Darwinism Design inference Evolutionary biology Intelligent Design

The War is Over: We Won!

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Here is the abstract from a Nature Review: Genetics paper:

The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.

Many years ago, I predicted that modern genome sequencing would eventually prove one side of the argument to be right. This review article indicates that ID is the correct side of the argument. What they describe is essentially what ID scientist, Michael Behe, has termed the “First Principle of Adaptation.” (Which says that the organism will basicaly ‘break something’ or remove something in order to adapt) This paper ought to be the death-knell of Darwinism, and, of course, “neo-Darwinism,” but, even the authors who report this new “perspective” have not changed their Darwinian perspective. Somehow, they will find a way to tell us that the Darwinian ‘narrative’ always had room in it for this kind of discovery. As Max Planck said, and I paraphrase, “a theory does not prove itself right; it’s just that the scientists who opposed it eventually die.”

Here is basically the first page of the article (which is all I had access to):

Great attention has in the past been paid to the mechanisms of evolution by gene duplication (that is, neofunctionalization and subfunctionalization). By contrast, gene loss has often been associated with the loss of redundant gene duplicates without apparent functional consequences, and therefore this process has mostly been neglected as an evolutionary force. However, genomic data, which is accumulating as a result of recent technological and methodological advances, such as next-generation sequencing, is revealing a new perspective of gene loss as a pervasive source of genetic change that has great potential to cause adaptive phenotypic diversity.

Two main molecular mechanisms can lead to the loss of a gene from a given genome. First, the loss of a gene can be the consequence of an abrupt mutational event, such as an unequal crossing over during meiosis or the mobilization of a transposable or viral element that leads to the sudden physical removal of the gene from an organisms’ genome. Second, the loss of a gene can be the consequence of a slow process of accumulation of mutations during the pseudogenitzation that follows an initial loss-of-function mutation. This initial mutation can be caused by nonsense mutations that generate truncated proteins, insertions or deletions that cause a frameshift, missense mutations that affect crucial amino acid positions, changes involving splice sites that lead to aberrant transcripts or mutations in regulatory regions that abolish gene expression. In this Review, the term ‘gene loss’ is used in a broad sense, not only referring to the absence of a gene that is identified when different species are compared, but also to any allelic variant carrying a loss-of-function (that is, non-functionalization) mutation that is found within a population.

Here, we address some of the fundamental questions in evolutionary biology that have emerged from this novel perspective of evolution by gene loss. Examples from all life kingdoms are covered, from bacteria to fungi and from plants to animals, including key examples of gene loss in humans. We review how gene loss has affected the evolution of different phyla and address key questions, including how genes can become dispensable, how many of our current genes are actually dispensable, how patterns are biased, and whether the effects of gene loss are mostly neutral or whether gene loss can actually be an effective way of adaptation.

So, let’s translate what they’re saying here: “speciation” (their term is “phenotypic adaptation”) is the result of a LOSS of INFORMATION! This points, of course, to the “front-loading” of the LCA of the various branches of the so-called “Tree of Life.” Absolute bad news for Darwinism. We no longer say: “Another day; another bad day for Darwinism.” We now say: “Another day since the time Darwinism was disproved.”

This is what one of the authors has to say in an interview:

“The genome sequencing of very different organisms has shown that gene loss has been a usual phenomenon during evolution in all life cycles. In some cases, it has been proven that this loss might mean an adaptive response towards stressful situations when facing sudden environmental changes” says Professor Cristian Cañestro.

“In other cases, there are genetic losses –says Cañestro- which even though they are neutral per se, have contributed to the genetic and reproductive isolation among lineages, and thus, to speciation, or have rather participated in the sexual differentiation in contributing to the creation of a new Y chromosome. The fact that genetic loss patterns are not stochastic but rather biased in the lost genes[pav: IOW, this is where you’re going to find the genomic differences between species you compare] (depending on the kind of function of the gen or its situation in the genome in different organism groups) stresses the importance of the genetic loss in the evolution of the species.

There you have it: “evolution” through “gene loss.” I.e., “evolution” through “loss of information.” Evolution does not PRODUCE “information”; it DESTROYS “information”. You can read about in the book: “Genetic Entropy.”

In sum: the war is over, and we won! Congratulations everyone!

168 Replies to “The War is Over: We Won!

  1. 1
    Dr JDD says:

    “But this is exactly what [insert favourite of Darwin, evolution, new-Darwinism, neutral theory, etc, etc] predicted”

    …..

  2. 2
    rvb8 says:

    I’m sorry PaV, but why does a gene which fails to function because of physical forces acting upon the gene, and then the resulting phenotype being expressed differently, prove Intelligent Design? Couldn’t the designer fabricate a stronger template to prevent this error accumulation?

    Or rather, with gene loss, and the resultant new expression, why can’t this new expression be beneficial to the individual?

  3. 3
    johnnyb says:

    rvb8 –

    “Couldn’t the designer fabricate a stronger template to prevent this error accumulation”

    Fairly irrelevant. You could take any design and say, “couldn’t this be done better?” Just because it could have (or you imagine it could have) has no real bearing on whether or not something was designed. By that criteria, we have definitive proof that there was no one on the design team for Windows.

    “Or rather, with gene loss, and the resultant new expression, why can’t this new expression be beneficial to the individual?”

    It totally can be, but it is totally beside the point.

    The point is, if evolution is about gene *loss*, then that indicates it *isn’t* about the gain of genes. If the observed pattern is that we *lose* information, then this isn’t a good theory of where it comes from. The core of Darwinism says that life started information-poor and increased in information-richness over time by accumulation. ID, on the other hand, says that we *started* with fully-developed information sources.

    If the process of evolution is merely the getting rid of existing information, then ID was the one that was right.

  4. 4
    Alicia Cartelli says:

    Evolution is not “about gene loss.”
    Are you guys completely incapable of detecting PaV’s sarcasm?
    He’s merely playing down another mechanism of evolution and even trying to spindoctor it into “support of ID.”

    Unfortunately for you guys, this review paper in no way helps ID, and neither does PaV’s misrepresentations of actual science.

  5. 5
    PaV says:

    Alicia C:

    Dear Alicia, I’m not being sarcastic. The war is now over. Your side has lost.

    What this review article presents is the complete ANTITHESIS of what Darwinian evolution should look like.

    Let me put it another way: Darwinism couldn’t have been MORE wrong.

    As to my “misrepresentations of actual science,” please consult Dr JDD’s post.

  6. 6
    PaV says:

    rvb8:

    As I mentioned in my response to Alicia, the paper I’m quoting presents results that are: (1) the complete opposite of what Darwinism should look like; (2) confirmation of what a principle made by an ID theorist; and (3) confirms what a supporter of ID has written in a book.

    There you have it: complete rejection of Darwinian expectations, and, simultaneously, confirmation of what ID thinking people have stated is going on.

    It’s not too late to switch sides.

  7. 7
    Alicia Cartelli says:

    Gene loss is just another mechanism of evolution. It is not THE mechanism of evolution. You guys love to blow up research that you don’t even understand.

  8. 8
    PaV says:

    Alicia:

    Your comment makes clear that it is you who do not fully understand the implications of this review article.

    It basically says that what Darwinists believe is “evolution”– you know, the “origin of species”–is driven by a “loss” of information, not a steady, gradual build-up of information. IOW, there is no foundation for Darwinism.

    But, of course, if an “intelligent agent” is involved, this “information” is infused, and this discontinuous infusion of “information” can also include mechanisms which allow for “adaptation” through a gradual LOSS of the infused, phyla-level “information,” as in NGE. This paper is fully consistent with ID; it is the death-knell of Darwinism.

    The war is over: we won! The only thing that remains is for a declaration of surrender to be ‘signed.’ You can be the first to sign!

  9. 9
    rvb8 says:

    The Adder’s Tongue fern has 1200 chromomes, the Human 46, the kingfisher 132, Great Apes and Hares 48, the Horse 64 etc. The thing is, the complete arbitrary nature in which these numbers vary, with a sea slug having maybe 400, and mushromm several hundred, and then an eathworm and Tibetan Fox sharing 36, tells me clearly there is no design.

    This utter randomness in the gene count, from the supposedly highest ‘human’, to the lowest bacteria points to chaos, not design.

  10. 10
    PaV says:

    rvb8:

    You’ve succeeded in making a “mountain out of molehill.” There could be lots of reasons for those numbers; meanwhile, the astronomically, infinitely small probabilities associated with even an average size de novo protein is enough to invalidate Darwinism.

    You “strain gnats, and swallow camels.”

  11. 11
    Alicia Cartelli says:

    PaV. Please.
    Gene loss is nothing new. They are saying it’s been over-looked and has an important role in evolution, just as gene duplication, mutations, transposable elements, chromosome rearrangements, etc. all do. No where does it say that “evolution is driven by a loss of information.”

    It’s funny you think you can claim the research paper says “this” and “that” when you have already admitted to not even having access to the actual paper.

  12. 12
    PaV says:

    Alicia:

    Please. Of course gene loss is nothing new.

    As to it’s saying “evolution is driven by a loss of information,” they would deny this; however, that is the import of the paper.

    Here’s what’s new: extensive sequencing of genomes! I said 7 or 8 years ago, at a time when sequencing was becoming quicker and less expensive, that the comparison of genomes would either confirm the Darwinian view, or, that of ID.

    The evidence is in: information actually drives speciation, a complete inverse of what neo-Darwinism expects. It’s the nail in the coffin.

    Holler all you want, but, the war is over: and we won!

  13. 13
    PaV says:

    Alicia:

    Here’s what one of the authors has said in an interview:

    “La visión hasta ahora es que al evolucionar ganábamos en complejidad, ganando genes. Así se pensó cuando se secuenciaron los primeros genomas, de mosca, de gusano y del ser humano. Pero hemos visto que no es así. La mayoría de nuestros genes está también en las medusas. Nuestro ancestro común los tenía. No es que nosotros hayamos ganado genes, es que los han perdido ellos. La complejidad génica es ancestral”, sentencia Cañestro.

    Here’s my translation:
    “The view up until now is that to evolve means a gain in complexity, a gain in genes. This is what was thought when they sequenced the first genomes, of the fly, of worms, and of human beings. However we have seen that this isn’t how things are. The majority of our genes can be found in sea anemones. Our common ancestor had them. It’s not that we have gained genes, rather, it’s that they have lost them. Genetic complexity is ancestral,” said Canestro.

    The war is over: we won!

  14. 14
    Cabal says:

    The war is over and I’d rather say it is everybody’s loss. If gene loss is allowed to go on for much longer, kids will be born without genes.

  15. 15
    Rennie says:

    Alecia:

    Lets make this easy for you to understand. To go from a fresh water drinking land animal, to a salt water swimming 15 000kg whale, would require an immense increase of novel genetic information. This paper indicates evolution by gene loss, which is counter intuitive the usual Darwinian paradigm.

    Time to dust of your white flag.

  16. 16
    tjguy says:

    I predict that creationists will have a field day with this new discovery as it seems to validate one of their main points they have been making for years. Evolution works, but the progression is not in the right direction needed to see a single cell turn itself into a human being. I haven’t read the paper either so this is simply based on the OP.

    Losing genes and breaking genes is simple. No one argues that evolution can do this. We are all in total agreement on that point! The evidence for it is incontrovertible.

    However, the evidence for evolution in the opposite direction is much more theory driven and unclear.

  17. 17
    Origenes says:

    From the website of the ‘Universitat de Barcelona’:

    Thinking of gene loss as an evolution force is a counterintuitive idea, for it is easier to think that only when we gain something –genes in this case- can we evolve. However the new work by these authors, who are members of the Research Group on Evolution and Development (EVO-DEVO) of the UB, paints the vision of gene loss as a great potential process of genetic change and evolutionary adaption.

    … “The genome sequencing of very different organisms has shown that gene loss has been a usual phenomenon during evolution in all life cycles. In some cases, it has been proven that this loss might mean an adaptive response towards stressful situations when facing sudden environmental changes” says Professor Cristian Cañestro.

    “In other cases, there are genetic losses –says Cañestro- which even though they are neutral per se, have contributed to the genetic and reproductive isolation among lineages, and thus, to speciation, or have rather participated in the sexual differentiation in contributing to the creation of a new Y chromosome. The fact that genetic loss patterns are not stochastic but rather biased in the lost genes (depending on the kind of function of the gen or its situation in the genome in different organism groups) stresses the importance of the genetic loss in the evolution of the species.

    … Gene loss can become a positive condition. This has been proved with laboratory experiments (in yeast or bacteria) and population studies on humans. Some of the best studied cases on humans are coding gene losses with cell receptors (CCR5 and DUFFY), which make individuals more resistant to HIV infection and to plasmodium caused by malaria. In nature, there are gene losses from which some organisms benefited: losses which made colour changes in flowers which attract new pollinators, losses which made warmness-resistant insects to be able to colonize new habitats, etc.

