Thursday, September 11, 2014

Is the Origin of New Genes “Basically a Solved Problem”?

De Novo Genes a Done Deal

It is no surprise that proteins—the essential machines of life—are not likely to have evolved. At least, that is, if you believe in science. Even according to evolutionists and the most optimistic assumptions possible, the evolution of proteins is so unlikely it is beyond practical consideration. While this conclusion is intuitive and hardly surprising, there are several reasons for it. One of the reasons is that the scenarios evolutionists typically envision involve the pre existence of proteins. For instance, proteins are needed to create proteins, at least in today’s biological world. Indeed, proteins are also required for life as we know it. So the first proteins would have had to evolved in a very different kind of biological world. Another reason why protein evolution is difficult is that the fitness landscape in protein sequence space is mostly flat and rugged. A few random mutations will quickly degrade protein function and most of the hyper-dimensional sequence space has little or no function and is far from a useful protein. It is extremely difficult for a random sequence to migrate via mutations close enough to a useful protein for natural selection to take over. In fact this challenge makes the protein evolution difficult regardless of whether proteins already exist. But in spite of this problem, evolutionists believe that protein evolution is not a significant problem. Recently an evolutionist commented that it is “basically a solved problem.”

It wasn’t too many years ago that evolutionists ruled out such protein evolution. Because the problem is so difficult, they believed proteins somehow evolved very early in evolutionary history, and have merely undergone various modifications ever since. As one recent paper explains:

In the pre-genomics era it was widely assumed that much of present-day genetic diversity could be traced by common ancestry to a molecular big bang, where all genes evolved at once.

Likewise another recent paper states:

The emergence of new genes has long been thought to be almost exclusively driven by duplication or recombination of existing gene fragments. The possibility of de novo evolution from intergenic non-coding sequences seemed remote.

But that has all changed now. Not because evolutionists have figured out how new proteins can evolve de novo, but because, if evolution is true, new proteins must have evolved de novo. For in this post-genomic era, we now know that the genomes of species are chocked full of unique, one-time, protein-coding genes. They are not found in allied species, which under evolutionary theory means those genes must have evolved relatively recently.

But how?

If you read the headlines, you would have the impression that the problem is well in hand. For instance, super-star science writer Carl Zimmer wrote in the New York Times earlier this year that “researchers have documented the step-by-step process by which a new gene can come into existence.”

Case closed right?

Well not quite. In fact, not even close. What Zimmer tells his readers is a “step-by-step process” is what scientists affectionately refer to as a cartoon. In fact, here it is:


Was it not a bit serendipitous that DNA segments could so easily become transcribed?

And once transcribed and translated, the resulting protein would most likely be worthless junk. It would be somewhere in the middle of that rugged protein sequence hyperspace, light years away from a design that would improve fitness.

Yet the protein would continue to be synthesized by the patient organism, waiting forever as mutations randomly sample the rugged hyperspace. If that was the case then such experiments would rapidly accumulate, and the organism would be producing a plethora of junk proteins.

For this evolutionists envision that the rapid rise of these experimental protein-coding genes is offset by their destruction:

This fast rate of gene emergence raises the question why the genomes do not fill up with such genes over time. In spite of huge variation in total genome size, genomes do not show a proportionally large variation in terms of protein-coding repertoires. Hence, the emergence rate of new genes must in some way be balanced with a corresponding loss rate.

So evolutionists must say that mutations halt the progress, for example, by creating stop codons somewhere in the middle of the gene.

But if that was the case, then the incredible problem of searching through the sequence space just became that much more impossible. Not only must we search through an astronomically huge, flat, rugged fitness landscape that makes finding a needle in a haystack seem trivial, but now the searches are routinely interrupted and must start all over again from scratch. It is an evolutionary treadmill where mutations are working furiously and getting nowhere as they are continually creating and destroying genes.

This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence.

So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes are observed over and over. And since evolution must be true, then those solo genes must evolved:

Several studies have by now also shown that de novo emerged transcripts and proteins can assume a function within the organism. All of this provided solid evidence that de novo gene birth was indeed possible.

And what exactly do these studies show? Did they really show that “de novo emerged transcripts and proteins can assume a function within the organism”?

Not exactly.

One study found a gene in a yeast species, but the corresponding genome location in allied species came up blank. Again, it is the belief that evolution must be true that does the heavy lifting. A gene is found in a species, it is not found in allied species, those species must share a common ancestor, that common ancestor must have existed relatively recently because the species are similar, therefore the gene must have evolved recently.

It all hinges on evolution being true.

