Sunday, January 1, 2017

A Salamander Two-fer: Non Homologous Development and an ORFan

A Faulty Foundation

Salamanders have their own way of doing things. For most animals, if an important body part, such as a limb, is lost, it is gone for good. But for salamanders, they just grow a new one. Also, salamanders use different embryonic development patterns. For example, their digits (fingers and toes for us humans) form in the wrong order—going, essentially, in the wrong direction. You can see this in the figure below (taken from this paper from Neil Shubin’s group, but note the labeling error, VI rather than IV). In the figure, the numbers across the top show the order in which the digits appear. Salamanders go against the common pattern. This “reverse polarity” in what otherwise is a highly conserved development pattern in the tetrapods is a quandary for evolution.



Early evolutionists who first seriously reckoned with this “striking deviance from an otherwise conserved pattern in tetrapods,” as the Shubin paper puts it, as well as other distinctive features of salamander limb development, concluded that the salamanders probably arose independently of the other tetrapods. In other words, these development inconsistencies were so profound they required an independent origins—there were two different origins of tetrapods.

The problem, however, is the set of similarities between the salamanders and their cousin tetrapods is so massive, that any such independent origins would be absurd from an evolutionary perspective.

So evolutionists were left needing an explanation for the profound divergence. Perhaps salamanders got their start with a loss of digits. If the first salamanders had only two digits, and then re-evolved the other digits (catching up to their ancestral forms), the development order could have been rearranged.

Unfortunately such a hypothetical evolutionary history, where the salamanders begin by losing digits, does not fit the data (both molecular and fossil) very well, even within the context of evolutionary theory.

Perhaps the salamander digit development deviance arose as a larval adaptation. Or perhaps the salamander development pattern is not a “deviance” at all, but rather is the nominal, ancient pattern, but is retained only in salamanders among living tetrapods.

But these hypotheses have problems as well. In fact the salamander character data are full of contradictions:

The evolution and phylogeny of crown group salamanders is plagued by homoplasy. In fact, a large a number of highly derived anatomical characters, including body elongation, tail autonomy, and life history pathways, have been demonstrated or are debated to have evolved multiple times.

[Note that these anatomical characters have not “been demonstrated” to have evolved multiple times. That is a misrepresentation of the science. They only have “been demonstrated” to have evolved multiple times if one assumes evolution at the outset.]

Yet another problem plaguing these evolutionary hypotheses is the finding of genes unique to the salamander that are crucial for its limb regeneration ability and unique embryonic development patterns. You can read more about these here and here, and this brings us to the second half of our two-fer.

Whether they are called unique genes, novel genes, orphans, ORFans, taxonomically-restricted genes (TRGs), lineage-specific genes (LSGs), or whatever, they are a problem for evolution. First, they counter the above hypotheses attempting to explain the salamander’s unique development. As one paper explains:

the notion of an ancient limb regeneration programme has been challenged by reports of salamander lineage-specific genes (LSGs) upregulated during regeneration. One salamander LSG in particular, the Prod1 gene, was shown to be required for proximodistal patterning during limb regeneration and for ulna, radius and digit formation during forelimb development. The existence of urodele LSGs expressed and involved in regeneration has lent support to the hypothesis that limb regeneration is a derived urodele feature.

In other words, the salamander gets it done using genes unique to its lineage, and that contradicts the hypothesis that the salamander’s unique capabilities were there all along.

It also contradicts the evolutionist’s long-standing, but rapidly fading, hope that ORFans would go away. As we have explained, evolutionists hoped that such lineage-specific genes would be found in other species as more genomes were decoded. But instead the number of ORFans just continued to grow.

Evolutionists next predicted that similar ORFan sequences would be found in the so-called non-coding DNA. Although that is sometimes the case, it is not generally, and the Prod1 gene is another example of this.

Evolutionists next predicted that ORFan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That also is wrong, and Prod1 is yet another example of an ORFan that is indeed a real protein.

The findings of unique (non homologous) development patterns, and lineage-specific genes make no sense on evolution. And attempts to explain these findings according to evolution with clever, detailed hypotheses just cause more problems.

If you try to build a house on a faulty foundation, it will just get worse. Evolution is a flawed theory, and the more we learn about biology, the more evident that becomes.

Evolution may be true, it may be false. That is debatable. What is not debatable, however, is that the empirical evidence contradicts the theory.

29 comments:

  1. "The findings of unique (non homologous) development patterns, and lineage-specific genes make no sense on evolution. And attempts to explain these findings according to evolution with clever, detailed hypotheses just cause more problems."

    The reality you describe should be sufficient to cause every evolutionist to sit up and take notice. Something is very wrong with Darwinian evolution.

    Instead, unfortunately, they close their eyes, and put their hands over their ears. Alas.

