Tuesday, January 21, 2014

Err, Remember That Little Problem About Novelty?

“Life is genomically complex”

The theory of evolution has made many predictions about what we should find in biology. Those predictions have routinely failed and that tells us there is something wrong with the idea. One such prediction is that the genomes and their protein products, from different species, should form a common descent pattern. The graphic above shows an example of this prediction from a high school textbook written by evolutionist George Johnson. In that example Johnson informs his young readers that the hemoglobin protein “reveals the predicted pattern.” That was a misrepresentation of the evidence at the time, and since then the failure of this prediction has only grown worse. Another more recent, but related, prediction is that evolution is largely driven by regulatory proteins which regulate the construction of other proteins. These regulatory proteins control the embryonic development stages and the idea was that species evolve by slight modifications to how these proteins function. This prediction has also failed, and even evolutionist are now admitting the evidence contradicts what they were claiming only a few years ago. Here is how one evolutionist explains the failure of these predictions:

The prevailing theory is that all animals are built from essentially the same set of regulatory genes—a genetic toolkit, and that phenotypic variation within and between species arises simply by using shared genes differently. Scientists are now generating a vast amount of genomic data from an eclectic mix of organisms. These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes. Instead, we need to turn our attention to the role of genomic novelty in the evolution of phenotypic diversity and innovation.

The idea of a conserved genetic toolkit of life comes from the 'evo-devo' (evolutionary and developmental biology) world. In short, it proposes that evolution uses the same ingredients in all organisms, but tinkers with the recipe.

That, however, is all wrong:

However. We can now sequence de novo the genomes and transcriptomes (the genes expressed at any one time/place) of any organism. We have sequence data for algae, pythons, green sea turtles, puffer fish, pied flycatchers, platypus, koala, bonobos, giant pandas, bottle-nosed dolphins, leafcutter ants, monarch butterfly, pacific oysters, leeches…the list is growing exponentially. And each new genome brings with it a suit of unique genes. Twenty percent of genes in nematodes are unique. Each lineage of ants contains about 4000 novel genes, but only 64 of these are conserved across all seven ant genomes sequenced so far.

Many of these unique ('novel') genes are proving important in the evolution of biological innovations. Morphological differences between closely related fresh water polyps, Hydra, can be attributed to a small group of novel genes. Novel genes are emerging as important in the worker castes of bees, wasps and ants. Newt-specific genes may play a role in their amazing tissue regenerative powers. In humans, novel genes are associated with devastating diseases, such as leukaemia and Alhzeimer's.

So whereas the genome was once just so much junk, evolutionists now must admit that “Life is genomically complex” and that Darwinian evolution, err, doesn’t actually explain how the eye, or anything else for that matter, originated:

Life is genomically complex, and this complexity plays a crucial role in evolving diversity of life. It's easy to see how an innovation can be improved through natural selection, e.g. once the first eye evolved, it was subject to strong selection to increase the fitness (survival) of its owner. It is more challenging to explain how novelty first originates, especially from a conserved genomic toolkit. Darwinian evolution explains how organisms and their traits evolve, but not how they originate. How did the first eye arise? Or more specifically how did that master regulatory gene for eye development in all animals first originate? The capacity to evolve novel phenotypic traits (be they morphological, physiological or behavioural) is crucial for survival and adaptation, especially in changing (or new) environments.

Not a problem however. Biology doesn’t follow evolutions patterns? We merely must reimagine evolution. It’s a whole new theory as “genomes are constantly producing new genes all the time”:

But the presence of unique genes in all evolutionary lineages studied to date now tells us that de novo gene birth, rather than a reordering of old ingredients, is important in phenotypic evolution. The over-abundance of non-coding DNA in genomes is less puzzling, if they are a melting pot for genomes to exploit and create new genes and gene function, and ultimately phenotypic innovation. The current thinking is that genomes are constantly producing new genes all the time, but that only a few become functional.

“Constantly producing new genes”? Evolutionists think nothing of the failure of fundamental predictions—they simply add more epicycles. Whatever is found in biology, evolution produced it, no matter how silly the theory becomes. For decades evolutionists proclaimed that biology revealed evolution’s common descent pattern. That turned out to be wrong and now evolutionists simply turn the story on its head. Once we were told that evolution was proven by its common descent patterns. Now evolutionists euphemistically describe biology’s designs as “taxonomically-restricted,” “lineage-specific,” and “phylogenetically widespread.” The exact opposite of evolutions predictions.

Nothing in biology makes sense in the light of evolution.

[h/t: The Man]

33 comments:

  1. "The current thinking is that genomes are constantly producing new genes all the time"

    LOL

    This should patch up quite a few holes in the theory. Forget that step-wise incrementally beneficial mutation.

    Still, you have to admire the Darwinist's ambition. Only a year or so ago they were mystified by the presence of orphan (taxonomically restricted) genes. But in true form, any biological mystery is automatically absorbed as new evidence of 'what evolution did'.

    So it sounds like the new story is that entire genes are hopeful monsters now?

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  2. ...... who suppress the truth in unrighteousness, because what may be known of God is manifest in them, for God has shown it to them. For since the creation of the world His invisible attributes are clearly seen, being understood by the things that are made, even His eternal power and Godhead, so that they are without excuse,.......

