Wednesday, October 8, 2014

Evolution Professor: We Evolved to be More Complex

Serendipity and Aristotelianism

We recently saw how evolutionists are elaborating on what they view as an evolutionary arms race within our genome. Rival elements battle it out as transposable elements invade and repressors seek to shut them down. The transposable elements are “continually evolving to escape repression,” while the repressors adjust and find new ways to defeat the transposable elements. It is “a never-ending race” according to one evolutionist. The backstory here is the on-going historical feud between those who view nature as perfect and those who view nature as evil. In the eighteenth century, for instance, the English natural theologians presented a decidedly optimistic, rosy version of the world, to which Hume responded that “A perpetual war is kindled amongst all living creatures,” and that nature is so arranged so as “to embitter the life of every living being.” So who is right? The answer, of course, is that both are right. Nature is both wonderful and dangerous at the same time. As usual the heresy is not in recognizing these obvious truths, but in emphasizing and dwelling on one side of the spectrum, to the exclusion of the other. Creation and Scripture—general revelation and special revelation—are studies in contrast. Science requires recognizing both sides of the contrast, and keeping them both in view together. Show me a cult, either religious or scientific, and I’ll show you people who are fixated on one end of a spectrum. The result is a lopsided theory that makes no sense.

Consider the genomic arms race idea, for example. First, it requires rapid evolution of astonishing complexity. Not likely. Second, it calls upon a monumental amount of serendipity. Humans and frogs have “basically the same 20,000 protein-coding genes as a frog, yet our genome is much more complicated, with more layers of gene regulation.” How did that happen? Those astonishing levels of sophistication and subtlety in the human genome arose with the help of these invading transposable elements. The incredible regulation machanisms that arose to repress them, just happened to take on other roles as well. This resulted in primates and ultimately humans. Really? Evolution just happened to produce transposable elements, and they then became evolutionary mechanisms? In other words, evolution created evolution. As the report summarizes, “repressor genes that originally evolved to shut down jumping genes have since come to play other regulatory roles in the genome.” That was lucky.

Furthermore, to understand and communicate this story, evolutionists dive deep into the waters of Aristotelianism. It is the ultimate internal contradiction, for the theory that is supposed to represent the triumph over teleology is, itself, immersed in it. Consider these examples:

a transposable element changed to become expressed and replicated itself throughout the genome

The way this type of repressor works, part of it binds to a specific DNA sequence and part of it binds other proteins to recruit a whole complex of proteins that creates a repressive landscape in the genome. This affects other nearby genes, so now you have a potential new layer of regulation available for further evolution.

the transposable elements are themselves continually evolving to escape repression

This paper shows how important it is to integrate computational and experimental approaches to fundamental scientific problems, such as how and why we continuously evolve to be more complex.

For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions.

KZNF genes rapidly evolved to repress these two distinct retrotransposon families

evolved earlier to repress the primate L1 lineage

followed by mutations in these retrotransposons to evade repression

Evolving to escape repression? Changed to become? We evolved to be more complex? This is not science, this is story telling. We need to stay with the evidence.

24 comments:

  1. Thank you Dr. H..

    I remember the days when the Berlin Wall fell.
    People hammered relentlessly, both figuratively and literally, on that wall for decades
    People who believed in freedom, who wanted freedom for their children and their friends and themselves hammered.
    For decades, the wall just stood there, seemingly impervious to assault.

    Then one day it fell.
    All at once.
    One day it seemed insurmountable.
    The next day it was rubble.

    I very much appreciate your relentless hammering on evolutionism's wall of ignorance, superstition, and rottenness.

    It will fall.

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  2. I can't comment on such higher intimacies of genetics.
    Yet this new stuff from evolutionists fits in a kind of prophecy.
    As we get smarter and greater skill in examination and analysis of genes takes place then evolutionists must start explaining how genes evolved.
    If genes never evolved, they didn't, then there would be no evidence of this in the genes.
    So it could only be that evolutionists can work with finished genes and THEN start the selection game guessing.
    They can't let genes and thier complexities go without explanation as to how they came about.
    Its possible genes are no friend to evolutionary biology.
    Its possible the closer they look the more bad it looks for old man Chuck.
    Yup. They must the machine of how genes evolved.
    I predict more problems as more is learned.