The same logic applies in the other studies, such as the one which found a gene in the mouse genome that is missing in other mammals.

Two more studies found more of these de novo genes in the fly genome, and upon testing discovered that such genes are often surprisingly essential. That doesn’t help. Now, the genes must not only have somehow evolved rapidly, they must have rapidly become essential. It was another surprise for evolutionists. Other studies have found genes in only some individuals, within a population.

Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.

This de novo gene story parallels the twentieth century evolutionary insistence that species adapt by random biological variation, not geared to help with the current environmental challenges. Those random variations are then subject to natural selection, and the resulting adaptation is the first step toward the large-scale change evolution requires to create the species.

Only recently have evolutionists begun to reckon with the failure of that narrative. I don’t know how genes arose, but once again evolutionists have made unscientific and unsubstantiated claims, and set themselves up for another failure. Only a few years ago they agreed that such evolution of new genes would be impossible. Now they have been forced to adopt it because the evidence unambiguously reveals solo genes, and evolutionists dogmatically insist that everything must have spontaneously evolved. So it is yet another false prediction followed by yet another epicycle, making the theory far more complicated and unlikely.

63 comments:

  1. a minimal system like a camera will need at least 3-4 parts. so a minimal eyespot will need the same (even an intellegent desgin cant made a vision system below 2-3 parts). so for start we will need 2-3 proteins. a minimal protein will need 50 aa(nature 2001 for atp binding only). so we will need at least 150 amino acid or a minimal chance of 2^150 if we consider the sequences that give the same function(synonymous sequences)

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    1. What good is an eyespot by itself? It must be part of a light sensing system that controls the organism in some manner. That system must also evolve in conjunction with the eyespot.

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  2. Even Michael Behe and David Berlinski agree that natural evolutionary processes can create new genes. Look up jingwei and sdic and the literature on their origin. Look up Long et al. 2003. Why can't you even get these totally obvious basic points right?

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    1. Nick:

      Wow. Thank you for the comment, you have proven my point for me. It is astonishing you would mention Long et. al. as there is literally nothing there at odds with the OP. Even more astonishing are your appeals to jingwei (exon shuffling) and scid (gene fusion and fission).

      Unfortunately this is a typical interaction with evolutionists. I've debated evolution professors who also gave just this sort of fallacious and vacuous response. It always seems to be a hurried sort of hand-waving, throwing out a few names as though it proves their case. The crowd applauses and the debate adjourns. This isn't about the empirical evidence, it is about an agenda.

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    2. Berlinski does not agree with Matzke. As a matter of fact he takes Matzke to task over those two genes.

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    3. Nick, you've been corrected about these kinds of mistakes over and over, yet you still continue to make them. Please, for the sake of your profession, stop embarrassing yourself and learn to actually address the points made.

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  3. Dr. Hunter, I soooo agree with you that De Novos are a BIG DEAL! I see them as a neo-Darwin crusher.

    Nick, rather than semi-site some out of context statement by Behe and Berlinski, please explain to me how random DNA sequence can luck into not just a sequence that has "function", but a sequence that as function which is called for by an organism.

    If I understand the state of De Novos at the moment, certain species have genes that the neighboring species in the same genus don't have. Often these species HAVE UNIQUE ABILITIES. They don't just need "some sort of function" from their unique proteins, they need the function that gives them a unique ability which is meaningful within their environmental context. The latter is a VASTLY greater challenge.

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    1. bFast: please explain to me how random DNA sequence can luck into not just a sequence that has "function", but a sequence that as function which is called for by an organism.

      Exon shuffling. Basically, taking known working components and rearranging them into new combinations.

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    2. Unfortunately unguided evolution cannot account for exons let alone exon shuffling.

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    3. Joe G: Unfortunately unguided evolution cannot account for exons let alone exon shuffling.

      That wasn't the question raised.

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    4. Zachreil, "Basically, taking known working components and rearranging them into new combinations."

      My understanding is that any time a gene's heredity can be figured out from "rearranging in new combinations" the resultant gene is not considered orphan.

      Cornelius Hunter, please correct me if I am wrong. Are you not saying that we are having genes appear out of non-functional space rather than merely out of cut and paste from functional space?

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    5. Here's a review article discussing various mechanisms. Tautz & Domazet-Lošo, The evolutionary origin of orphan genes, Nature 2011.

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    6. How did they determine that those various mechanisms are blind watchmaker mechanisms?

      Unfortunately unguided evolution cannot account for exons let alone exon shuffling.

      That wasn't the question raised.

      Yes, it was. Obviously you have reading comprehension issues.