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  3. Someone seems to have already forgotten that de novo genes aren't made from scratch. And that they can be found in sister species.

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    1. Oleg, why do you think evolutionists had such a surprised reaction to this discovery? (look up Tautz or Ken Weiss, etc.)

      The point is that entire complex genetic sequences are relatively suddenly becoming functional. As directly opposed to function being built up incrementally by selected mutations.

      And no, most of them have no detectable signal of common ancestry in a sister taxa.

      Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all genes in a genome.

      http://www.ncbi.nlm.nih.gov/pubmed/23348040

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    2. lifepsy,

      There are known cases of de novo gene that were broken in an ancestral species (non-coding portions of the DNA) and then were turned on by a mutation. One such case was described in a paper discussed in this thread. The researchers found human proteins that are entirely absent from chimpanzee and orangutan. That's a de novo origination of a protein.

      They have also found that the genes coding for those proteins in man also exist in chimpanzee and orangutan but are broken and therefore not expressed. A simple mutation in humans turned them on.

      Not exactly rocket science.

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    3. oleg:

      If humans, then, are descendants of chimps, what was the purpose of their "broken" genes?

      If the answer is that these genes were functional in the chimp ancestors, then the fact that they were retained, and not eliminated, suggests 'stasis' as a minimum, and points in the direction of "front-loading"---or, to put it another way, in the direction of teleology.

      What say you?

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    4. Front loading is an interesting hypothesis, Lino. How would you test it? Say, how would you distinguish front loading from a situation where a mutation broke a gene, making it non-coding, and another mutation subsequently restored it?

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    5. How does one test unguided evolution, oleg? That isn't even an interesting idea, more like a desperate one.

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    6. oleg:
      The researchers found human proteins that are entirely absent from chimpanzee and orangutan. That's a de novo origination of a protein.

      Only if you believed/ assumed that the three groups shared a common ancestor. IOW it's only a de novo origination of a protein in your imagination.

      Maybe you think that is enough for science, but we know better. Sorry, try again...

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  4. So, are is the genome creating novelty or, to put it another way, is it creating new information? I only ask because the denizens of Uncommon Descent seemed to reject that notion as I remember.

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  5. chemicals cannot create information, therefore a designer must have created the capacity for novelty.

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    1. Chemicals can create information,therefore a designer is not necessary for novelty.

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    2. How a random bag of chemicals can claim something as a truth? You are a foolish

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    3. Only creationists think it is random, Juan .

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    4. awstar January 23, 2014 at 2:20 AM
      chemicals cannot create information, therefore a designer must have created the capacity for novelty.


      That rather depends on what you mean by information.

      What we all write here is a form of information. The growth rings in a tree's trunk also provide information, at least, to a dendrochronologist. They are not the same thing, We have good reason to think that these posts are directly created by intelligent agents (although the amount of intelligence might vary) but we have no reason to think each tree was created by some intelligent agency.

      So just what is this information we all talk so glibly about?

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    5. Ian: "but we have no reason to think each tree was created by some intelligent agency. "

      Sure we do. each tree starts as a single seed full of all the encoded "information" necessary to transform it into a mature tree over time. That's a reason to think it was created by some intelligent agency.

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    6. awstar January 25, 2014 at 12:11 AM

      [...]

      Sure we do. each tree starts as a single seed full of all the encoded "information" necessary to transform it into a mature tree over time. That's a reason to think it was created by some intelligent agency.


      Do we? When we read posts on this blog, although it's possible they were created by soem sort of text generator, we have good reason to think they were actually created by intelligent agents, in this case, other human beings. We can read them and they convey information that makes sense to us. We can't "read" what's in the genome of the seed. Even if it were fully sequenced, those long strings of A,T,C and G wouldn't mean anything to us.

      Yes, you can call what's in the genome "information" if you want but you need to understand that it's very different from the information we exchange through these posts. While the latter is a form of information that we have good reason to think is the product of intelligent agents, the same is not true for the former. Of course, it might be. We can't absolutely rule it out but you need rather more than what is at best a flimsy analogy to make the case.

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    7. Yes the information that runs cells is much more complex and intricate than anything we use to communicate. Yeah, it's differant and it screams for a more advanced desogner.

      Mother Nature can't even produce something as relatively simple as Stonehenge.

      Put up Ian- show us unguided processes putting together a coded process- start by telling us how to test such a premsie.

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    8. Ian said: "in this case, other human beings. We can read them and they convey information that makes sense to us. We can't "read" what's in the genome of the seed. Even if it were fully sequenced, those long strings of A,T,C and G wouldn't mean anything to us."

      But the designer didn't write them for human beings understanding, they were written for the intelligent agent within the cell to understand and operate on. We know this because of the similitude of how we were designed to share information with one another. Kind of like "in the image of"

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    9. Joe G January 26, 2014 at 1:47 PM

      [...]

      Mother Nature can't even produce something as relatively simple as Stonehenge.


      Sure, she can. She built us and we built Stonehenge. We're as much a part of Nature as anything else.

