Friday, June 01, 2012

Cornelius, Meet Johnnyb

Cornelius Hunter doesn't like anything about evolution. He especially doesn't like us to say that Evolution Is a Fact.

Here's the latest from Cornelius [When I Pointed Out the Evolutionary Tree Has Failed Two Professors Gave Me Pushback ].
If you are new to the evolution debate you might wonder why evolutionists do not simply acknowledge the painfully obvious fact that evolution is not a fact. It is not as sure gravity and in fact there are significant questions and problems with evolution. Why don’t evolutionists admit to the truth of how the science bears on their theory?

The answer is that evolution is not about the science. At issue here is not merely the status of another scientific theory. Evolutionists won’t be swayed by the evidence because doing so—and confessing that evolution is not overwhelmingly supported by the evidence—would immediately expose evolutionists to all kinds of possibilities which they simply cannot accept. An evolutionist can no more change his mind than could a cultist. Evolution is underwritten by a religious worldview—it is a metaphysical theory, not at scientific theory. As such it may lose every battle, but it cannot lose the war.
Contrast this with what Johnnyb said a few weeks ago on Uncommon Descent [see All IDiots Believe in Evolution! ].
So what is one to do? Well, thankfully, our friends the evolutionists have given us a way out. In their zeal to claim consensus on the “fact of evolution,” they have had to steamroll together such a large diversity of opinion into the single term “evolution”, that the word “evolution” no longer has the grand meaning it used to. The only real meaning everyone can agree on is “change in allele frequency over time” – and that is a definition that literally everyone can agree with.

In other words, even if you are a young earth creationist, if your professor asks if you believe in evolution, the legitimate answer is “yes”. Given the common definition of “evolution,” the only thing they are really asking with that question is, “do you believe in genetics?”
Cornelius Hunter and Johnnyb really should get together and agree on the facts.


20 comments :

  1. Yes, the definition of evolution as the “change in allelic frequencies over time” is next to useless because even YECs accept this as fact.

    I think we should learn to differentiate between inevitable "evolution" at the molecular level and universal common ancestry. The two are not co-substantial with each other and YECs firmly deny the existence of the LUCA.

    However, many ID proponents (like Behe) accept universal common ancestry even if there are those who do not (like Dembski). They just take issue with the mechanism of evolution. They reject Darwinian natural selection as a valid explanation for the diversity of life on earth but instead regard it as a mostly conserving force in biology. There is a mountain of genomic evidence to support their conclusion. I'm sorry.

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  2. I don’t know if Cornelius and Johnnyb believe or not in evolution. But what seems to be true is that they, as well as many self-proclaimed evolutionists, have legitimate problems with the mechanisms of evolution and with the fundamental evolutionary principles as described in some of the current prevalent evolutionary views.

    At a recent post by Larry, “All IDiots Believe in Evolution!”, I brought up one of these issues, the origin of life on Earth according to the “RNA world” hypothesis, which, despite lack of a coherent rationale or model, has dominated the thinking and the scientific textbooks for decades.

    Here, I want to bring up another modern evolutionary problem, that regarding the prevalent current views about the Tree of Life (TOL) which question its value and validity and create tremendous confusion (and, in my ‘humble opinion,’ they might be flirting with pseudoscience). As previously discussed, the problem might not be with the TOL, but with the current reductionist approach of generating a TOL based on phylogenetic analysis of DNA or protein sequences:

    The intent of the TOL, however, is to establish the line of descent among groups of organisms or species, not necessarily the evolutionary relationships among their genes. Certainly, each of the millions of cellular and viral genes has an evolutionary history that can be revealed by a sequence-based phylogenic tree, but many of these gene-based trees do not represent a TOL that reflects the line of descent among the species

    This excerpt is from a section of a paper (http://precedings.nature.com/documents/3888/version/1) discussing the merits of including viruses, which are prone to intense lateral gene transfer and have high evolutionary rates, in the TOL. Indeed, over long periods of evolution, most if not all the genes in some viral lineages have been replaced by genes from other viruses or from other sources, possibly several times over. Evidently, in these cases, the line-of-descent of extant viruses cannot be established by sequence-based phylogenetic analysis. But, the lack of methods or approaches for representing viruses on the TOL should not nullify their right to be a part of the TOL.

    Similarly, the fact that scientists studying evolution do not understand well the mechanisms behind evolution, or misrepresent them, it doesn’t mean that evolution doesn’t exist or that it is not true!

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  3. "and confessing that evolution is not overwhelmingly supported by the evidence—would immediately expose evolutionists to all kinds of possibilities which they simply cannot accept."
    What possibilities does Cornelius have in mind with this?