    Some studies also suggest that gene loss has been decisive in the origins of the human species. Chimpanzees and humans share more than the 98% of their genome –something which has always been of great interest- and in this context it is tempting to speculate that perhaps it would be necessary to look for the differences not in the shared genes but in the lost ones- the ones which have been lost in a different way through the human and primate evolution. “For example, it is believed that gene loss reduced the jaw muscular structure, which allowed the human brain to grow its size, or that gene losses were important in the improvement of our defense system against illnesses”, says Cristian Cañestro. …

  18. 18
    EugeneS says:

    PaV,

    Thanks for drawing attention to this remarkable scientific finding.

    Without getting into much detail, the message is clear. The evolutionist claim regarding the natural development from simpler forms to more complex is under threat. Fortunately, the scientific process is free from emotions that overload some of the responses from our Darwinist friends 🙂

    Now the question is, where did the initial complexity come from?

    Game over.

  19. 19
    bornagain77 says:

    As long as they stay within lineages of a specific species, they are correct in their conclusion that gene loss was integral to adaptation to specific environments

    No Positive Selection, No Darwin: A New Non-Darwinian Mechanism for the Origin of Adaptive Phenotypes – November 2011
    Excerpt: Hughes now proposes a model he refers to as the plasticity-relaxation-mutation (PRM) model. PRM suggests that adaptive phenotypes arise as follows: (1) there exists a phenotypically plastic trait (i.e., one that changes with the environment, such as sweating in the summer heat); (2) the environment becomes constant, such that the trait assumes only one of its states for a lengthened period of time; and (3) during that time, deleterious mutations accumulate in the unused state of the trait, such that its genetic basis is subsequently lost.
    ,,, But if most adaptations result from the loss of genetic specifications, how did the traits initially arise? One letter (Chevin & Beckerman 2011) of response to Hughes noted that the PRM “does not explain why the ancestral state should be phenotypically plastic, or why this plasticity should be adaptive in the first place.”
    http://www.evolutionnews.org/2.....52941.html

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    IMHO, where they go off the rails in the study is where they try to extrapolate the loss of genetic information witnessed within lineages of a specific species to try to claim that gene loss was integral to macro-evolution between species.
    The large percentage of ORFan genes found in every new genome sequenced, by itself, refutes that notion.

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,,
    The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.
    http://ccsb.dfci.harvard.edu/w.....n_2013.pdf

    Of related note to the ‘rotting Y chromosome’ hypothesis they alluded to:

    Theory of the ‘Rotting’ Y Chromosome Dealt a Fatal Blow – February 2012
    Excerpt: “the sequence of the rhesus Y, shows the chromosome hasn’t lost a single ancestral gene in the past 25 million years. By comparison, the human Y has lost just one ancestral gene in that period, and that loss occurred in a segment that comprises just 3% of the entire chromosome”, “,,,earlier work comparing the human and chimpanzee Ys revealed a stable human Y for at least six million years. “Now our empirical data fly in the face of the other theories out there. With no loss of genes on the rhesus Y and one gene lost on the human Y, it’s clear the Y isn’t going anywhere.”
    http://www.sciencedaily.com/re.....154359.htm

    Genes on the Y chromosome prove essential for male survival – April 23, 2014
    Excerpt: Moreover, the vast majority of these tenacious genes appear to have little if any role in sex determination or sperm production.,,,
    “There are approximately a dozen genes conserved on the Y that are expressed in cells and tissue types throughout the body,” he continues. “These are genes involved in decoding and interpreting the entirety of the genome. How pervasive their effects are is a question we throw open to the field, and it’s one we can no longer ignore.”
    Page believes this research will at last allow his lab to transition from proving the so-called rotting Y theorists wrong to a new era in Y chromosome biology.,,,
    http://www.sciencedaily.com/re.....132421.htm

  20. 20
    Bob O'H says:

    The review is interesting (you can see it all via the naughtiness that is sci-hub), but it doesn’t put deletion into context compared to other mechanisms of genomic evolution. So gene duplication (for example) could be much more important and prevalent.

    Declaring that the war is over because of this could be like saying that the Golden State Warrior are NBA champions because they scored 89 points in game 7.

  21. 21
    Alicia Cartelli says:

    The main idea of the paper is that gene loss is an important evolutionary force, just as gene duplication, mutations, transposable elements, chromosome rearrangements, etc. all are.
    Period.
    There is no massive overthrow of evolutionary thought, as you would like to believe. Don’t you think more of your friends would be jumping up and down and stomping their feet if it was?
    Sorry to burst your bubble.

  22. 22
    PaV says:

    Bob and Alicia:

    Almost all mutations are deleterious. When you compare species, you find de novo genes, which, probabilistically, cannot be explained, and is far beyond anything that gene duplication can explain.

    When you add to this the growing body of knowledge spawned by sequencing that tells us gene loss is a prevalent method of speciation, then little is left of Darwinian notions.

    When I say the war is over, I mean that Darwinism doesn’t have a leg to stand on. But you can’t tell that to Darwinists. So, it will probably take 20 years for this latest finding to sink in.

    But, watch out, because the ENCODE project still continues, and they have a plan for elucidating function throughout the genome. And then what?

    No junk-DNA; pseudogenes that have regulatory function; epigenetics demonstrating the tremendous dialougue between environment and genome. No, the war is over.

  23. 23
    PaV says:

    BTW, I left out the whole new area of transposons, which, as we know, have a non-random character.

  24. 24
    Alicia Cartelli says:

    Almost all mutations are deleterious?
    So humans all have identical genomes?
    How have scientists been altering the genome of organisms and cells for years without them all immediately dying?

    “de novo genes, which, probabilistically, cannot be explained”
    What about the explanations we already have for de novo genes? Are we ignoring those?

    Please, you think encode is going to find function in the entire genome? They won’t even come close.
    And what happens when they find that some of these functions are important for evolution, and not necessarily the individual organism? Are you guys going to count those?

  25. 25
    RexTugwell says:

    “explanations we already have for de novo genes?”
    Care to share?

  26. 26
    Alicia Cartelli says:

    Just go onto pubmed and search “de novo genes”
    Do I need to walk you guys through everything?

  27. 27
    RexTugwell says:

    Thanks for the non answer. Typical

  28. 28
    Alicia Cartelli says:

    It took more typing and clicking to post that comment than to go to pubmed and search “de novo genes”

    Just another classic case of a creationist not wanting to learn.

  29. 29
    RexTugwell says:

    I have neither the time nor the patience for what probably amounts to a literature bluff from Alicia. Is anyone familiar with these “explanations” and what is your opinion.

  30. 30
    Alicia Cartelli says:

    Right, instead of doing a simple literature search, you decide to ask the most unscientific community on the internet about….science.

    I would expect nothing less from UD.

  31. 31
    bornagain77 says:

    RexTugwell, The so-called ‘explanation’ for new genes from Darwinists is just the same ole hand-waving just-so story that Darwinists are notorious for whenever a finding contradicts their theory. (which is often)

    Is the Origin of New Genes “Basically a Solved Problem”? – Cornelius Hunter – Sept. 11, 2014
    Excerpt: 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:,,,
    ,,,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 must have evolved because solo genes are observed over and over:
    “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.”,,,
    Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.,,,
    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.,,
    http://darwins-god.blogspot.co.....olved.html

    Could Chance Arrange the Code for (Just) One Gene?
    “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
    http://www.creationsafaris.com/epoi_c10.htm

    Can new genes arise from junk DNA? – August 2015
    Excerpt: Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.,,,
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....-junk-dna/

    Can new genes arise from junk DNA? – August 24, 2015
    Excerpt: Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said.
    BA77: Moreover, the essential genes were somehow incorporated into the ‘bicycle’ while the bicycle was being peddled, i.e. while the cell was busy being alive.
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....ent-577484

  32. 32
    bornagain77 says:

    Alicia Cartelli, since you are so concerned with being properly grounded in science, perhaps you would like to lay out the precise falsification criteria for Darwinian evolution so as to establish it as a testable hypothesis that is firmly grounded in science?

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    Dubitable Darwin? Why Some Smart, Nonreligious People Doubt the Theory of Evolution By John Horgan on July 6, 2010
    Excerpt: Early in his career, the philosopher Karl Popper ,, called evolution via natural selection “almost a tautology” and “not a testable scientific theory but a metaphysical research program.” Attacked for these criticisms, Popper took them back (in approx 1978). But when I interviewed him in 1992, he blurted out that he still found Darwin’s theory dissatisfying. “One ought to look for alternatives!” Popper exclaimed, banging his kitchen table.
    http://blogs.scientificamerica.....evolution/

    It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    Darwinian Evolution is a Unfalsifiable Pseudo-Science – Mathematics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater

  33. 33
    Seqenenre says:

    RexTugwell:
    25, 27 and 29 must be the most embarrassing ‘triplet’ of posts ever seen on the internet.

  34. 34
    bmaque12 says:

    Alicia Cartelli, It took more typing and clicking to post that comment than to go to pubmed and search “de novo genes”

    Just another classic case of a creationist not wanting to learn.

    We just want to articulate using your words . How de novo genes are well understood . That’s the insertion that you made . We don’t feel that they are well understood , So it’s not for us to make your case. So we just want you to back that up . Can you ?

  35. 35
    Andre says:

    Hahahahaha Dr Behe was right… again!

  36. 36
    RexTugwell says:

    Many thanks, BA77. Now was that so hard, Alicia?

    @Seqenenre: Not so embarrassing when my suspicions are ultimately confirmed. Nice try though. Maybe you’re willing to make a case for known mechanisms of de novo genes. Hmmm?

  37. 37
    Seqenenre says:

    @Rex Tugwell:

    Thanks for the non answer. Typical

    I have neither the time nor the patience for what probably amounts to a literature bluff from Alicia. Is anyone familiar with these “explanations” and what is your opinion.

  38. 38
    RexTugwell says:

    I used to love cartoons but then I grew up.

  39. 39
    bill cole says:

    Seqenenre
    Hi
    There are pub med papers on di novo genes. The challenge for all the papers is identifying a mechanism that can account for their origin within reasonable population sizes and generations. According to Mychael Lynch’s paper in 2010 it takes over 1 million generations and a population size of 10^11to fix an adaption requiring 5 specific mutations. So based on this how does a di novo gene arrive in a human that is not in a chimp that requires more then 5 specific mutations? This is a very real and unresolved problem for the theory of common decent. The genome is an organized sequence and sequences have almost unlimited possible ways of being organized. How they get organized into a gene coding sequence is quite a mystery.

  40. 40
    wd400 says:

    So.. what’s the argument here?

    At the moment it reads like

    1. Gene loss can be adaptive
    2 …
    3. also de novo genes are common and mutations are bad
    4 ….
    5 Victory

  41. 41
    Bob O'H says:

    PaV @ 22 – I see you don’t rise to the challenge of asking whether gene duplication is more prevalent than gene loss.

    I’m wondering what this probabalistic proof is that de novo gene can’t evolve.

    I also don’t see ENCODE as a problem – the consensus is that they were being overly optimistic about function. I also don’t see why pseudo-genes having a regulatory function is a problem: evolution is messy, and whatever works will work. Epigenetic is just (!) the mechanism by which the environment affects gene expression, but we knew is did already – “G by E” isn’t controversial.

    So, you can declare victory. If anyone notices, they’ll just shrug.

  42. 42
    Andre says:

    I have to mention this. YEC’s have stated for years that speciation is as a result of information loss. I think this paper vindcates them too.

  43. 43
    Andre says:

    Bob

    Whatever works works….. hahahahahaha…. Darwinian evolution explains everything but really explains nothing….

  44. 44
    Andre says:

    Bob

    It is not the consensus that disagrees with ENCODE it’s the dogmatists

  45. 45
    Borne says:

    Alicia posted, “the most unscientific community on the internet about….science.”

    That is worthy of a heart felt ROTFL

  46. 46
    bill cole says:

    Bob O’H

    I’m wondering what this probabalistic proof is that de novo gene can’t evolve.

    How would you evolve my cell phone number with a random unguided process? How about a number that would contact 1 of my 50 friends on my direct dial.

    How would this change if phone numbers increased from 10 to 50 digits?

  47. 47
    bornagain77 says:

    That adaptation is driven by loss of genetic information is overwhelmingly supported by many lines of evidence. Whereas the evidence that adaptation is driven by gain of information, as is presupposed in Darwinian thought, is slim to non-existent. The only reason this finding would even be controversial is because it flies directly in the face of Darwinian presupposition.

