes, the more it will find.

    And, of course, this is to say nothing of the ENCODE project.

    But religion drives science, and it has consequences. Down with those Epicureans!! :)

    ReplyDelete