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  3. All of which tends to confirm just how much ID/creationists don't "get" science.

    The excitement of new and unexpected discoveries is what scientists live for. Far from being downcast, they are fascinated by being able to study a facet of the natural world that no one has ever seen before. So what if it forces a rethink of previous theory? That's how science advances.

    You're also apparently oblivious to something that's staring you right in the face. One measure of a good scientific theory is the quantity of new research it inspires. Almost every paper that CH so assiduously excavates from the literature comes from evolutionary biology. Thus almost every new paper reviewed here is further evidence for the scientific fertility of evolution and the sterility of ID/creationism.

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    1. Well I guess that's one way to put lipstick on it.

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    2. NO. Its not signs of a GOOD "scientific" 'theory"
      Its signs indeed that its unsatisfying. That they grasp at any new idea because they smell evolutionary biology is unsupported and not soon supported.
      They do have a problem with the new knowledge of the flory of genes.
      Genes threaten evolution if evolution is not true.
      faith in selectionism on genes etc for explaining biology is a tall order.
      I think its not the way they would like genes to act if evolution was true.
      New ideas are needed again.

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    3. Robert Byers NO. Its not signs of a GOOD "scientific" 'theory"

      Really? There are those who disagree.

      In his 1981 book The Rationality of Science the Canadian philosopher of science W H Newton-Smith listed eight properties of a good scientific theory, one of which was "Fertility" described as follows:

      A theory ought to have scope for future development. It should contain ideas to guide research. This is akin to but more nebulous than Lakatos’s notion of a positive heuristic. This may come from a metaphorical component in the theory as in the early days of the ideal gas theory. Gases were thought to be like collections of small hard balls colliding in space. The metaphorical component suggests exploration of the similarities and dissimilarities with the phenomenon to which it has been likened. Fertility may also come from a novel idea as when, for example, Planck introduced the quantum of action in the course of explaining the distribution of radiation given off by a black body. This suggested the possibility of applying the idea of the quanta to other unexplained phenomena. The justification for including this factor comes from a well- supported meta-induction on past science. Theories are evolving historical entities which rarely spring into existence fully fleshed out. Those that have tended to be ultimately successful have as a matter of fact come with association ideas for further development. This factor, like the others to be advanced, are only fallible inductive indicators of ultimate success. A fertile theory may not in the end deliver the goods. Freud’s theory of psychoanalysis certainly was fertile. It suggested a host of possible developments and applications. Cynics about psychoanalytic theories may well argue it is to be held against the theory that while apparently fertile it has not borne fruit.

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    4. Another example includes Newton, whose theories spawned entire fields of study, as did Darwin.

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    5. ID, in contrast, spawns nothing but rhetoric.

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    6. The rhetoric is all yours.

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  4. It seems like all this research tat evolution is inspiring is creating problems for evolution. Its like when Michelson and Morley tries to prove Aether.

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    1. natschuster: It seems like all this research tat evolution is inspiring is creating problems for evolution.

      Sure all scientific theories are necessarily tentative and incomplete. They can only capture part of the whole. Today's Theory of Evolution is not the same as the theory originally proposed by Darwin, though it certainly traces its roots to Darwin. Nothing thus far indicates design, though.

      natschuster: Its like when Michelson and Morley tries to prove Aether.

      Sure, and how anomalies in predictions of Newton's Theory led to General Relativity. Or how work in mechanics led to theories of entropy.

      However, pointing the anomalies doesn't support 'design'. That requires scientific evidence, that is, entailments derived from the hypothesis, confirming observations, and comparison with competing hypotheses.

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    2. There isn't any theory of evolution.

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  5. What would you consider acceptable evidence for design?

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    1. natschuster: Excellent question!

      What is evidence? Evidence is the available body of facts indicating whether a belief or proposition is true or valid. In other words, evidence is not just facts, but facts in support of a proposition.