    For prime example of how this flies in the face of Darwinian presuppositions we need look no farther than humans themselves.

    Darwin presupposed that the Caucasian race was more evolutionarily advanced than the African race:

    “At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate, and replace, the savage races throughout the world. At the same time the anthropomorphous apes, as Professor Schaaffhausen has remarked, will no doubt be exterminated. The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilised state, as we may hope, even than the Caucasian, and some ape as low as a baboon, instead of as now between the negro or Australian and the gorilla”
    ? Charles Darwin, The Descent of Man, 1874, p. 178

    In fact, the belief that Caucasians were the most advanced race was an integral part of Nazi racial ideology.

    The Role Of Darwinism In Nazi Racial Thought – Richard Weikart – October 2013
    Excerpt: The historical evidence is overwhelming that human evolution was an integral part of Nazi racial ideology.
    http://www.csustan.edu/history.....hought.pdf

    Yet contrary to that Darwinian presupposition of racial superiority, which was at the root of so much misery in the world in WWII, the fact of the matter is that, genetically specking, Caucasians are actually genetically inferior to Africans. Whites are not genetically superior as Darwin and the Nazis presupposed.

    Human Genetic Variation Recent, Varies Among Populations – (Nov. 28, 2012)
    Excerpt: Nearly three-quarters of mutations in genes that code for proteins — the workhorses of the cell — occurred within the past 5,000 to 10,000 years,,,
    “One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,”,,,
    The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,,
    http://www.sciencedaily.com/re.....132259.htm

    “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.”
    Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.-

    New analysis provides fuller picture of human expansion from Africa – October 22, 2012
    Excerpt: A new, comprehensive review of humans’ anthropological and genetic records gives the most up-to-date story of the “Out of Africa” expansion that occurred about 45,000 to 60,000 years ago.
    This expansion, detailed by three Stanford geneticists, had a dramatic effect on human genetic diversity, which persists in present-day populations. As a small group of modern humans migrated out of Africa into Eurasia and the Americas, their genetic diversity was substantially reduced.
    per physorg

    In fact, Blue eyes, light skin, Blond hair and lactase persistence, contrary to what Nazis thought, are the result of the loss of genetic information, not a gain:

    Daily thought: blue eyes and other gene mutations, April 25, 2013
    Excerpt: “Research on blue-eyes has led many scientist to further affirm that humans are truly mere variations of the same origin. About 8% of the world’s total population has blue eyes so blue eyes are fairly rare. In fact, blue eyes are actually a gene mutation that scientist have researched and found to have happened when the OCA2 gene “turned off the ability to produce brown eyes.”
    http://www.examiner.com/articl.....-mutations

    Melanin
    Excerpt: The melanin in the skin is produced by melanocytes, which are found in the basal layer of the epidermis. Although, in general, human beings possess a similar concentration of melanocytes in their skin, the melanocytes in some individuals and ethnic groups more frequently or less frequently express the melanin-producing genes, thereby conferring a greater or lesser concentration of skin melanin. Some individual animals and humans have very little or no melanin synthesis in their bodies, a condition known as albinism.
    – per wikipedia

    Subtle change in DNA, protein levels determines blond or brunette tresses, study finds – June 1, 2014
    Excerpt: The researchers found that the blond hair commonly seen in Northern Europeans is caused by a single change in the DNA that regulates the expression of a gene that encodes a protein called KITLG, also known as stem cell factor. This change affects how much KITLG is expressed in the hair follicles without changing how it’s expressed in the rest of the body. Introducing the change into normally brown-haired laboratory mice yields an animal with a decidedly lighter coat — not quite Norma Jeane to Marilyn Monroe, but significant nonetheless.
    http://www.sciencedaily.com/re.....150924.htm

    Got milk? Research finds evidence of dairy farming 7,000 years ago in Sahara
    Excerpt: In premature babies, the gene coding for lactase is sometimes not yet active. And in much of the world’s population, the gene is downregulated after weaning, eventually producing some degree of lactose intolerance. Those whose genes are not downregulated are said to have “lactase persistence.” However, even lactose-intolerant people still have genes coding for lactase enzyme; they are just switched off.
    In an adult with lactase persistence, one or both alleles of the lactase gene remain switched on.
    http://www.answersingenesis.or.....e-07072012

    Critic ignores reality of Genetic Entropy – Dr John Sanford – 7 March 2013
    Excerpt: Where are the beneficial mutations in man? It is very well documented that there are thousands of deleterious Mendelian mutations accumulating in the human gene pool, even though there is strong selection against such mutations. Yet such easily recognized deleterious mutations are just the tip of the iceberg. The vast majority of deleterious mutations will not display any clear phenotype at all. There is a very high rate of visible birth defects, all of which appear deleterious. Again, this is just the tip of the iceberg. Why are no beneficial birth anomalies being seen? This is not just a matter of identifying positive changes. If there are so many beneficial mutations happening in the human population, selection should very effectively amplify them. They should be popping up virtually everywhere. They should be much more common than genetic pathologies. Where are they? European adult lactose tolerance appears to be due to a broken lactase promoter [see Can’t drink milk? You’re ‘normal’! Ed.].
    African resistance to malaria is due to a broken hemoglobin protein [see Sickle-cell disease. Also, immunity of an estimated 20% of western Europeans to HIV infection is due to a broken chemokine receptor—see CCR5-delta32: a very beneficial mutation. Ed.] Beneficials happen, but generally they are loss-of-function mutations, and even then they are very rare!
    http://creation.com/genetic-entropy

    Moreover, contrary to what the Nazis believed about humans evolving into some sort of master race, the fact of the matter is that humans, all humans, are devolving instead of evolving:

    If Modern Humans Are So Smart, Why Are Our Brains Shrinking? – January 20, 2011
    Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.”
    “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,,
    He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.”
    http://discovermagazine.com/20.....-shrinking

    Scientists Discover Proof That Humanity Is Getting Dumber, Smaller And Weaker By Michael Snyder, on April 29th, 2014
    Excerpt: An earlier study by Cambridge University found that mankind is shrinking in size significantly.
    Experts say humans are past their peak and that modern-day people are 10 percent smaller and shorter than their hunter-gatherer ancestors.
    And if that’s not depressing enough, our brains are also smaller.
    The findings reverse perceived wisdom that humans have grown taller and larger, a belief which has grown from data on more recent physical development.
    The decline, said scientists, has happened over the past 10,000 years.
    http://thetruthwins.com/archiv.....and-weaker

    The evidence for accumulating detrimental mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.

    “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.”
    John C. Avise – Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57

    I went to the mutation database website cited by John Avise and found:

    The Human Gene Mutation Database
    The Human Gene Mutation Database (HGMD®) represents an attempt to collate known (published) gene lesions responsible for human inherited disease.

    Mutation total (as of May 23, 2016) – 183,500

    Again, The evidence for ‘devolution’, and/or adaptation by loss of genetic information is overwhelming. The only reason this is controversial is because it flies directly in the face of Darwinian presuppositions.

  48. 48
    Querius says:

    The Theory of Evolution is absolutely brilliant. It can predict anything in retrospect!

    You see, evolutionary change in a genome has actually gotta be Oscillating Over Time(tm). It expands and contracts depending on the type of selective pressure or lack thereof.

    Oh my! I feel the unmistakable tremor of a PhD eruption! 😉

    -Q

  49. 49
    buffalo says:

    Remember John Sanford and Genetic Entropy. –
    “over 90% of the genome is actively transcribed”
    “the genome has multiple overlapping messages”
    “data compression on the most sophisticated level”
    “more and more the genome looks like a super super set of programs”
    “more and more it looks like top down design”
    “the reality is everybody is mutant”
    “the selection process really has nothing to grab hold of”
    “so it’s kind of a trade secret amongst population geneticists,any well informed population geneticist understands man is degenerating”
    “so in deep geological time we should have been extinct a long time ago”
    “the human race is degenerating at 1-5% per generation”

    http://idvolution.blogspot.com.....y-and.html

  50. 50
    rvb8 says:

    After rereading all the posts and PaV’s article again, and having visited several websites (Harvard, BBC, Wikipedia, Encyclopedia Britannica, Cambridge, Science Daily, Nature, etc), I have to conclude that PaV and bornagain77 have actually done it; they have successfully refuted and confounded Evolutionary Biology.

    In a mere 700 words or so, s/he has overturned what Theodosius Dobzhansky explained as the unifying theory of life. Well done! Tell us about your Stockholm travel arrangements so that we can share in your success.

  51. 51
    Querius says:

    Bornagain77,

    Mutation total (as of May 23, 2016) – 183,500

    This data is child’s play for any Darwinist to accommodate!

    It simply demonstrates how long humans have been evolving, since more evolved species obviously accumulate more mutations between Massive Evolutionary Upswings. 😉

    -Q

  52. 52
    bornagain77 says:

    rvb8, since Darwinian evolution is. in reality, a religion instead of a testable/falsifiable science, then there is no falsification that will ever be allowed to falsify Darwinian evolution in the minds of the faithful.

    Theodosius Dobzhansky, whom you mentioned favorably, proves as much:

    Nothing in biology makes sense except in light of theology? – Dilley S. – 2013
    Abstract
    This essay analyzes Theodosius Dobzhansky’s famous article, “Nothing in Biology Makes Sense Except in the Light of Evolution,” in which he presents some of his best arguments for evolution. I contend that all of Dobzhansky’s arguments hinge upon sectarian claims about God’s nature, actions, purposes, or duties. Moreover, Dobzhansky’s theology manifests several tensions, both in the epistemic justification of his theological claims and in their collective coherence. I note that other prominent biologists–such as Mayr, Dawkins, Eldredge, Ayala, de Beer, Futuyma, and Gould–also use theology-laden arguments. I recommend increased analysis of the justification, complexity, and coherence of this theology.
    http://www.ncbi.nlm.nih.gov/pubmed/23890740

    Methodological Naturalism: A Rule That No One Needs or Obeys – Paul Nelson – September 22, 2014
    Excerpt:,,,with respect to one of the most famous texts in 20th-century biology, Theodosius Dobzhansky’s essay “Nothing in biology makes sense except in the light of evolution” (1973).
    Although its title is widely cited as an aphorism, the text of Dobzhansky’s essay is rarely read. It is, in fact, a theological treatise. As Dilley (2013, p. 774) observes:
    “Strikingly, all seven of Dobzhansky’s arguments hinge upon claims about God’s nature, actions, purposes, or duties. In fact, without God-talk, the geneticist’s arguments for evolution are logically invalid. In short, theology is essential to Dobzhansky’s arguments.”,,
    http://www.evolutionnews.org/2.....89971.html

    If you disagree with the fact that Darwinian evolution is a pseudo-scientific religion, instead of a testable/falsifiable science, then please present the exact falsification criteria that will allow an experimentalist to test its claims.

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    Dubitable Darwin? Why Some Smart, Nonreligious People Doubt the Theory of Evolution By John Horgan on July 6, 2010
    Excerpt: Early in his career, the philosopher Karl Popper ,, called evolution via natural selection “almost a tautology” and “not a testable scientific theory but a metaphysical research program.” Attacked for these criticisms, Popper took them back (in approx 1978). But when I interviewed him in 1992, he blurted out that he still found Darwin’s theory dissatisfying. “One ought to look for alternatives!” Popper exclaimed, banging his kitchen table.
    http://blogs.scientificamerica.....evolution/

    Darwinian Evolution is a Unfalsifiable Pseudo-Science – Mathematics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater

    It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
    Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.

    In fact, not only is Evolution not based on any known universal law, as other overarching theories of science are based upon known universal laws, (including ID being based upon the ‘law of conservation of information’), Entropy, a law with great explanatory power in science, almost directly contradicts Darwinian claims that increases in functional complexity and/or information can be easily had,,,

    “Gain in entropy always means loss of information, and nothing more.”
    Gilbert Newton Lewis – preeminent Chemist of the first half of last century

    Why Tornados Running Backward do not Violate the Second Law – Granville Sewell – May 2012 – article with video
    Excerpt: So, how does the spontaneous rearrangement of matter on a rocky, barren, planet into human brains and spaceships and jet airplanes and nuclear power plants and libraries full of science texts and novels, and supercomputers running partial differential equation solving software , represent a less obvious or less spectacular violation of the second law—or at least of the fundamental natural principle behind this law—than tornados turning rubble into houses and cars? Can anyone even imagine a more spectacular violation?
    http://www.uncommondescent.com.....econd-law/

    So rvb8 how exactly is one suppose to overturn a ‘scientific’ theory that doesn’t even a qualify as a testable scientific theory in the first place? Evidence is useless against such a ill-begotten contraption that is called Darwinian evolution!