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    1. The possibility that they might be going insane?

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    2. As Larry knows full well, but is reluctant to admit it, the vast majority of the coding DNA (and a fair amount of ncDNA) of living organisms is highly conserved both in terms of sequence and function. This is not evolution but stasis.

      Let me just repeat this for the benefit of the intellectually challenged here: Natural selection is a force for conservation in biology.

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    3. As one of the intellectually-challenged here, I'm really not sure how conservation would contradict that natural selection can also be a force for change.

      In simple terms, if something works then why wouldn't natural selection select conserve in the same way that if an improvement or a change of function would mean change? Would a mutation that changes the colour of the fur of a mouse, for example, that better camouflages it be as much an expected result of natural selection as a well camouflaged pigment in fur remain in stasis?

      And following from that, if there's highly conserved function and sequence, shouldn't we be able to see the products of neutral theory in looking at common descent - that is if a gene is highly conserved in function and sequence because its job is highly concerned, then wouldn't evolution predict a tree-like pattern of neutral mutations when comparing sequences?

      Highly-conserved patterns, at least to me, doesn't prima facie seem at odds with evolution nor evolutionary mechanisms. Can you elaborate, please?

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  4. @Atheistoclast

    Sounds like a tautology to me, by definition natural selection will select against mutations to conserved sequences given that most mutations will be deleterious.

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    1. In a sense it is. Natural selection will conserve functional sequences because they are functional. However, anyone who has looked at coding sequences will be surprised at the extent to which they are conserved despite billions of years of evolutionary divergence.

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    2. However, anyone who has looked at coding sequences will be surprised at the extent to which they are conserved despite billions of years of evolutionary divergence.

      At the extremes, all genomes would either be identical, or all completely 'random'. They are neither - genomes display both conservation and divergence in different parts. Short-term conservation is simply due to replication; longer-term is probably due to negative NS. The divergent fraction, meanwhile, can be caused by both positive and negative NS and drift. Which is really to say that there is a continuum of selective advantage, and all parts of it outside of lethality can lead to change. The allele with the highest selective advantage is not always the resident one.

      I really don't know why that is so hard to grasp, o intellectually-challenged one.

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    3. Natural selection is pervasive right across the proteome, but is biased towards conservation rather than any innovation. Where significant divergence may have occurred in protein-coding sequences is in gene duplicates. This is often because the selection regime is much weaker than for singletons because of the presence of a backup.

      The basic issue is that organisms of diverse morphology and psychology use essentially the same proteins in their cells. This is where evolutionary theory is in danger of collapsing because the basis for phenotypic diversity does not seem to be encoded in the DNA molecule. This is where I part company with the IDiots.

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    4. Psychology???

      I presume you are looking at multicellular organisms. It appears that the diversity within these is largely mediated by rather few genes, as a proportion of the whole, controlling the development from fertilised zygote. So you aren't necessarily going to get a strong correlation between perceived "difference" in mature form and the underlying coding genome. The Mkl cellular maintenance genes are likely to be highly conserved. Life long ago evolved effective electron transport pathways, DNA replication, cell cycle control &c. From ineffective precursors, 'positive' NS is likely to have selected improvements, but the returns from further improvement diminish. The elephant that develops a better cytochrome c is unlikely to have much advantage over its fellows; that which develops a worse one is unlikely to prevail.

      So an historic pattern of optimisation by positive NS would lead to 'core genes' now preserved by negative NS. The rest - those responsible for phenotypic diversity - are needles in that haystack. Epigenetics may be nothing more than the phenotype of 'conventional' DNA-genes - but either way, it does not mean that evolutionary theory is in imminent danger of collapse (after all, it did not depend on DNA in the first instance).

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    5. "but either way, it does not mean that evolutionary theory is in imminent danger of collapse"
      That was the bit that most confused me, I'm really not sure how evolutionary theory was actually threatened by such findings. I would have hoped that Atheistoclast would have spent more time on describing the ways in which the pillars of evolutionary theory are in danger from such a finding, because it's really not evident as to how to get from what he's saying about sequence preservation to what would be threatening to evolutionary theory.

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    6. it's really not evident as to how to get from what he's saying about sequence preservation to what would be threatening to evolutionary theory.

      What seems to come from the anti-evo side is a general incapacity to think in evolutionary terms - which is perhaps partly what makes them anti-evo in the first place. It's like this so it must always have been like this, therefore it can't possibly have evolved to get like this. NS in its current form must have been an overwhelmingly conservative force since the day the first replicator emerged in the Designer's test-tube, because many modern highly-evolved genes (having, one assumes, squeezed as much adaptation as is possible out of the locally-accessible fitness landscape) are conserved.