      For a simplified version of science, you have the hypothesis, the proposition. From the hypothesis you derive empirical predictions, the entailments. If the entailments are confirmed, then it is considered support for the hypothesis. If the entailments are contradicted by the facts, then the hypothesis is considered falsified. In the former case, we might try other experiments to try and extend the hypothesis. In the latter case, we might modify or discard our hypothesis.

      So let's take design. What does 'design' entail? It entails an artifact, art, and artisan. However, without specific notions of these facets, the concept is far too vague to lead to specific entailments. In other words, it's too vague and unconstrained.

      If, on the other hand, you said the Earth was made up of garbage dumped by three-eyed aliens from Alpha Centauri, then you might have the beginnings of a testable hypothesis.

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    2. Unguided evolution cannot muster testable hypotheses. And if you want vague and unconstrained, just look at evolutionism.

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  6. Curiously Zachriel,

    Can you explain how organisms 'recruit'?

    Can you explain how organisms 'repress'?

    Can you explain how organisms 'prevent'?

    ...without using the words recruit, repress, prevent, or their synonyms?

    Can the explanation be done by simply describing the series of interactions caused by physics and chemistry?? If so, how does the result of one interaction directly trigger the next interaction??

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    1. Steve: Can you explain how organisms 'prevent'?

      It's the same way a river *runs* to the sea, or rainwater *finds* the cracks in your roof, or how a mass *seeks* the lowest level. Old words are often coopted by science. So air *fills* a container, even though air is nothing but individual particles, each answering its own imperative.

      As for evolution, genomes are known to change over time due to mechanisms such as mutation and recombination. Those organisms which have a reproductive advantage tend to increase their share of the population. So, if a mutation *prevents* an antibiotic from killing a bacterium, then that bacterial strain will tend to increase its share of the population when in the presence of antibiotics. We then say the bacteria evolved to protect itself from the antibiotic. We express it as if it were a teleonomic process, even though we can trace it back to a mutation and the ensuing reproductive advantage.

      Steve: If so, how does the result of one interaction directly trigger the next interaction??

      Not sure your question, but certainly one change can lead to another.

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    2. Z:
      As for evolution, genomes are known to change over time due to mechanisms such as mutation and recombination.

      Sounds like baraminology.

      Those organisms which have a reproductive advantage tend to increase their share of the population.

      Which organisms are those?

      So, if a mutation *prevents* an antibiotic from killing a bacterium,

      By making it less specific, ie by losing information.

      We then say the bacteria evolved to protect itself from the antibiotic.

      Under evolutionism, that is wrong and misleading

      We express it as if it were a teleonomic process, even though we can trace it back to a mutation and the ensuing reproductive advantage.

      Mutation could very well be telic.

      Not sure your question, but certainly one change can lead to another.

      Then it shouldn't be any problem for you to provide the probabilities. We await your equations.

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    3. Joe G: Mutation could very well be telic.

      The evidence supports mutation being random with respect to need.

      Joe G: Then it shouldn't be any problem for you to provide the probabilities.

      See Lenski's E. coli Long-term Experimental Evolution Project Site. They showed the existence of potentiating mutations. Their results are consistent with mutation random with respect to need.

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    4. Z:
      The evidence supports mutation being random with respect to need.

      No, it doesn't- see Shapiro "Evolution: A View from the 21st Century"- see also Spetner "Not By Chance" and "The Evolution Revolution".

      See Lenski's E. coli Long-term Experimental Evolution Project Site.

      Seen it. Does tat mean you cannot provide the calculations I asked for?

      Their results are consistent with mutation random with respect to need.

      That is only your opinion.

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    5. Z:
      Those organisms which have a reproductive advantage tend to increase their share of the population.

      Which organisms are those?

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  7. Bacteria. They are simple. They are still here. #NowWhat

    Evolution does not imply complexity. <- Stephen Jay Gould

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  8. followed by mutations in these retrotransposons to evade repression

    and then ... The Selfish Retrotransposon: Why Selfish Genes Jump About In Ways That Appear Designed
    And then we could discover some unexpected pseudogene complex in DNA that coordinates adaptations after processing RNA messages about environmental change ...
    The Selfish Heterochronocybernon: How Genes Were Adapted Into Computer Programs Because Programs Are Beneficial
    Why there is just no end to what Selection can explain!

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