      Put up Ian- show us unguided processes putting together a coded process- start by telling us how to test such a premsie

      I think we could put something together, if you have a few million years to spare. That sort of thing doesn't happen overnight.

      And while we're waiting you can tell us exactly why and how your Intelligent Designer did what he, she or it did.

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    10. awstar January 27, 2014 at 3:52 AM

      [...]

      But the designer didn't write them for human beings understanding, they were written for the intelligent agent within the cell to understand and operate on. We know this because of the similitude of how we were designed to share information with one another. Kind of like "in the image of"


      It's a nice story, without a shred of evidence except a weak analogy going for it. Kind of like 'just so' story.

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    11. Ian:
      Sure, she can. She built us

      Evidence please. Your wishful thinking means nothing.

      I think we could put something together, if you have a few million years to spare.

      If that is what you need then you have left science behind.

      And while we're waiting you can tell us exactly why and how your Intelligent Designer did what he, she or it did.

      So you don't know how science operates. Tat is what I thought.

      Ya see Ian, science dictates that in the absence of direct observation or designer input, the only possible way to make any scientific determination as to the who, how, when, where and why, is by studying the design and all relevant evidence. And ID is the study of design in nature, meaning those other questions are irrelevant to ID.

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    12. Ian said: "It's a nice story, without a shred of evidence except a weak analogy going for it. Kind of like 'just so' story."

      I guess that's what it all comes down to, doesn't it. We each get to choose which "just so" story we buy into.
      As for me, I'm going with the "just so" story of redeeming grace as recorded in the Bible because of 1) it's wonderful hope, 2) what I've experienced since believing in it, --- AND 3) it just happens to explain what we see -- far better than anyone else's "just so" story.

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    13. Ian:
      It's a nice story, without a shred of evidence except a weak analogy going for it.

      How do you know that there isn't any evidence for it? You don't seem to able to assess evidence.

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    14. Joe G January 28, 2014 at 4:01 AM
      Ian:
      Sure, she can. She built us

      Evidence please. Your wishful thinking means nothing.


      Start here and work your way forward.

      I think we could put something together, if you have a few million years to spare.

      If that is what you need then you have left science behind.


      You wanted to be shown " unguided processes putting together a coded process". That could take rather a long time. Nature isn't broken up into handy human bite-sized pieces. You'll just have to be patient.

      Ya see Ian, science dictates that in the absence of direct observation or designer input, the only possible way to make any scientific determination as to the who, how, when, where and why, is by studying the design and all relevant evidence. And ID is the study of design in nature, meaning those other questions are irrelevant to ID.

      Science would be trying to determine whether or not the appearance of design in nature is not just pareidolia on a grand scale. would be intensely interested the nature of any putative designer, not try to pretend it's of no concern.

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    15. awstar January 28, 2014 at 5:18 AM

      I guess that's what it all comes down to, doesn't it. We each get to choose which "just so" story we buy into.
      As for me, I'm going with the "just so" story of redeeming grace as recorded in the Bible because of 1) it's wonderful hope, 2) what I've experienced since believing in it, --- AND 3) it just happens to explain what we see -- far better than anyone else's "just so" story.


      If it makes your life better and the Universe a better place in which to live it then that's fine by me.

      If I am right and we live a brief, fragile existence in a vast and mostly hostile Universe that can - and often does - snuff us out in an instant then who am I to deny people whatever they can lay their hands on to get them through?

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    16. Joe G January 28, 2014 at 6:07 AM

      [...]

      How do you know that there isn't any evidence for it? You don't seem to able to assess evidence.


      Give us some evidence and we'll assess it.

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    17. Ian:
      Start here and work your way forward.

      Nice bluff.

      You wanted to be shown " unguided processes putting together a coded process". That could take rather a long time. Nature isn't broken up into handy human bite-sized pieces. You'll just have to be patient.

      If all you have is to hide behind father time then you don't have any science.

      Science would be trying to determine whether or not the appearance of design in nature is not just pareidolia on a grand scale. would be intensely interested the nature of any putative designer, not try to pretend it's of no concern.

      You have problems. Just because the nature of the designer is a separtate wuestion from whether or not something is designed, does not mean it is of no concern.

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    18. Ian,

      Present the evidence for unguided evolution producing a bacterial flagellum- any bacterial flagellum- so I can see what type of evidence you will accept.

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  6. OT: James Shapiro - video playlist
    https://vimeo.com/humbirdfilms/videos

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    1. This must be a candidate for the shortest BA77 post ever. Did hit the "Publish" button by accident?

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  7. OK, with evolutionism novelty arises via the mechanism of badda-bing, badda-boom, and if it isn't lethal it has a chance to get passed on. If it is helpful it has a better chance of being passed on and modified.

    So it starts with badda-bing, badda-boom and then it's accidentally refined. Any questions?

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  8. Great article, CH.

    What's startling about Neo-Darwinism is that they basically seem to have gotten absolutely nothing right.

    1. Gradualism? Oops, not so much.
    2. Mutations random? Err, scratch that.
    3. Selection caused it? Um, doesn't even make sense.

    Nothing about evolution makes sense in the darkness of Darwinism.

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