      But only if there are NO beneficial mutations can adaptation cease.

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    7. All the evidence shows that genomes are subject to constant conservation by natural selection. We can look at many ancient genes and observe that they have diverged little in hundreds of millions of years.

      "Beneficial" mutations do exist, but we can classify them as the following:

      1) Loss-of-function: mutations that result in the loss or degradation of a biological function which, under certain circumstances, can help increase survival chances.

      2) Compensatory: mutations that restore the function of a gene that has been degraded by deleterious mutations.

      3 Optimizing: mutations that improve or adjust an existing function but do not significantly alter it.

      I have yet to see how natural evolution can generate genuine novelty. That is because it is stupid, dumb and blind - just like its proponents.

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    8. I have yet to see how natural evolution can generate genuine novelty. That is because it is stupid, dumb and blind - just like its proponents.

      Yes, you clearly have all the best intellects on your side. Do you have an example of an unevolvable 'genuine' novelty (clearly distinguishable from one whose history is obscure)?

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    9. Everything has the capacity to "evolve". But I make a distinction between "evolution" and "origination". The two are quite different: this is because the origin of something is separate to how that thing changes subsequently. Saying that a protease digestive enzyme has evolved tell us nothing about how that gene/protein came to exist in the first place.

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    10. Ah, you're a word-gamer. OK, by "unevolvable" I mean "could not arise by evolution", which one could distinguish from "arise by design" or "arise by single-step random amino-acid mixing". I didn't mean "incapable of subsequent evolution", which I think was clear.

      In an evolutionary scenario, the 'origin' of a protease, say, would be rather diffuse. There may be no discrete point at which one could say "today, there is a protease, where yesterday there was none". Rather like the Speciation Issue. Feeble proteolytic activiy could be better than none.

      Proteins are rather modular, and LGT, or donations from elsewhere in the genome, would form part of the history whose end-point we see today as (name your favourite enzyme here).

      Saying that a protease digestive enzyme has evolved tell us nothing about how that gene/protein came to exist in the first place.

      I don't think you add anything by insisting on a discrete Origin, unless you have some specific information to impart in regard to when, where and how. It is difficult to declare the impossibility of 'new protein function' (eg the first enzymatic cleavage of the peptide bond) if we know nothing of the organism or its pre-existing chemical arsenal.

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    11. "We can look at many ancient genes and observe that they have diverged little in hundreds of millions of years."
      Have you tested common ancestry against these genes? That is, does the tree of life pattern show? If so, then there's one evolutionary pillar that the evidence would be in support of.

      "I have yet to see how natural evolution can generate genuine novelty."
      What do you mean by "genuine novelty"? Would you count the evolution of limbs from fins as evolutionary novelty? What about bacteria developing an enzyme that breaks down nylon? I'm surprised that you earlier mentioned gene duplication, yet now can't see how natural evolution cannot create genuine novelty.

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  5. Why are you surprised that functional sequences are conserved ?

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  6. Cornelius Hunter is a professor (LOL) at Biola and the first thing that stands out on the Biola website is:

    BIOLA UNIVERSITY

    BIBLICALLY CENTERED EDUCATION

    If that oxymoron isn't enough, they offer this:

    "Biola University's M.A. in Christian Apologetics is a premier graduate degree in the defense of the Christian faith. Currently, there are no other degree programs like this one. The accredited 36-unit curriculum is flexible and offers students the opportunity to study broadly in the field of Christian apologetics."

    A college degree in defending religious fairy tales? I wonder if they offer degrees in astrology, witchcraft, and psychic spoon bending too?

    Cornelius does a class called Darwin, Evolution & Design. Considering what he spews on his website that must be one seriously UN-educational class.

    Want to see why Cornelius is so against the theory of evolution and the very idea that evolution has ever occurred? He agreed with this doctrinal statement to work at Biola:

    http://offices1.biola.edu/hr/ehandbook/1.2/?h=duty


    And this is from the page about requirements for applicants who want to enroll as students at Biola:

    "Note to Applicants

    For nearly 100 years, Biola University has equipped students academically and spiritually to impact the world for Christ. We're excited that you are ready to add to this rich heritage of cultural influence!

    As a Biola student, it's important that you possess a Christian commitment and character that match that of the University. We welcome all applicants who are personally committed to faith in Christ.

    Biola offers equal access to applicants regardless of race, color, national origin, sex, or disability."

    Unless of course your 'disability' is that you live in reality and aren't a delusional bible thumper.

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