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    1. What's your "design" explanation for this phenomenon PaV? The Designer just decided on a whim to make salamander digits develop in reverse order because he was feeling a bit contrary that day?

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    2. The designer must have been partaking in that other designed compound; alcohol.

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    3. Umm evolutionism doesn't have a mechanism capable of explaining embryonic development. So that would be a problem for you two yet I am sure it will be ignored.

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    4. You can always count on Joke to evade questions with his stock "your side has no evidence!!" tirade. What a blustering coward.

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    5. Joke: "Umm evolutionism doesn't have a mechanism..."

      Evolution has several mechanisms. What are ID's mechanisms?

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    6. LoL! Wee willie has to chop off what I said and post a desperate quote-mine and ghostdork can only stomp its little feet and flail away at a strawman.

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    7. GR - "What's your "design" explanation for this phenomenon PaV?"

      I keep seeing you go to this argument. The idea that ID doesn't have a mechanism so ToE is valid. Isn't that Arguementum Absurdum? I've been told over and over again that lack of evidence for evolution isn't proof of creation. How is it that lack of evidence for creation is proof of evolution?

      Ultimately, both claim the same evidence. Life exists in diversity. Something had to cause it unless of course its not real and we all live in a Matrix world.

      If evolution is falsified, then what? Where do evolutionists turn? Where do anti-theists turn? If evolution is falsified and creation isn't proven, what?

      "if you remove the impossible, whatever remains, however improbable, must be true" - Spock

      The more I read the more likely evolution, as taught, is impossible. The question becomes, what remains?

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    8. "I've been told over and over again that lack of evidence for evolution isn't proof of creation."

      It isn't. But since there are mountains of evidence for evolution, I wouldn't lose sleep over it.

      "How is it that lack of evidence for creation is proof of evolution?"

      It isn't. It just points a finger at the vacuity of creationism.

      See, that was simple.

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    9. But since there are mountains of evidence for evolution,

      That all depends on how you are defining "evolution". Equivocation is big business for evolutionists.

      There is a mountain of evidence that allele frequency changes over time. There isn't any evidence that natural selection and drift can produce vision systems.

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    10. ohandy1

      GR - "What's your "design" explanation for this phenomenon PaV?"

      I keep seeing you go to this argument. The idea that ID doesn't have a mechanism so ToE is valid.


      No one made that argument. Evolution has provided sufficient positive evidence to be beyond any reasonable doubt. I just think it's funny Creationists like PaV love to scream "evolution is WRONG WRONG WRONG!" but can't even begin to tell us what's right.

      The paper reference in the OP offered several plausible explanations for the reversed digit development. Did you notice not a single creo offered any evidence they are wrong or offered any alternative ID reason?

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    11. Ghost, "The Designer just decided on a whim to make salamander digits develop in reverse order because he was feeling a bit contrary that day?"

      Um, first, you seem to think that challenges that are good for one theory are automatcially good for the other. However, they are not. If we presumed that Hamlet was developed via Darwinian means, we could come up with all sorts of "how 'bout this, how 'bout that" reasoning. However, as we know that some smart guy wrote it, the questions become mute. Shakespeare wrote any portion of Hamlet as he did simply because it pleased him to do so. It may have made aesthetic or logical sense, but down at its core, it pleased him to write it that way, so he did. This is the creative person's right.

      Now to the challenge at hand, could it be that the Designer wanted to create a mystery, a challenge for the simple minded to puzzle about as they purused this theory called the Darwinian synthesis? Does the designer need anything more than this "entertainment" to make such a decision?

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    12. bFast

      Um, first, you seem to think that challenges that are good for one theory are automatically good for the other


      Funny how one theory - ToE - consistently answers such challenges while the ID side - it isn't a theory by any stretch - consistently can't offer a thing except "The Designer made it that way JUST BECAUSE!"

      ID is impotent. It has zero predictive power, zero explanatory power, can identify zero mechanisms for the physical manipulation of matter. It's so lame it can't even come up with any testable hypotheses.

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    13. GR "Creationists like PaV love to scream "evolution is WRONG WRONG WRONG!" but can't even begin to tell us what's right."

      You appeal to "mountains of evidence" to justify your faith in evolutionary theory. Ok, so you believe. But whenever you're presented with an argument where the evidence is against you, out comes this mantra again, "Well its not like ID has a mechanism".

      As though that were at issue.

      If evolution has failures, they belong to that theory. They don't equal proof for an alternative, only reason to doubt the theory at hand. It would be intellectually honest to say "I don't know" and look for viable alternatives. It's not intellectually honest to stamp your feet and squeal about how much evidence you have. Like WS also likes to do.

      I'm just a lowly MBA in this crowd. Maybe the really smart people of the world don't require consistency in their worldviews.

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    14. bFast: "Um, first, you seem to think that challenges that are good for one theory are automatcially good for the other."