  53. 53
    rvb8 says:

    The LAWs that prove the THEORY, thus making the THEORY fact:

    “These laws,taken in the largest sense, being Growth with Reproduction; (I think living things follow these LAWs. rvb8) Variability from the indirect and direct action of the external conditions of life, and from use and disuse; (Another law. rvb8)a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms.” (so many LAWs here; desire for sex-more off spring-competition-success-more sex etc etc)

    I’m sorry BA77 but your constant twittering on a subject already confirmed, and the absurd title of this piece are embarassments for your position, which, to quote Wolfgang Pauli is, ‘not even wrong’.

  54. 54
    bornagain77 says:

    What is that gibberish you wrote? Are you drunk?

    Moreover, Wolfgang Pauli was certainly no friend of ‘very irrational’ evolutionists:

    “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.'”
    Wolfgang Pauli (pp. 27-28) – Letter by Pauli to Bohr of February 15, 1955

  55. 55
    rvb8 says:

    Heh:) “that gibberish”, is from ‘The Origin of Species‘ you may have heard of it? Try reading it slowly. It actually makes a lot of sense, try this: living things like to reproduce, in many instances they even find the act fun. Having reproduced they next want to live. If the inherited traits of one living thing give it an advantage over another living thing, then that living thing will be more successful in sex.

    Honestly, I don’tknow how to dumb down Darwin’s “gibberish” (Heh:)) any more.

  56. 56
    bornagain77 says:

    So the law of ‘having fun’ by ‘wanting to reproduce’ and the law of ‘wanting to live’ form the basis of evolution in science? 🙂

    Can you show me exactly where those constants/laws of ‘having fun’ by reproducing and ‘wanting to live’ are in the NIST table? 🙂

    NIST Reference – Constants
    http://physics.nist.gov/cuu/Constants/index.html

    To repeat, there is no natural ‘law of evolution’ within physical science:

    The Evolution of Ernst: Interview with Ernst Mayr – 2004
    Excerpt: biology (Darwinian Evolution) differs from the physical sciences in that in the physical sciences, all theories, I don’t know exceptions so I think it’s probably a safe statement, all theories are based somehow or other on natural laws. In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences.,,,
    in this book. I show that the theoretical basis, you might call it, or I prefer to call it the philosophy of biology, has a totally different basis than the theories of physics.
    http://www.scientificamerican......-ernst-in/

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Evolution is True – Roger Highfield – January 2014
    Excerpt:,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology.
    Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation.
    http://www.edge.org/response-detail/25468

    Moreover, the mechanism of random mutation that Darwinists imagine to be the ultimate creator of all life on earth is actually the primary reason why all living things eventually grow old and die:

    Entropy Explains Aging, Genetic Determinism Explains Longevity, and Undefined Terminology Explains Misunderstanding Both – 2007
    Excerpt: There is a huge body of knowledge supporting the belief that age changes are characterized by increasing entropy, which results in the random loss of molecular fidelity, and accumulates to slowly overwhelm maintenance systems [1–4].,,,
    http://www.plosgenetics.org/ar.....en.0030220

    And no, natural selection does not help:

    Can Purifying Natural Selection Preserve
    Biological Information?
    Excerpt: Across all reasonable parameters settings, we observed that high impact mutations were selected away with very high efficiency, while very low impact mutations accumulated just as if there was no selection operating
    http://www.worldscientific.com.....08728_0010

    Genetic Entropy – peer reviewed references
    http://www.geneticentropy.org/.....08728_0013

  57. 57
    PaV says:

    Alicia C:

    Almost all mutations are deleterious?

    Yes. They’ve known this since the 60’s. Maybe you can read up on it.

    So humans all have identical genomes?

    I have no idea what you’re talking about. Please clarify.

    How have scientists been altering the genome of organisms and cells for years without them all immediately dying?

    Did I say they were “deleterious,” or did I say they were “deadly”? Your strawman argument will get you nowhere.
    BTW, I have thalassemia.

    “de novo genes, which, probabilistically, cannot be explained”
    What about the explanations we already have for de novo genes? Are we ignoring those?

    But Darwinists have explanations for all kinds of things. But are they plausible? In the really important cases, usually not.

    A portion of de novo genes are “novel” genes, and of considerable length. They are termed “novel” because they don’t match up with any annotated genes. How did these genes arise? What was the mechanism?

    To put together a new protein of average length requires an improbability of more than 1 in 4^900, roughly, just to give a ball park figure. This is simply another way of saying that an average size protein cannot be made using random processes. It’s simply impossible. Everyone know this. But if you want to deceive yourself badly enough, you can believe the impossible happens.

    Please, you think encode is going to find function in the entire genome? They won’t even come close.
    And what happens when they find that some of these functions are important for evolution, and not necessarily the individual organism? Are you guys going to count those?

    They found some kind of function for what, 82% of the genome. And, they said that this percentage would rise. Why? Because some portions of the genome are expressed only for short periods of time during development, and, through improving their assaying techniques, they hope to confirm functions for those segments that, once development has ended, no longer function. So, it’s worse than you think.

    Ask yourself this question Alicia: what will make me stop believing in Darwin’s theory? What does the answer to this question look like exactly?

  58. 58
    PaV says:

    Bob O’H:

    PaV @ 22 – I see you don’t rise to the challenge of asking whether gene duplication is more prevalent than gene loss.

    Does gene duplication increase the information content of the genome? Does gene loss?
    When will you recognize that that’s the way to argue with someone who holds the ID position?

    Will the mechanism of duplication and subsequent degradation help? Can it bring about a “novel” gene? Answer: No.

    I’m wondering what this probabalistic proof is that de novo gene can’t evolve.

    Nucleotides are chemically interchangeable. Chemistry can’t explain the entirely “new” sequence of a “novel” gene. Random mechanisms can’t do this either. That leaves intelligent agency. Simple as that. And logically compelling.

    I also don’t see ENCODE as a problem – the consensus is that they were being overly optimistic about function.

    The consensus now. And then when that consensus is completely undermined by evidence, the “new consensus” will be that you knew this all along, and that this isn’t anything new at all.

    I also don’t see why pseudo-genes having a regulatory function is a problem: evolution is messy, and whatever works will work.

    They were called “pseudogenes” because they didn’t have function. So, when you find function for this putative “pseudogenes,” then it looks like you didn’t properly understand what you were looking at.

    Epigenetic is just (!) the mechanism by which the environment affects gene expression, but we knew is did already – “G by E” isn’t controversial.

    This is not a very forthright answer. Of course everyone knew that the environment affected the genome: but not to the degree that it does. But what really makes your answer devious is the fact that you know that it is now known that epigenetics can have long-term inheritable effects. This is new; and a game-changer. Who are you trying to fool? Those looking in on this discussion?

    So, you can declare victory. If anyone notices, they’ll just shrug.

    Well, of course, Darwinists will shrug. They always do. No matter what evidence is discovered undermining the strange thinking they hold, they just shrug, invent some new amendment to their on-going narrative, and move on.

    But your days are numbered. Why? Genome sequencing.

    Darwinism, and neo-Darwinism, will never stand up to this test. ID, OTOH, will be vindicated.

    It’ll just take a number of prominent evolutionary biologists to enter the pearly gates.

  59. 59
    PaV says:

    wd400:

    So.. what’s the argument here?

    At the moment it reads like

    1. Gene loss can be adaptive
    2 …
    3. also de novo genes are common and mutations are bad
    4 ….
    5 Victory

    Information, my dear wd400, information. Where does it come from? How does it arise?

  60. 60
    rvb8 says:

    “Almost all mutations are deleterious?”

    I agree, but whether I agree or not is pretty unimportant, the facts are much more important. Large and random mutations in the genotype, producing new and radically altered offspring, and that this saltation is ruinous to the individual, is the accepted position in evolutionary science. Big and quick change at the level of saltation has always been accepted as harmful to life.

    Why would you think this in any way undermines evolution, which is nothing, if not a fan of gradualism?

  61. 61
    Querius says:

    PaV,

    Did I say they were “deleterious,” or did I say they were “deadly”? Your strawman argument will get you nowhere.

    Actually, both words start with the letters “de” and can easily be confused. Beside deleterious sounds much more serious.

    That explains why Alicia asked the question

    So humans all have identical genomes?

    on the assumption that deleterious means deadly. Or is it delirious? Delicious? Desirous? Anyway, one of those long words. 🙂

    Make sense now?

    -Q

  62. 62
    Querius says:

    rvb8,

    Big and quick change at the level of saltation has always been accepted as harmful to life.

    The LAWs that prove the THEORY, thus making the THEORY fact

    LOL!

    C’mon you’re Spearshake or one of his sock puppets, right? You know—the guy who claimed he was an “expert” in statistics? Please say yes.

    -Q

  63. 63
    rvb8 says:

    There was once a poster here in the early days who was called answersingenitals which I thought funny on many levels; sorry not Spearshake as I claim to be an expert in very little, and following the example of Socrates I am smart enough to know I know very little.

    However large mutations are almost always, if not always deadly to the individual organism, I don’t need to be an expert to know this. And evolution is most certainly the science of gradualism by definition; why is this a silly statement?

  64. 64
    Querius says:

    rvb8,

    Since saltation, by definition, is a big and quick evolutionary change . . .

    Also look up punctuated equilibrium.

    Look up the definitions for theory, law, and fact. Toss in hypothesis for good measure.

    Are you sure you’re not Spearshake?

    -Q

  65. 65
    rvb8 says:

    Saltation has never been documented in biology and my remarks concerning the gradualism of evolution remain.

    ‘Punctuated equilibrium’ is a theory within the theory of evolution put forward by Niles Eldredge and Stephen Jay Gould. It merely notes that ‘stasis’ is probably the normal order in evolution, punctuated by periods of increasing bio-diversity; Cambrian Explosion as one famous example.

    Large mutations in genes producing freakish off spring are almost always, or even always deadly to the individual organism. This is not ‘saltation’, which along with Ken Ham’s absurd cladistic invention ‘kinds’, is never mentioned by serious scientists.

  66. 66
    Bob O'H says:

    bill cole @46 – Is your phone number a de novo gene? I suspect not.

    rbv8 @ 50 – bad news. I’m not sure this would fit under the rubric of any of the Nobel prizes. Literature, maybe.

    Pav @ 58 – I see you are still punting on whether gene duplication is more prevalent than gene loss. You’re also still punting on the proof that de novo genes can’t arise.

    Incidentally, I can’t use the information argument because I’ve never seen a definition of information from IDists that makes sense biologically. I’d rather not go round the “calculate the information for the flagellum” carousel again.

    Oh, one thing:

    So, when you find function for this putative “pseudogenes,” then it looks like you didn’t properly understand what you were looking at.

    I agree – that’s the wonderful thing about science, we often don’t understand what we’re looking at, so we figure it out.

  67. 67
    EugeneS says:

    Bob #66,

    “I agree – that’s the wonderful thing about science, we often don’t understand what we’re looking at, so we figure it out.”

    Yes, sure. But acknowledging a falsified hypothesis and moving on is way different from pretending the hypothesis still holds and modifying it as if nothing happened.

  68. 68
    bornagain77 says:

    To reiterate, since Darwinian evolution is, in reality, a religion instead of a testable/falsifiable science, then there is no falsification that will ever be allowed to falsify Darwinian evolution within the minds of the Darwinian faithful.
    http://www.uncommondescent.com.....ent-611045

    Evolution, You’re Drunk (Go Home) – January 30. 2014
    Excerpt: When asked whether de-evolution, a reversal from the complex to the simple, happens frequently, Dunn replies, sure. “But,” he adds, “I wouldn’t call that de-evolution, I’d call it evolution.”
    http://nautil.us/issue/9/time/.....oure-drunk

    No matter how contrary a finding may be to Darwinian claims, the contrary finding is simply crammed into the Theory of evolution by the addition of ad hoc ‘epicycles’ that try to ‘explain away’ the contradictory finding.

    Inquiry-Based Science Education — on Everything but Evolution
    – Sarah Chaffee – January 22, 2016
    Excerpt: As Thomas Kuhn wrote in The Structure of Scientific Revolutions, when faced with an anomaly, a theory’s defenders “will devise numerous articulations and ad hoc modifications of their theory in order to eliminate any apparent conflict.”
    http://www.evolutionnews.org/2.....02534.html

    In fact, the only actual evidence ever witnessed for the unlimited plasticity of species predicted by Darwinian evolution has been within the theory itself. The theory is forever plastic, able to morph itself into whatever shape it needs to in order to avoid falsification by empirical observation!