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    7. Zachriel, I have been googling this topic. (That's how the common man expands his knowledge base.) It would appear that ORFan, or orphan, genes can be created via duplications, splicing "errors" etc. However, the term de novo seems to be held exclusively for genes that develop out of non-functional dna. As CH is referring to de novo genes in his article, your "they come from shuffling working components" view is invalid.

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    8. Zachriel, how much true de novo (new gene sourced from dna that doesn't have precursor function) activity is permitted within the theory? At what frequency does de novo challenge the current paradigm?

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    9. bFast: However, the term de novo seems to be held exclusively for genes that develop out of non-functional dna.

      Non-functional dna was often once functional, that is, it's not random.

      bFast: At what frequency does de novo challenge the current paradigm?

      All sorts of things challenge the prevailing paradigm. That's why biology is such an active field of study. However, ID has never added anything to the field.

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    10. Z:
      Non-functional dna was often once functional, that is, it's not random.

      Non-answer, Unguided evolution can't account for DNA. So that would be a problem.

      Z;
      However, ID has never added anything to the field.

      How would you know? Functional sequence complexity is being discussed in peer-review and FSC = CSI.

      Blind watchmaker evolution has been an obstruction to science but you seem to be OK with that.

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    11. Joe G: Unguided evolution can't account for DNA.

      Again, that wasn't the question being raised.

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    12. Here's the question:

      bFast: please explain to me how random DNA sequence can luck into not just a sequence that has "function", but a sequence that as function which is called for by an organism.

      This question presupposes the existence of dna, contrary to your assertion otherwise.

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    13. I did NOT assert otherwise. My point is that if unguided evolution cannot account for DNA then it has nothing to say about it.

      Also it is obvious that this:
      please explain to me how random DNA sequence can luck into not just a sequence that has "function", but a sequence that as function which is called for by an organism.

      and this:

      Unfortunately unguided evolution cannot account for exons let alone exon shuffling.

      Are the same thing and you sed they weren't.

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    14. Z:
      Non-functional dna was often once functional, that is, it's not random.

      It doesn't follow that even if non-functional DNA was once functional that means it's non-random. You have no idea what you are saying.

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    15. Joe G: My point is that if unguided evolution cannot account for DNA then it has nothing to say about it.

      If evolution cannot account for the origin of DNA, it may still, given the existence of DNA, inform about how DNA sequences evolve over time.

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    16. Joe G: It doesn't follow that even if non-functional DNA was once functional that means it's non-random.

      Of course it does. As an analogy, take a bit of literary text, and change some of the letters. The result will not be random, but the altered text will exhibit all sorts of patterns.

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    17. Z:
      If evolution cannot account for the origin of DNA, it may still, given the existence of DNA, inform about how DNA sequences evolve over time.

      LoL! Evolution isn't being debated.

      It doesn't follow that even if non-functional DNA was once functional that means it's non-random.

      Of course it does.

      Nope. And your "analogy" is nothing of the kind.

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    18. Joe G: Evolution isn't being debated.

      Evolution is found 50 times in the original post.

      Joe G: And your "analogy" is nothing of the kind.

      Instead of waving your hands, you might explain why the analogy fails.

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    19. Z:
      As an analogy, take a bit of literary text, and change some of the letters. The result will not be random, but the altered text will exhibit all sorts of patterns.

      LoL! Of course it wouldn't be random if an intelligent agency deliberately changed the text.

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    20. Z:
      Evolution is found 50 times in the original post.

      Yes and CH has explained how he uses the word- as blind watchmaker evolution.

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    21. Joe G: Of course it wouldn't be random if an intelligent agency deliberately changed the text.

      Take a literary text and change a few letters randomly. The result will not be random. If you prefer, take a DNA sequence of a functional protein, change a few bases. The result will not be random.

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    22. Z:
      Take a literary text and change a few letters randomly. The result will not be random.

      Why not?

      If you prefer, take a DNA sequence of a functional protein, change a few bases. The result will not be random.

      How do you know?

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    23. Joe G: Why not?

      Because it will exhibit many of the patterns in the original sequence.

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    24. Joe G: How do you know?

      It's easy enough to test. Let's try it:

      Original:
      "To be, or not to be- that is the question:
      Whether 'tis nobler in the mind to suffer
      The slings and arrows of outrageous fortune
      Or to take arms against a sea of troubles,
      And by opposing end them."


      After 10 random letter mutations:
      To be, or not tb be- that is the question:
      Whethel tis nobler in the mindrto suffer
      Thelslings and arrowsqif outrageous fortune
      Or to take arms against a sea of troubles,c
      And y oiposivg end them.