      The journals are full of thousands of original research papers on evolution. I don't recall any of these arguing that because ID doesn't have a mechanism that evolution must be right. On the other side, the journals do not contain many original research papers on ID. Most of the heavy lifting is done by the DiscoTute, UD, Darwin's God and other ID blogs. Anyone looking at the articles and OPs posted on these web sites will conclude that they are all about documenting gaps in evolutionary theory and disagreements amongst evolution scientists. So, tell me again which side thinks that challenges for one theory is automatically good for the other.

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    15. The equivocation is in full bloom. The journals are devoid of papers singing the virtues of natural selection and drift. No one knows how to test the claim that vision systems evolved let alone that they evolved by means of natural selection and drift.

      Evolution is not a scientific theory because it does not make testable claims. Evolutionism is impotent, it doesn't make testable claims and no one uses it as a research heuristic.

      And BTW, design is a mechanism by definition. And it is as valid a mechanism as natural selection. Dr Spetner's "built-in responses to environmental cues" is another mechanism of ID. And it is as valid a mechanism as anything evolutionism has.

      The evos here think their equivocation and willful ignorance are actual arguments- desperation is thy name, evos.

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    16. Ghost equivocator:
      Evolution has provided sufficient positive evidence to be beyond any reasonable doubt.

      How are you defining "evolution"? There isn't any evidence that vision systems can evolve and no one knows how to test the claim.

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    17. WS: What is your premise? What if evolution were falsified? Where would you go? What option remains for you? How much of your faith in evolution is driven by your antithesis for the alternatives?

      I've asked this of others and always get the same answer; "there are no scientific alternatives". So when there's nowhere else to go, you do what you have to to accept where you are.

      You can claim that evolution hasn't been falsified, but if there were a scientific (I could just as easily say atheistic) alternative it would already be heralded with sighs of relief. The fact is, evolution is the only game in town for the materialist.

      It seems to me you believe evolution had to happen because there are no viable alternatives.

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    18. ohandy1: "WS: What is your premise? What if evolution were falsified? Where would you go?"

      Ask me again when it has been falsified.

      "How much of your faith in evolution is driven by your antithesis for the alternatives?"

      I don't think that words means what you think it means.

      "I've asked this of others and always get the same answer; "there are no scientific alternatives"."

      There have been scientific alternatives. Lamarck, preformation, saltation, etc. but they have not stood up to scrutiny and are not supported by the evidence. There have also been non-scientific alternatives such as creationism and scientific creationism, and pseudo-scientific alternatives such as ID. Again, not supported by any evidence.

      "The fact is, evolution is the only game in town for the materialist."

      It is the only game in town for anyone who has examined the evidence.

      "It seems to me you believe evolution had to happen because there are no viable alternatives."

      That's how science works. You may start with several possible explanations. Slowly, as they are tested and evidence gathered, one or more may be excluded. If you are lucky, only one remains. Right now, the last man standing is evolution. If you think that ID is a better explanation, feel free to do the research and publish the papers.

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    19. Ask me again when it has been falsified.

      Tell us when it can be tested.

      Again, not supported by any evidence.

      ID is supported by the evidence. Experiments have uncovered a multitude of irreducibly complex systems, subsystems and structures. Basic cellular division is IC.

      It is the only game in town for anyone who has examined the evidence.

      Except you fail to mention what evidence supports natural selection and drift producing protein machines, vision systems, macroevolution.

      The bottom line is no one knows how to test the claims of evolutionism, ie darwinism and all of its variants.

      All William can do is equivocate- how are you defining "evolution", William?

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    20. WS yup wrong word.

      "It is the only game in town for anyone who has examined the evidence."

      No, its the only game in town for people who adhere to the philosophy of materialism. We don't know all that exists in the natural universe beyond what we can see or touch. To call God or spirit unnatural is wrong and supernatural is to place arbitrary limitations on what is natural. Radio broadcasts would have been supernatural once upon a time.

      We lack the capacity to study what is spiritual, but that doesnt limit our ability to hypothesize any more than Tesla was prohibited from theorizing wireless energy transmission. I've read he was called a quack at the time.

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    21. I will help William out:

      1. Change over time; history of nature; any sequence of events in nature


      2. Changes in the frequencies of alleles in the gene pool of a population

      3. Limited common descent: the idea that particular groups of organisms have descended from a common ancestor.

      4. The mechanisms responsible for the change required to produce limited descent with modification, chiefly natural selection acting on random variations or mutations.

      5. Universal common descent: the idea that all organisms have descended from a single common ancestor.

      6. “Blind watchmaker” thesis: the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection
      acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms.

      The way "evolution" has been portrayed by Darwin, Mayr, Dawkins, Coyne, and countless others theirs is #6. That is the "evolution" that is being taught. Yet that is a philosophical claim with no founding in science.