    Who would have thought that it would be biologists that came up with the first Theory of Everything?
    Biological divergence? Evolution. Biological convergence? Evolution. Gradual variation? Evolution. Sudden variation? Evolution. Stasis? Evolution. Junk DNA? Evolution. No Junk DNA? Evolution. Tree of life? Evolution. No tree of life? Evolution. Common genes? Evolution. Orfan genes? evolution. Cell with little more than a jelly-like protoplasm? Evolution. Cell filled with countless, highly-specified nano-machines directed by a software code? Evolution. More hardy, more procreative organisms? Evolution. Less hardy, less procreative organisms? Evolution.
    – Evolution explains everything. –
    William J Murray

    Dr. Hunter puts the unfalsifiable situation with Darwinian evolution like this.

    “Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought.”
    ~ Cornelius Hunter

    “When their expectations turn out to be false, evolutionists respond by adding more epicycles to their theory that the species arose spontaneously from chance events. But that doesn’t mean the science has confirmed evolution as Velasco suggests. True, evolutionists have remained steadfast in their certainty, but that says more about evolutionists than about the empirical science.”
    ~ Cornelius Hunter

    “With each new absurdity another new complicated just-so story is woven into evolutionary theory. As Lakatos explained, some theories simply are not falsifiable. But as a result they sacrifice realism and parsimony.”
    – Cornelius Hunter – Here’s That Algae Study That Decouples Phylogeny and Competition – June 17, 2014

    Dr. Hunter also has a site listing many of the fundamentally failed predictions of evolution:

    Darwin’s (failed) Predictions – Cornelius G. Hunter – 2015
    This paper evaluates 23 fundamental (false) predictions of evolutionary theory from a wide range of different categories. The paper begins with a brief introduction to the nature of scientific predictions, and typical concerns evolutionists raise against investigating predictions of evolution. The paper next presents the individual predictions in seven categories: early evolution, evolutionary causes, molecular evolution, common descent, evolutionary phylogenies, evolutionary pathways, and behavior. Finally the conclusion summarizes these various predictions, their implications for evolution’s capacity to explain phenomena, and how they bear on evolutionist’s claims about their theory.

    *Introduction
    Why investigate evolution’s false predictions?
    Responses to common objections

    *Early evolution predictions
    The DNA code is not unique
    The cell’s fundamental molecules are universal

    *Evolutionary causes predictions
    Mutations are not adaptive
    Embryology and common descent
    Competition is greatest between neighbors

    *Molecular evolution predictions
    Protein evolution
    Histone proteins cannot tolerate much change
    The molecular clock keeps evolutionary time

    *Common descent predictions
    The pentadactyl pattern and common descent
    Serological tests reveal evolutionary relationships
    Biology is not lineage specific
    Similar species share similar genes
    MicroRNA

    *Evolutionary phylogenies predictions
    Genomic features are not sporadically distributed
    Gene and host phylogenies are congruent
    Gene phylogenies are congruent
    The species should form an evolutionary tree

    *Evolutionary pathways predictions
    Complex structures evolved from simpler structures
    Structures do not evolve before there is a need for them
    Functionally unconstrained DNA is not conserved
    Nature does not make leaps

    *Behavior
    Altruism
    Cell death

    *Conclusions
    What false predictions tell us about evolution
    https://sites.google.com/site/darwinspredictions/home

    Why investigate evolution’s false predictions?
    Excerpt: The predictions examined in this paper were selected according to several criteria. They cover a wide spectrum of evolutionary theory and are fundamental to the theory, reflecting major tenets of evolutionary thought. They were widely held by the consensus rather than reflecting one viewpoint of several competing viewpoints. Each prediction was a natural and fundamental expectation of the theory of evolution, and constituted mainstream evolutionary science. Furthermore, the selected predictions are not vague but rather are specific and can be objectively evaluated. They have been tested and evaluated and the outcome is not controversial or in question. And finally the predictions have implications for evolution’s (in)capacity to explain phenomena, as discussed in the conclusions.
    https://sites.google.com/site/darwinspredictions/why-investigate-evolution-s-false-predictions

    The strength of a theory in science is in its predictive power. In fact, the predictions of General Relativity and Quantum Mechanics are tested to absurd levels of precision. Darwinian evolution is a joke in terms of its predictive power.

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    – Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003

    As mentioned previously, the reason why Darwinian evolution seemingly floats serenely above experimental reproach is that it has no falsification criteria.

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    Darwinian Evolution is a Unfalsifiable Pseudo-Science – Mathematics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater

    Yet, despite the pseudo-scientific nature of Darwinian evolution, and despite the unwillingness of Darwinists to accept any falsifying evidence against their theory, as far as empirical science itself is concerned, Darwinian evolution is falsified in its most foundational claim. Specifically, Darwinian evolution is empirically falsified in its foundational claim that RM & NS can generate functional complexity.

    Michael Behe – Experimentally Observed (1 in 10^20) Edge of Evolution – video – Lecture delivered in April 2015 at Colorado School of Mines
    25:56 minute quote – “This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not.”
    https://www.youtube.com/watch?v=9svV8wNUqvA

    relevant Feynman quote:

    The Scientific Method – Richard Feynman – video
    Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
    https://www.youtube.com/watch?v=OL6-x0modwY

  69. 69
    tragic mishap says:

    Pretty sure Behe called it “The First Rule of Adaptive Evolution” in his QRB paper.

  70. 70
    bornagain77 says:

    Of related note:

    Common Descent: An Obituary – Lee M. Spetner – June 21, 2016
    Excerpt: Common Descent (CD) has been offered as a scientific theory and must therefore be judged as such. Its status as a scientific theory, however, has never been properly established. Without a theory showing that speciation is reasonably probable in the available time, all the circumstantial evidence proffered for CD by its advocates is for naught, and the evidence of proteins such as vitellogenin (the subject of some discussion here lately) is no more than circumstantial evidence. Circumstantial evidence can support a conclusion only when there is a theory to connect the evidence with the conclusion.

    By the beginning of the twentieth century, Charles Darwin’s suggestion for the variation on which he meant for natural selection to act was rejected because it turned out to be nonheritable. In the first third of the 20th century several replacement suggestions for the variation were offered only to be later rejected. In 1941 a project was launched to establish the theory of evolution on a sound basis by bringing together facts and methods from all branches of science, and a decade later was considered fully established. The modern synthesis (MS) embraced natural selection and took the variation to be mutations and recombinations in the chromosomes, although exactly what these were was not clearly understood at the time.

    The discovery of the structure of the DNA in the mid 20th century was thought to solidify the MS. The random mutations were identified with random changes in the DNA sequence attributed to DNA-copying errors and genetic recombination. The variation was no longer a vague genetic effect that it had been: it was now an understood random process.

    With a known random mechanism now available for the variation on which natural selection could operate, the randomness became subject to mathematical investigation. Mutation rates could be measured and in principle the probability of an evolutionary event could be calculated. For the first time it became possible to check if Darwin’s celebrated mechanism of random variation and natural selection could really account for CD. But the advocates of CD never picked up the challenge to publish any probability calculations. Some who questioned CD, however, did calculate and found the probabilities of speciation under random mutation and natural selection in the available time to be negligibly small and essentially zero. These results were never competently rebutted. The conclusion is inescapable that CD has no theoretical backing, has been refuted, and is not a valid scientific theory.,,,
    http://www.evolutionnews.org/2.....02937.html

  71. 71
    Alicia Cartelli says:

    Bmaque, my “insertion” was that scientists have come up with a partial explanation for how de novo genes arise and a simple pubmed search will get you a few recent articles right at the top of the list, feel free to even go into the references of those papers if you want to learn more.

    So PaV, almost all mutations are deleterious, yet humans have thousands of genetic variations across the population? My point is that most mutations, though they may be slightly deleterious, are not immediately culled by natural selection. They can accumulate and contribute to evolution, like in thalassemia; what is deleterious in one environment, may be beneficial in another.

    “an average size protein cannot be made using random processes.” Good thing no one is claiming this.

    ENCODE’s results are very much up for debate, but I have no doubt that there is a good portion of unknown functionality in the genome. Depending on the perspective you take, organismal vs. evolutionary, you can get different amounts of function in the genome. I’m sure some evolutionary scientists somewhere at some point will even try to make the claim that because the genome is passed on to the next generation, the entire thing represents the potential for evolution and is therefore 100% functional. The scientific community is filled with people with slightly different ideas about each area of research, we feed off of controversy and constantly try to dispute each other, and yet we all seem to agree that evolution explains the diversity of species we see today.

    What will make me “stop believing in Darwin’s theory?”
    Well, first let’s put aside that it isn’t a “belief” and that it’s not even “Darwin’s theory” anymore.
    But what would it take?
    Hmm, let’s say take the number of things we have at least a partial explanation for in evolutionary biology, now take 1% of that, and that’s the number of things that if we had absolutely no explanation for or completely went against everything we know, then I would begin to question evolution.

  72. 72
    bornagain77 says:

    “yet humans have thousands of genetic variations across the population?”

    You fail to distinguish between non-random, i.e. ‘directed’, variation in humans and random mutations in humans. Directed mutations are non-Darwinian since they are not random (and since they still reduce overall information), and truly random mutations are overwhelmingly deleterious

    Duality in the human genome – Nov. 28, 2014
    Excerpt: The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word.
    The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time.,,,
    According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe.
    http://medicalxpress.com/news/.....enome.html

    Human Mutation Clock Half Off – October 20, 2012
    Excerpt: New studies have shown about 36 mutations between generations in Icelandic families. The rates seem to be converging on “1.2 × 10?8 mutations per generation at any given nucleotide site,” or “1 in 2.4 billion mutations per site per year,” which is less than half the previous estimate.
    http://crev.info/2012/10/human.....-half-off/

    Human evolution or extinction – discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) – video
    http://www.youtube.com/watch?v=aC_NyFZG7pM

    “it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained…
    it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection…
    it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements.”
    Hermann Muller quoted by John Sanford; Appendix 1, Genetic Entropy

    Human Genetic Variation Recent, Varies Among Populations – (Nov. 28, 2012)
    Excerpt: Nearly three-quarters of mutations in genes that code for proteins — the workhorses of the cell — occurred within the past 5,000 to 10,000 years,,,
    “One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,”,,,
    “Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older.” (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,,
    The report shows that “recent” events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers.
    The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,,
    http://www.sciencedaily.com/re.....132259.htm

    Also of note:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    http://www.worldscientific.com.....08728_0006

  73. 73
    PaV says:

    Bob O’H:

    Pav @ 58 – I see you are still punting on whether gene duplication is more prevalent than gene loss. You’re also still punting on the proof that de novo genes can’t arise.

    In the article I cited, they downplay the role of gene duplication. I think that’s a good idea.

    As to “de novo” genes arising, the more critical question is how do “novel” genes arise, those that cannot be connected to other known sequences. How do you explain it, Bob?

    Incidentally, I can’t use the information argument because I’ve never seen a definition of information from IDists that makes sense biologically. I’d rather not go round the “calculate the information for the flagellum” carousel again.

    Who’s punting here, actually? Entropy is connected to information. All of science accepts this. Entropy is all about degrees of freedom. And, any nucleotide sequence has 4 degrees of freedom at each site. Do the math. It’s quite straightforward and easy.

    But, of course, if someone chooses to be willfully ignorant, no one can help them “see.”

    Oh, one thing:

    PaV:
    So, when you find function for this putative “pseudogenes,” then it looks like you didn’t properly understand what you were looking at.

    I agree – that’s the wonderful thing about science, we often don’t understand what we’re looking at, so we figure it out.

    And, as EugeneS has already pointed out, when you “figure it out,” you should be willing to live with the consequences. But, no, the ‘Darwinian narrative’ must conquer all. So, it’s not falsifiable. Therefore, it is no longer a scientific theory, or even a postulate.

  74. 74
    Dr JDD says:

    rvb8 @55:

    “living things like to reproduce, in many instances they even find the act fun. Having reproduced they next want to live. If the inherited traits of one living thing give it an advantage over another living thing, then that living thing will be more successful at sex”

    So why did sexual reproduction even evolve? What advantage does it offer? What advantage does needing 2 separate individuals to have sexual relations actually bring to the table? If evolution is about survival and most likely to reproduce then it should have stopped at bacteria. They are far better at it than any multicellular organism. Plus they can do it in all sorts of environments – hot, cold, high salt, low salt, oxide, anoxic….

  75. 75
    bill cole says:

    Bob O’H

    bill cole @46 – Is your phone number a de novo gene? I suspect not.

    Both a phone number and a gene are sequences. The english language is also a sequence. This is why Richard Dawkins used a line of Shakespeare to simulate a protein search. By trying to visualize how difficult this is you will better understand the arguments that you are dealing with.