      Is the resultant string random? Not at all.

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    25. Z:
      Because it will exhibit many of the patterns in the original sequence.

      That does not make it non-random.

      Is the resultant string random?

      Yes, the pattern of typos is random

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    26. Joe G: Is the resultant string random?

      Heh. Really?

      To be, or not tb be- that is the question:
      Whethel tis nobler in the mindrto suffer
      Thelslings and arrowsqif outrageous fortune
      Or to take arms against a sea of troubles,c
      And y oiposivg end them.


      You can't detect any significant patterns?

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    27. LoL! Zachriel quotes himself and makes it appear that I said it.

      The pattern of typos is random- yes, really.

      But more to the point what Zachriel is saying has absolutely nothing to do with bFast's inquiry.

      And it doesn't follow that even if non-functional DNA was once functional that means it's non-random.

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    28. Joe G: The pattern of typos is random

      Yes, but not the altered string itself.

      Z: Is the resultant string random?
      J: Yes

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    29. Zachriel continues to prove that she is dishonest.

      Z: Is the resultant string random?

      Yes, the pattern of typos is random

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    30. Joe G: the pattern of typos is random

      But that's not the question. Is the resultant string random?

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    31. It is random in that you cannot predict what letter will come next. However this has NOTHING to do with anything we were discussing. It is just another one of your attempts to obfuscate.

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    32. Joe G: It is random in that you cannot predict what letter will come next.

      That is incorrect. We can predict with reasonable probability which letter will come next in the sequence.

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    33. And you will be wrong at every random change. So going from a 100% certainty to less than that means it is random with respect to the original.

      But again all of this is moot as it has nothing to do with what you were trying to respond to.

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    34. Joe G: And you will be wrong at every random change.

      Which means 97% of the time we would be correct. That means it is not a random sequence.

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    35. It is definitely random with respect to the original.

      But anyway this is where it started:

      If you prefer, take a DNA sequence of a functional protein, change a few bases. The result will not be random.

      How do you know?

      Shakespeare is not a DNA sequence of a protein.

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    36. Joe G: It is definitely random with respect to the original.

      No, it's not. It strongly resembles the original sequence. So you are wrong again.

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    37. If 97 < 100 then I am correct. And 97 < 100

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    38. Joe G: If 97 < 100 then I am correct.

      Add random to the concepts you do not understand. For something to be random, it means the chance of guessing the next in the sequence is no better than chance. With 27 characters, that would be about 4%, not 97%.

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    39. I said random with respect to the original. If you have to lie and misrepresent, why bother?

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    40. Joe G: I said random with respect to the original.

      It's not random with respect to the original. The original predicts the altered version with 97% accuracy.

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    41. It is random with respect to the original.

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    42. I can predict the unaltered original to 100%. I cannot do the same with the altered version.

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    43. Joe G: I cannot do the same with the altered version.

      So if someone can predict lottery numbers with 97% accuracy, you would consider that random?

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    44. Z:
      So if someone can predict lottery numbers with 97% accuracy, you would consider that random?

      In context that would mean someone looked at the winning numbers and couldn't repeat them correctly.

      What is wrong with you?

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    45. Joe G: that would mean someone looked at the winning numbers and couldn't repeat them correctly.

      So not random.

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    46. So not random

      So not a prediction.

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    47. Joe G: So not a prediction.

      The question is whether the string was random or not.

      In any case, someone who could predict 97% of the lottery numbers would win the jackpot on four out of five lotteries of six numbers, and when losing the jackpot would almost certainly win one of the lesser prizes.

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    48. In any case, someone who could predict 97% of the lottery numbers would win the jackpot on four out of five lotteries of six numbers, and when losing the jackpot would almost certainly win one of the lesser prizes.

      When that person exists you will have something to talk about.

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    49. Joe G: When that person exists you will have something to talk about.

      So you have abandoned your position. Fair enough.

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    50. So you have abandoned everything. Very good.

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  6. Zachriel:

    I'm assuming that by rearrainging exons you mean yorua re rearrainging functional domains, or tertiary structures. But to the best of my knowledge, that isn't there isn't 1: correspondence between exons and domains. Sometimes a number iof exons is needed to make one domain. And they might nit fit together to make a functioning domain if the order is change. Tertiary stucture depends on quaternary structure. So just shuffling exons doesn;t really solve the problem. Its like taking apart a machine, shuffling the parts, randomkling rearrainging them, and hpoing to get something that works.

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  7. natschuster: So just shuffling exons doesn;t really solve the problem.

    It dramatically reduces the combinatorial problem.

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    1. And it significantly increases the bullshit factor

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