      William and GR may beg to differ but they will do so without any reasoning. And they will never tell us how to test the claim that vision systems evolved via the processes in #6. They will bluff their way through it and say others have already done so, which is a lie. No one even knows how to test such a claim.

      ID is OK with definitions 1-5 above, with the caveat that organisms were designed to evolve and evolved by design. With the advent of genetic algorithms we have seen the power of evolution by design. No one knows how to model evolution #6.

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    22. ohandy1: "WS yup wrong word."

      Not to worry. We all do this on occasion. If we were all perfect and infallible, we would all be Joe.

      "No, its the only game in town for people who adhere to the philosophy of materialism."

      There are many non-materialists who also believe that evolution is the only game in town.

      "We don't know all that exists in the natural universe beyond what we can see or touch."

      True. But if it is in the natural world, it is not beyond detection.

      "To call God or spirit unnatural is wrong and supernatural is to place arbitrary limitations on what is natural."

      No, natural and supernatural have very clear definitions. If God is a physical being, then he would be considered natural but extremely powerful. If he is not a physical being then he is supernatural and very powerful. But, overtime I ask ID proponents to speculate on the nature of the designer, I am always told that ID is not about the designer, it is about the detection of design.

      "Radio broadcasts would have been supernatural once upon a time."

      As was lighting, thunder, the tides, etc. Over the centuries, the realm where the supernatural has been used as an explanation has gotten smaller and smaller. there is no reason to believe that this trend will not continue.

      "We lack the capacity to study what is spiritual,..."

      This is where we disagree. If anything has an impact on the physical universe, it is within our capacity to study. We cannot see electrons or subatomic particles, yet we are able to study them.

      "...but that doesnt limit our ability to hypothesize any more than Tesla was prohibited from theorizing wireless energy transmission."

      Agreed. But for an hypothesis to be of value, it must be testable. So far, ID has done very little other than identify gaps in evolutionary theory and cheer any time there are disagreements amongst scientists. There have been noble efforts to make it a true science (e.g., irreducible complexity, FIASCO, etc.), but whenever these are examined in detail, they fall apart.

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    23. But for an hypothesis to be of value, it must be testable.

      ID is testable whereas evolutionism is not. Well if the claim is that allele frequencies change over time, that has been tested. But that is hardly a mechanism capable of producing the diversity of life.

      First, a lesson from Dr Behe:
      The conclusion that something was designed can be made quite independently of knowledge of the designer. As a matter of procedure, the design must first be apprehended before there can be any further question about the designer. The inference to design can be held with all firmness that is possible in this world, without knowing anything about the designer.—Dr Behe

      The following is one design hypothesis:

      ID is based on three premises and the inference that follows (DeWolf et al., Darwinism, Design and Public Education, pg. 92):
      1) High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
      2) Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
      3) Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
      4) Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.


      Premise one is based on all of our observations and experiences. Premise 2 is based on observations and experiments. And if anyone could demonstrate premise 3 is wrong and that naturalistic mechanisms or undirected causes suffice to explain the origin of information (specified complexity) or irreducible complexity, then ID would be falsified.

      OTOH no one knows how to test the claim that vision systems evolved let alone evolved via natural selection and drift.

      The design is in the natural world and has been detected.

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    24. ohandy1

      It seems to me you believe evolution had to happen because there are no viable alternatives.


      Wrong. Evolution is accepted due to the quality and quantity of its positive evidence. You or anyone else is free to propose a scientific alternative. If you find one that explains the empirical data better than ToE, has more predictive power than ToE then it will become the accepted idea. Sorry but POOF the Designer did it by MAGIC!! isn't going to cut the muster. Neither is having IDiots like Joke endlessly C&P the same IDiot claims which have been soundly refuted for over a decade.

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    25. And still the equivocators refuse to define how they are using the word "evolution".

      What is William and GR so afraid of?

      Ranting on like a lunatic isn't evidence for you alleged ToE. Refusing to answer questions about your alleged ToE is evidence that you don't know what you are talking about. Refusing to say what this alleged supporting evidence is is proof that you are bluffing.

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    26. IRONY ALERT!!!

      Joke: "Ranting on like a lunatic isn't evidence for you alleged ToE."

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    27. Wee Willie clucking like a chicken, as usual. This is what wee willie is reduced to when its bluff is called.

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  2. Dr. Hunter, thanks for this post. I do believe that de novo genes (the term I prefer) are an absolute darwin killer. NDE* should produce extremely few of 'em.

    I remember on another post dialoguing with a biologist who assured me that as genes were studied the de novo count would go down. In his opinion the human lineage may be able to support one or two de novos, and that these would be small and not in important systems. I can buy his estimate of what NDE* is capable of.

    * I use NDE to imply all the wonderful techniques that have been uncovered within the naturalistic framework.

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