  76. 76
    wd400 says:

    JDD,

    Good quesiotn. I’d start with Sally Otto’s article here

    Pav

    In the article I cited, they downplay the role of gene duplication. I think that’s a good idea.

    Where? They mention more focus has been placed on duplication that loss, but that’s all. There is also quite a lot of discussion about the importance of duplication for gene loss (i.e. ancestral duplication followed by differential loss of daughter genes).

  77. 77
    Andre says:

    Wow so information is gained by losing it according to the Darwinists commenting here. Are we seriously entertaining this nonsense?

  78. 78
    Alicia Cartelli says:

    “In the article I cited, they downplay the role of gene duplication.”
    If they really did do that, it shouldn’t surprise you, unless you have no experience in research, PaV.
    Of course the researchers are going to make their work sound like the best thing since sliced bread while downplaying everyone else’s work. That’s what most research groups do, only to different degrees.
    This site posts all the time about the current state of research, and for once you guys are actually right: it is, in part, a business.

  79. 79
    Andre says:

    Some people take it very personal when their world view is challenged.

  80. 80
    Bob O'H says:

    PaV @ 73 –

    In the article I cited, they downplay the role of gene duplication. I think that’s a good idea.

    Actually, they barely mention it, and make no comment on the relative importances. My guess is that they were asked to write a review about gene loss, and either decided comparing gene loss and gain would be too much, or had written something and were asked to take it out (to save space or not make the paper unwieldy).

    As to “de novo” genes arising, the more critical question is how do “novel” genes arise, those that cannot be connected to other known sequences. How do you explain it, Bob?

    By googling. And finding two papers that discuss just this. There are probably more too: these were from the first page of results.

    Who’s punting here, actually? Entropy is connected to information. All of science accepts this. Entropy is all about degrees of freedom. And, any nucleotide sequence has 4 degrees of freedom at each site. Do the math. It’s quite straightforward and easy.

    Yes, I can count too. But so what? How does this relate to evolution, other than saying there is a very large genotype space? This is the problem I have – you can calculate these numbers, but I haven’t seen anything which suggests they’re meaningful with respect to evolution.

  81. 81
    Bob O'H says:

    bill cole – lots of things are sequences. But they can be produced in lots of different ways. Frankly, I have difficulty seeing how phone numbers mate and recombine, especially when within a longer string of sequences.

  82. 82
    J-Mac says:

    “The war is over. We won!”
    Whoever wrote this is very naive…

    One example comes to my mind when Jesus performed a miracle and yet the Jewish scribes while acknowledging his miracle they were still seeking to kill him… Why?

  83. 83
    bill cole says:

    Bob O’H

    lots of things are sequences. But they can be produced in lots of different ways. Frankly, I have difficulty seeing how phone numbers mate and recombine, especially when within a longer string of sequences.

    How are sequences like phone numbers and languages produced? What happens if they are changed randomly?

  84. 84
    Mung says:

    Bob O’H:

    lots of things are sequences. But they can be produced in lots of different ways. Frankly, I have difficulty seeing how phone numbers mate and recombine, especially when within a longer string of sequences.

    Ah, the old “I cannot imagine” defense. I could write a program in which phone numbers mate and recombine. Incredulity is not an explanation.

  85. 85
    Mung says:

    Alicia Cartelli:

    Of course the researchers are going to make their work sound like the best thing since sliced bread while downplaying everyone else’s work. That’s what most research groups do, only to different degrees.

    Alicia’s posts are the best thing since sliced bread. Or at least they sound that way.

  86. 86
    HeKS says:

    Dr JDD @74

    So why did sexual reproduction even evolve? What advantage does it offer? What advantage does needing 2 separate individuals to have sexual relations actually bring to the table? If evolution is about survival and most likely to reproduce then it should have stopped at bacteria. They are far better at it than any multicellular organism. Plus they can do it in all sorts of environments – hot, cold, high salt, low salt, oxide, anoxic….

    The belief is that sexual reproduction offers a chance at genetic diversity that is not offered by asexual reproduction, thereby giving the offspring of sexual reproduction a better chance at dealing with disease and potentially harmful microorganisms.

    That said, your point is completely valid. What we regularly see with evolutionary explanations for the arrival of some feature of biology is a description of some benefit it confers. The problem is that these sorts of explanations are blatantly teleological: Feature A evolved because it conferred advantage X. This might explain why a feature ended up being retained by natural selection after it arose, but it doesn’t explain why the complex feature arose in the first place, unless we want to assign intelligence to evolution (as has been recently suggested).

    However, with regard to sexual reproduction, as you noted, it is far less efficient than asexual reproduction, so whatever advantages it confers, it carries some very significant evolutionary disadvantages as well. It offers an evolutionary advantage with respect to one set of considerations (genetic diversity), but an evolutionary disadvantage with respect to another set of considerations (reproductive success and larger populations). One wonders why the advantages should have outweighed the disadvantages in this case, since reproductive success is supposed to be the primary measure of fitness and main predictor of what traits will be passed on and fixed, while drastically reduced reproductive success and population sizes significantly decreases the potential for ongoing evolution in populations that rely on sexual reproduction. Meanwhile, asexually reproducing organisms may be more susceptible to disease and microorganisms, but they typically deal with these problems simply by having very large population sizes, and they are doing quite well to this day.

    So, in short, the reasons given for why sexual reproduction has hung around are dubious at best, considering reproductive success is supposed to be primary measure of fitness, but these reasons do nothing to explain why or how it actually arose in the first place.

  87. 87
    Arthur Hunt says:

    Hmmm…

    If gene duplication doesn’t add information, then the duplicates have no information. But if a duplicate is lost, then information is lost.

    That’s some sort of funny math there.

  88. 88
    rvb8 says:

    You are correct HeKS, asexual reproduction is far more successful than sexual reproduction. That is why some plants, and some fungi, and all archaebacteria, eubacteria, and protists are far more abundent and therefore evolutionarily successful than us.

    It seems that everyone here is hell bent on asking, ‘then why are we here, why are we so special?’ If this is your question, then it sadly fails to understand Darwinian Evolution. We reproduce sexually because we inherited this method from ancient ancestors. The ligitimate question of why we went down this evolutionarily less efficient method, is what science is trying to answer. I have no idea what an ID question looks like, therefore ID also has zero answers.

    Bacteria reproduce asexually, they were probably the first life, they have existed for billions of years, and it is absolutely certain that when we dissapear, or destroy the planet, they will still be happily chugging along, and definately producing random gene errors that will possibly lead to the next sentient beings.

  89. 89
    PaV says:

    Please type out your comment below.

    Bob O’H:

    PaV:
    In the article I cited, they downplay the role of gene duplication. I think that’s a good idea.

    Actually, they barely mention it, and make no comment on the relative importances. My guess is that they were asked to write a review about gene loss, and either decided comparing gene loss and gain would be too much, or had written something and were asked to take it out (to save space or not make the paper unwieldy).

    If you read interviews of the authors, they seem to be very excited to have found a new way of looking at evolution, one driven by ‘gene loss.’

    PaV:
    As to “de novo” genes arising, the more critical question is how do “novel” genes arise, those that cannot be connected to other known sequences. How do you explain it, Bob?

    By googling. And finding two papers that discuss just this. There are probably more too: these were from the first page of results.

    But, Bob, those are about “de novo” genes, not “novel” genes, per se. “Novel” genes are a subset of “de novo” genes, and they don’t match up to annotated genes; hence, their entire, sizable length have to be explained. Any ideas?

    Pav:
    Who’s punting here, actually? Entropy is connected to information. All of science accepts this. Entropy is all about degrees of freedom. And, any nucleotide sequence has 4 degrees of freedom at each site. Do the math. It’s quite straightforward and easy.

    Bob O’H:
    Yes, I can count too. But so what? How does this relate to evolution, other than saying there is a very large genotype space? This is the problem I have – you can calculate these numbers, but I haven’t seen anything which suggests they’re meaningful with respect to evolution.

    Isn’t the real “problem” that you’re accepting the “theory” of evolution as a “fact”? IOW, you say that when we look at organisms, their genomes are different, so we know that the ‘long odds’ against this happening are overcome. And, then, you attribute this to a purely materialistic mechanism. But that’s an assumption.

    The only known “mechanism” of overcoming huge odds that we know of is the use of intelligence. That’s a big part of what Stephen Meyer argues in “Darwin’s Dilemna.”

    You can’t use what you assume to prove that which is in dispute.

  90. 90
    PaV says:

    Arthur, this is from memory, and I only had the first two pages to look at:

    I believe their argument was that gene duplication allowed for that gene to lose part of its function. Then, when the original gene lost its promoter region function through a mutation within that region, then the new phenotype emerged.

    So, it’s gene duplication at the service of ‘gene loss.’ No information is added, and then some is lost. And, overall, speciation occurs when this happens. Who would have thought? (Hope you’re paying attention wd400)

  91. 91
    Bob O'H says:

    PaV – wrt novel genes, once more google is your friend. Again, first page of results.

    You’re still punting the problem of gene loss/gain, so I guess we’re done there. And I still haven’t seen any maths from you about overcoming long odds, so I guess we’re done there too.

  92. 92
    Origenes says:

    Dr.JDD: If evolution is about survival and most likely to reproduce then it should have stopped at bacteria.

    HeKS: It [sexual reproduction] offers an evolutionary advantage with respect to one set of considerations (genetic diversity) ….

    The ‘genetic diversity’ argument doesn’t work wrt bacteria:
    Andreas Wagner:

    In another difference from sex as we know it, gene transfer occurs not just between similar organisms but also between baker’s yeast and fruit flies, between microbes and plants, and especially among bacteria, which can be as different from one another as humans are from oak trees.20 This is why gene transfer is so powerful, and the most important reason why bacteria are masters of metabolic innovation.

  93. 93
    bornagain77 says:

    Besides the obvious problem for Darwinian theory that sexual reproduction is far less efficient than asexual reproduction, there is also the burning question, on the Darwinian perspective of ‘survival of the fittest’, of why bacteria don’t eat us.

    If evolution by natural selection were actually the truth about how all life came to be on Earth then the only ‘life’ that should be around would be extremely small organisms with the highest replication rate, and with the most ‘mutational firepower’, since only they, since they greatly outclass multi-cellular organism in terms of ‘reproductive success’ and ‘mutational firepower’, would be fittest to survive in the dog eat dog world where blind pitiless evolution ruled and only the fittest are allowed to survive. The logic of this is nicely summed up here in this Richard Dawkins video::

    Richard Dawkins interview with a ‘Darwinian’ physician goes off track – video
    Excerpt: “I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly — a few hours sometimes, they can reproduce themselves — that they can evolve very, very quickly. And we’re stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?”
    http://www.evolutionnews.org/2.....62031.html

    In other words, since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but efficient reproduction be realistically ‘selected’ for? Any other function besides efficient reproduction, such as much slower sexual reproduction, sight, hearing, thinking, etc.., would be highly superfluous to the primary criteria of efficient reproduction, and should, on a Darwinian view, be discarded, and/or ‘eaten’, by bacteria, as so much excess baggage since it would slow down efficient reproduction.

    Humorously, the real world example that Dawkins gave to Dembski, (in Dembski’s critique of the hidden teleology within Dawkin’s “WEASEL” program), illustrates exactly this point, i.e. the point that natural selection can only ‘see’ efficient reproduction and will ‘discard’ any excess baggage:

    “Perhaps you should look at the work of Spiegelman and others on evolution of RNA molecules in an RNA replicase environment. They have found that, repeatedly, if you ‘seed’ such a solution with an RNA molecule, it will converge on a particular size and form of ‘optimal’ replicator, sometimes called Spiegelman’s minivariant.”
    Richard Dawkins to William Dembski
    http://www.evolutionnews.org/2.....63671.html

    Yet when we look at ‘Spiegelman’s minivariant’ we find:

    Spiegelman Monster is the name given to an RNA chain of only 218 nucleotides that is able to be reproduced by an RNA replication enzyme. It is named after its creator, Sol Spiegelman, of the University of Illinois at Urbana-Champaign.
    Spiegelman introduced RNA from a simple bacteriophage Q? (Q?) into a solution which contained Q?’s RNA replication enzyme, some free nucleotides, and some salts. In this environment, the RNA started to replicate. After a while, Spiegelman took some RNA and moved it to another tube with fresh solution. This process was repeated.
    Shorter RNA chains were able to replicate faster, so the RNA became shorter and shorter as selection favored speed. After 74 generations, the original strand with 4,500 nucleotide bases ended up as a dwarf genome with only 218 bases. Such a short RNA had been able to replicate very quickly in these unnatural circumstances.
    In 1997, Eigen and Oehlenschlager showed that the Spiegelman monster eventually becomes even shorter, containing only 48 or 54 nucleotides, which are simply the binding sites for the reproducing enzyme RNA replicase.
    http://www.revolvy.com/main/in.....%20Monster

    In a classic experiment, Spiegelman in 1967 showed what happens to a molecular replicating system in a test tube, without any cellular organization around it. … these initial templates did not stay the same; they were not accurately copied. They got shorter and shorter until they reached the minimal size compatible with the sequence retaining self-copying properties. And as they got shorter, the copying process went faster.
    – Stephen Meyer – The Nature of Nature: Examining the Role of Naturalism in Science (Wilmington, DE: ISI Books, 2011), p. 313–18.

    Needless to say, Dawkins real world example of ‘Spiegelman’s minivariant’, i.e. loss of information to gain a reproductive advantage, to support his WEASEL program to Dembski is NOT what Dawkins needed to prove his point. But in actuality Dawkins’ real world example proved Dembski’s ‘hidden teleology’ critique of Dawkins’ WEASEL to be right on the mark and also shows that ‘survival of the fittest’ is primarily concerned with efficient reproduction and nothing else.

    Moreover, contrary to this central ‘survival of the fittest’ assumption of Darwinian evolution, instead of eating us, time after time we find micro-organisms helping each other, and us, in ways that have nothing to with their own ‘survival of the fittest’’ concerns. The following researchers said they were ‘banging our heads against the wall’ by the contradictory findings to Darwinian theory that they had found:

    Doubting Darwin: Algae Findings Surprise Scientists – April 28, 2014
    Excerpt: One of Charles Darwin’s hypotheses posits that closely related species will compete for food and other resources more strongly with one another than with distant relatives, because they occupy similar ecological niches. Most biologists long have accepted this to be true.
    Thus, three researchers were more than a little shaken to find that their experiments on fresh water green algae failed to support Darwin’s theory — at least in one case.
    “It was completely unexpected,” says Bradley Cardinale, associate professor in the University of Michigan’s school of natural resources & environment. “When we saw the results, we said ‘this can’t be.”‘ We sat there banging our heads against the wall. Darwin’s hypothesis has been with us for so long, how can it not be right?”
    The researchers ,,,— were so uncomfortable with their results that they spent the next several months trying to disprove their own work. But the research held up.,,,
    The scientists did not set out to disprove Darwin, but, in fact, to learn more about the genetic and ecological uniqueness of fresh water green algae so they could provide conservationists with useful data for decision-making. “We went into it assuming Darwin to be right, and expecting to come up with some real numbers for conservationists,” Cardinale says. “When we started coming up with numbers that showed he wasn’t right, we were completely baffled.”,,,
    Darwin “was obsessed with competition,” Cardinale says. “He assumed the whole world was composed of species competing with each other, but we found that one-third of the species of algae we studied actually like each other. They don’t grow as well unless you put them with another species. It may be that nature has a heck of a lot more mutualisms than we ever expected.
    “,,, Maybe Darwin’s presumption that the world may be dominated by competition is wrong.”
    http://www.livescience.com/452.....f-bts.html

    Moreover, instead of eating us, as would be expected an a Darwinian view, time after time different types of microbial life are found to be helping us in essential ways,,,

    NIH Human Microbiome Project defines normal bacterial makeup of the body – June 13, 2012
    Excerpt: Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival.
    http://www.nih.gov/news/health.....gri-13.htm

    We are living in a bacterial world, and it’s impacting us more than previously thought – February 15, 2013
    Excerpt: We often associate bacteria with disease-causing “germs” or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them.,,,
    I am,, convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens.”
    http://phys.org/news/2013-02-b.....tml#ajTabs

    “Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides.”
    – Paul G. Falkowski – Professor Geological Sciences – Rutgers

  94. 94
    bornagain77 says:

    Moreover, there is very good reason to believe that pathogens were benign for most of their history and only recently became pathogenic

    From friend to foe: How benign bacteria evolve to virulent pathogens, December 12, 2013
    Excerpt: “Bacteria can evolve rapidly to adapt to environmental change. When the “environment” is the immune response of an infected host, this evolution can turn harmless bacteria into life-threatening pathogens. …It is thought that many strains of E. coli that cause disease in humans evolved from commensal strains.”
    http://medicalxpress.com/news/.....volve.html

    Setting a Molecular Clock for Malaria Parasites – July 8, 2010
    Excerpt: The ancestors of humans acquired the parasite 2.5 million years ago.
    “Malaria parasites undoubtedly were relatively benign for most of that history (in humans), becoming a major disease only after the origins of agriculture and dense human populations,” said Ricklefs.
    http://www.nsf.gov/news/news_s....._id=117259

    “the AIDS virus originated relatively recently, as a mutation from SIV, the simian immuno-deficiency virus. According to Wikipedia, this virus was also benign in its original form:.. Unlike HIV-1 and HIV-2 infections in humans, SIV infections in their natural hosts appear in many cases to be non-pathogenic. Extensive studies in sooty mangabeys have established that SIVsmm infection does not cause any disease in these animals, despite high levels of circulating virus.”
    http://www.uncommondescent.com.....ent-448372

    Moreover, contrary to Darwinian thought, there is also good reason to believe that many pathogenic viruses and bacteria are caused by a loss of functional complexity not a gain.
    For instance, a genetic study has shown that bubonic plague (Black Death) was caused by loss of genes and streamlining (genetic entropy) of a non-pathogenic bacteria:

    The independent evolution of harmful organisms from one bacterial family – April 21, 2014
    Excerpt: “We commonly think bacteria must gain genes to allow them to become pathogens. However, we now know that the loss of genes and the streamlining of the pathogen’s metabolic capabilities are key features in the evolution of these disease-causing bacteria,”
    http://phys.org/news/2014-04-p.....erial.html

    Frankly, it is very good that there is a strict limit to what evolution can create, (Behe: 2 protein/protein binding site limit; Edge of Evolution), since it allows us to develop drug treatments that are beyond the capacity of Darwinian processes to overcome:

    Guide of the Perplexed: A Quick Reprise of The Edge of Evolution – Michael Behe – August 20, 2014
    Excerpt: If there were a second drug with the efficacy of chloroquine which had always been administered in combination with it (but worked by a different mechanism), resistance to the combination would be expected to arise with a frequency in the neighborhood of 1 in 10^40 — a medical triumph.
    http://www.evolutionnews.org/2.....89161.html

    The multiple drug cocktail that has been so effective in controlling HIV uses much the same strategy of being beyond the ‘edge of evolution’ that Dr. Behe has elucidated:

    When taking any single drug, it is fairly likely that some mutant virus in the patient might happen to be resistant, survive the onslaught, and spawn a resistant lineage.
    But the probability that the patient hosts a mutant virus that happens to be resistant to several different drugs at the same time is much lower.,,,
    it “costs” a pest or pathogen to be resistant to a pesticide or drug. If you place resistant and non-resistant organisms in head-to-head competition in the absence of the pesticide or drug, the non-resistant organisms generally win.,,,
    This therapy has shown early, promising results — it may not eliminate HIV, but it could keep patients’ virus loads low for a long time, slowing progression of the disease.
    http://evolution.berkeley.edu/.....edicine_04

    And it is also very good that genetic entropy is true. Sanford has shown that the destructive effects of pathogens on humans are fairly quickly are modulated by information loss.

    Evolution and the Ebola Virus: Pacing a Small Cage – Michael Behe – October 24, 2014
    Excerpt: The high rate of mutation of Ebola is similar to what John Sanford has demonstrated for the H1N1 virus that caused the influenza pandemic after World War I. He makes a compelling case that the accumulating mutations there were degradatory could not be eliminated easily by selection, and eventually caused the virus’s extinction in 2009.
    http://www.evolutionnews.org/2.....90621.html

    Biological Information – Positive Genetic Entropy (Mutational Meltdown, i.e. extinction, of pathogenic viruses over relatively short times) 2-7-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=W17lVqYQzq4&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ&index=15

  95. 95
    Bob O'H says:

    ba77 @93 –

    Besides the obvious problem for Darwinian theory that sexual reproduction is far less efficient than asexual reproduction, there is also the burning question, on the Darwinian perspective of ‘survival of the fittest’, of why bacteria don’t eat us.

    But they do. Well, a few do.

  96. 96
    bornagain77 says:

    ‘But they do. Well, a few do.’

    Take your dogma glasses off so you can read for comprehension for goodness sake. That concern was addressed.

  97. 97

    We no longer say: “Another day; another bad day for Darwinism.” We now say: “Another day since the time Darwinism was disproved.” Love it!!!!

  98. 98

    Bornagain77: Can’t thank you enough for all of your comments, not just in this thread but in all threads on this site. Great work!

  99. 99
    bornagain77 says:

    TWSYF, can’t really take credit for it. I shamelessly steal from others on UD and use their insights! 🙂

  100. 100
    HeKS says:

    rvb8 @88

    You are correct HeKS, asexual reproduction is far more successful than sexual reproduction. That is why some plants, and some fungi, and all archaebacteria, eubacteria, and protists are far more abundent and therefore evolutionarily successful than us.

    It seems that everyone here is hell bent on asking, ‘then why are we here, why are we so special?’ If this is your question, then it sadly fails to understand Darwinian Evolution.

    Did you actually see me say anything like that? No, you didn’t. In fact, you have sadly failed to understand my point.

    My point is actually the opposite of what you’ve suggested. My point is that because Darwinian evolution is held to be a purposeless process lacking in any goals, evolutionary explanations for why some biological feature evolved are typically empty and misleading, because there is no reason that any biological feature evolved. There are only possible reasons why already evolved, functional features might be selected for.

    The thing is, in my experience, most casual believers in evolution ultimately think of evolution as a purposeful process. They think this because 1) they are constantly given teleological explanations for why biological features evolved (e.g. Feature A evolved because it has benefit X), and 2) their common sense tells them that ‘just because’ is an insufficient explanation for how a complex system could have arisen and been in a position to be selected for in the first place.

    These kinds of teleological explanations are common among science popularizers as well. For example, Bill Nye, in his debate with Ken Ham a couple years ago, talked about this very issue of the evolution of sexual reproduction. He started off by saying how it initially made no sense to scientists, because it was so inefficient when compared to asexual reproduction (there’s a joke in there somewhere), but then they realized that it offered the chance at greater genetic diversity and could help in coping with disease. Because of this potential benefit, Bill Nye then said that sexual reproduction was a fulfilled prediction of evolution.

    Of course, Nye clearly didn’t mean that sexual reproduction is a prediction of evolutionary theory in any specific sense. What Nye was saying was simply that evolution predicts that advantageous things will evolve. But this isn’t true. Evolution doesn’t predict that advantageous things will evolve. It predicts that, assuming all other things are equal, already evolved features will be selected if they are advantageous with respect to increased survival and reproduction. Explanations for the selection of features are not the same thing as explanations for the evolution of those features in the first place.

    Teleological explanations for the evolution of biological features are a blatant cheat, but they are used because they help sell the plausibility of evolutionary theory to the public. Noting that some feature confers a particular benefit is a perfectly reasonable explanation for why something would have been designed. It is not a reasonable explanation for why it would have been initially produced by a purposeless process that didn’t have the benefit in view or the feature as a goal.

    We reproduce sexually because we inherited this method from ancient ancestors. The ligitimate question of why we went down this evolutionarily less efficient method, is what science is trying to answer. I have no idea what an ID question looks like, therefore ID also has zero answers.

    Um, an ID question would be identical, but would not simply assume that the feature exists in humans solely because it was inherited from some ancient ancestor and served no particular purpose in humans themselves. ID would also offer teleological answers that are not strictly confined to issues of reproductive fitness. And teleological answers under ID could actually serve as legitimate explanations for why some feature might have been designed and implemented, rather than simply selected for after it has managed to arrive on the scene through a series of happy accidents.

  101. 101
    Dr JDD says:

    This statement from rvb8 sums up the whole debate nicely:

    “It seems that everyone here is hell bent on asking, ‘then why are we here, why are we so special?’ If this is your question, then it sadly fails to understand Darwinian Evolution. We reproduce sexually because we inherited this method from ancient ancestors. The ligitimate question of why we went down this evolutionarily less efficient method, is what science is trying to answer.”

    In other words, Darwinian evolution has become truly an unquestionable religion. It has come to the point of being able to substitute the word “God” for evolution and it would not read any differently.

    Of course if we are good scientists we must question why something happens. Any scientific theory must hold up to all challenges. So if we cannot explain humans through RM&NS then those mechanisms are falsified for our existence and the whole theory fails.

    Yet we are told we reproduce sexually because we had ancestors who did. It’s all an a priori assumption. Do not dare question the sacred evolutionary tale! Prove how our ancestors developed sexual reproduction and prove we actually could arise through chance from those ancestors. I was never asking why humans reproduce sexually, I was asking why any organism came about from an asexual ancestor through accident to reproduce sexually, it makes no sense by the definition of what evolution is about.

  102. 102
    PaV says:

    Bob O’H:

    PaV – wrt novel genes, once more google is your friend. Again, first page of results.

    Couple of problems, Bob: first, what they consider to be “novel” genes, are really “de novo” genes. Second, which confirms the first point, here’s what they say:

    In Table 1 is summarized the information on a sample of novel genes that reveals a picture of the events involved in their origin and their function. The sample is limited to genes that originated less than 50 million years ago to avoid confounding events of origination with effects of later evolution;. . .

    So, what has really “evolved” since 50 million years ago? Not much, and mostly mammals. And they study flies mostly.

    Sorry, this doesn’t help your cause.

    You’re still punting the problem of gene loss/gain, so I guess we’re done there. And I still haven’t seen any maths from you about overcoming long odds, so I guess we’re done there too.

    Duplicating a gene is not a gene “gain.” They have genomic sequence data that demonstrates–not just theorizes–that what differentiates species is the “loss” of genes. You’ll just have to learn to live with it.

    As to the maths, it is you who must provide the recipe for overcoming long odds, not me. I still await.

    To simply grandstand and say “evolution” happened, and therefore long odds were overcome, is to simply put the cart before the horse. This is convincing to no one.

  103. 103
    Bob O'H says:

    PaV – you’re clearly not using “de novo” and “novel” in the way they are used in the literature to describe genes, so can you explain what you mean by these terms please.

  104. 104
    PaV says:

    Bob:

    I’m now wondering if there is equivocation going on within the literature itself.

    In the article I’ve cited, “novel” means that there is no connection to annotated sequences. To me this means that the gene is entirely new. It the paper you cited, the two terms seemed to be used in the opposite sense.

    So, to me, I’m using “novel” to mean that it is a gene that has no connection to already known, and annotated, sequences, and so cannot represent a product of duplication and degradation, or inversion.

  105. 105
    PaV says:

    Bob:

    Let me add that the way “de novo” is used in the literature amounts to equivocation. “De novo” means, more or less, something that is utterly new. When you have a piece from here, and a backwards piece from over there, that’s not “de novo.”

    It only helps to obfuscate things.

    Here, for example, is the very first sentence of an abstract from April of last year:

    The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages.

    This sloppiness is unfortunately not uncommon in evolutionary literature.

  106. 106
    bornagain77 says:

    Of related note to ORFan genes.

    Alternative splicing is very different between species. Even very different between chimps and humans:

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013
    Excerpt: Although humans and chimpanzees share,, similar genomes, previous studies have shown that the species evolved major differences in mRNA (messenger RNA) expression levels.,,,
    http://www.sciencedaily.com/re.....144632.htm

    ,,,Alternative splicing,,, may contribute to species differences – December 21, 2012
    Excerpt: After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns—which determine the segments of those genes included or excluded—vary from species to species.,,,
    The results from the alternative splicing pattern comparison were very different. Instead of clustering by tissue, the patterns clustered mostly by species. “Different tissues from the cow look more like the other cow tissues, in terms of splicing, than they do like the corresponding tissue in mouse or rat or rhesus,” Burge says. Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says,,,
    Excerpt of Abstract: To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified;
    http://phys.org/news/2012-12-e.....wires.html

    Moreover, alternative splicing allows for the same gene to code for multiple different protein products:

    Time to Redefine the Concept of a Gene? – 2012
    Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins!
    While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25.
    http://networkedblogs.com/BYdo8

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].
    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.
    http://www.worldscientific.com.....08728_0006

    Moreover, “Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes.”

    Frequent Alternative Splicing of Human Genes – 1999
    Excerpt: Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes.
    http://www.ncbi.nlm.nih.gov/pm.....PMC310997/

    Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing – 2016
    In Brief
    Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,
    Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013).
    http://iakouchevalab.ucsd.edu/.....M_2016.pdf

    Thus, since alternative splicing is very different between different species, even very different between chimps and humans, and since alternative splicing produces up to a million polypeptides that appear “as if encoded by distinct genes rather than as minor variants of each other”, then it is very reasonable to conclude that the “ORFan gene problem” is actually far more problematic than Darwinists pretend that it is.

    Supplemental notes:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
    http://www.worldscientific.com.....08728_0006

    Unexpected features of the dark proteome – Oct. 2015
    We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ~14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.
    http://www.pnas.org/content/ea.....1508380112

  107. 107
    PaV says:

    Alternative splicing is a very big part of what we’re discussing here, and yet it doesn’t seem to factor into the notion of “de novo” gene.

    Thanks for the citations.

  108. 108
    MatSpirit says:

    Has anybody read vjtorley’s June 6th “Consider the opossum: the evidence for common descent” thread? Apparently all of us mammals have lost our genes for making egg yolks. Are we thus doomed?

  109. 109
    harry says:

    Hello, bornagain77,

    Thank you for your posts. You routinely expose the mere sophistry at the core of the doctrines promulgated by the apostles of the Church of Darwin and demonstrate that what has been masquerading as science for so long is in actuality only irrational, blind-faith-based atheism.

  110. 110
    rvb8 says:

    HeKS, “The thing is, in my experience, most casual believers in evolution ultimately think of evolution as a purposeful process.”

    No! “You couldn’t be more wrong”, if you tried. Firstly we don’t “believe” in evolution, we accept it, for the robust science it is. Secondly, how do you ‘casually’ believe something, I don’t even ‘casually’ accept evolution, I rigorously accept it. Finally ‘teleology’ is a strictly religious dogma, it has no place in, inferred from the evidence, or observational science.

    The whole of this post by HeKS which slurs science with religious sentamentalism is quite outrageous. We do not accept the supernatural because we can’t test for that. We do not accept a hiarchy of life because there is no evidence change has stopped, and we don’t know what will come next. We do make predictions (Tiktalik etc) and we do observe and test.

    For years I have been reading this site, since your Waterloo, and I have yet to hear of any science comming out of Anne Gauger’s lab. Please stop insulting scientists with teleological motives, they don’t have them, that’s your sphere.

    Heh:) You mentioed Ken Ham on a ‘science’ web site, good luck with that referrance to science:)

  111. 111
    Querius says:

    Yes, thank you bornagain77. You post a lot of great links.

    Incidentally, I made my “Darwexit” in college as a result of studying biochemical reactions.

    -Q

  112. 112
    HeKS says:

    rvb8,

    Do you actually read what people say or are you just a troll?

    Yes, I mentioned Ken Ham’s name to give you context for where Bill Nye made the comments I was referring to. What’s your point? I wasn’t citing Ham for anything and wouldn’t, since I’m not a YEC.

    As for teleology, there is nothing inherently religious in the word. You don’t seem to have the slightest clue what you’re talking about.

    tel·e·ol·o·gy

    noun PHILOSOPHY

    the explanation of phenomena by the purpose they serve rather than by postulated causes.

    People regularly offer teleological explanations for why things evolved, which is a practice that is in fundamental conflict with evolutionary theory. What don’t you understand about this?

    And what is a ‘casual believer’ in evolution? Someone who accepts it because they’ve been told it’s true but has never actually bothered to understand the theory, the evidence that is cited in its favor, or the evidence that is cited against it. Most people have a very poor understanding of any and all parts of the theory. They believe it because they were told it was true in school and they never really cared to question that one way or the other.

    Your comment is full of bluster and even more nonsense. You didn’t bother to seriously address any of the things I actually said, so why are you bothering to direct comments to me? Go troll someone else.

  113. 113
    Bob O'H says:

    PaV – I don’t think it’s equivocation, more that most geneticists use ‘de novo‘ and ‘novel’ in different ways to the way you are using them. But if you want references to the way novel genes (in your terminology) come about, read the papers I linked to @80.

    FWIW, the paper (I assume you mean the one cited in the OP) doesn’t use de novo to reference gene origin, and the only relevant use of ‘novel’ is in a sentence about “novel ‘patchy’ orthologues that reveal previously hidden origins of ancestral gene families”, so clearly it doesn’t mean ” that there is no connection to annotated sequences”.

    For me, a ‘novel’ gene would (probably) mean one with a novel function. But YMMV, depending on context.

  114. 114
    bornagain77 says:

    as yo:

    “Please stop insulting scientists with teleological motives, they don’t have them, that’s your sphere.”

    UMM no, they do have them regardless of whether they admit to them or not

    Design Thinking Is Hardwired in the Human Brain. How Come? – October 17, 2012
    Excerpt: “Even Professional Scientists Are Compelled to See Purpose in Nature, Psychologists Find.” The article describes a test by Boston University’s psychology department, in which researchers found that “despite years of scientific training, even professional chemists, geologists, and physicists from major universities such as Harvard, MIT, and Yale cannot escape a deep-seated belief that natural phenomena exist for a purpose” ,,,
    Most interesting, though, are the questions begged by this research. One is whether it is even possible to purge teleology from explanation.
    http://www.evolutionnews.org/2.....65381.html

    Of related note:

    The ‘Mental Cell’: Let’s Loosen Up Biological Thinking! – Stephen L. Talbott – September 9, 2014
    Excerpt: Many biologists are content to dismiss the problem with hand-waving: “When we wield the language of agency, we are speaking metaphorically, and we could just as well, if less conveniently, abandon the metaphors”.
    Yet no scientist or philosopher has shown how this shift of language could be effected. And the fact of the matter is just obvious: the biologist who is not investigating how the organism achieves something in a well-directed way is not yet doing biology, as opposed to physics or chemistry. Is this in turn just hand-waving? Let the reader inclined to think so take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness1.
    One reason this cannot be done is clear enough: molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself.
    http://natureinstitute.org/txt.....ell_23.htm

    The formal Darwinism project – June 2015
    Excerpt: Today, as molecular biologists choose to call some of their discoveries ‘mechanisms’, and ascribe ‘functions’ to enzymes, they use purposive language and so they also adopt the design approach. It is arguably impossible to undertake work in many areas of biology without doing so: purpose in explanations has great power, and attempts to do without it in ethology,,, have long ago been abandoned as unworkable.
    of note: *Ethology is the scientific and objective study of animal behaviour
    https://scientiasalon.wordpress.com/2015/06/15/the-formal-darwinism-project/

    This working biologist agrees:

    Life, Purpose, Mind: Where the Machine Metaphor Fails – Ann Gauger – June 2011
    Excerpt: I’m a working biologist, on bacterial regulation (transcription and translation and protein stability) through signalling molecules, ,,, I can confirm the following points as realities: we lack adequate conceptual categories for what we are seeing in the biological world; with many additional genomes sequenced annually, we have much more data than we know what to do with (and making sense of it has become the current challenge); cells are staggeringly chock full of sophisticated technologies, which are exquisitely integrated; life is not dominated by a single technology, but rather a composite of many; and yet life is more than the sum of its parts; in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology–we simply cannot avoid them.
    Furthermore, I suggest that to maintain that all of biology is solely a product of selection and genetic decay and time requires a metaphysical conviction that isn’t troubled by the evidence. Alternatively, it could be the view of someone who is unfamiliar with the evidence, for one reason or another. But for those who will consider the evidence that is so obvious throughout biology, I suggest it’s high time we moved on. – Matthew
    http://www.evolutionnews.org/2.....nt-8858161

    as well:

    Can Darwinian Evolutionary Theory Be Taken Seriously?
    – Stephen L. Talbott – May 16, 2016
    Excerpt: it would have been hard to find even a slight blush of embarrassment when Stephen Jay Gould, countering the sort of doubt voiced above by his peers, asked, “Why was natural selection compared to a composer by Dobzhansky; to a poet by Simpson; to a sculptor by Mayr; and to, of all people, Mr. Shakespeare by Julian Huxley?” The answer, according to Gould, is that the allusions to poetry, musical composition, and sculpture helpfully underscore the “creativity of natural selection”:,,,

    And so it is possible for leading theorists of evolution to declare an abstract algorithm — natural selection — a capable artist, even though the only place where we observe an actual creative and artistic activity going on is in the organism itself. And even though the explanatory appeal to natural selection simply hides the fact, as we saw above, that the explanation assumes this very same creative activity in the organism. ,,,

    What we do have is a god-like power of natural selection whose miracle-working activity in creating ever-new organisms is vividly clear to eyes of faith, but frustratingly obscure to mere empirical investigators. This is not a science ready for submission to a larger public along with a demand for acquiescence. Not if this public has yet to dull its sensitivity to fundamental questions in the way that the research community seems to have done.
    http://natureinstitute.org/txt.....ogy_30.htm

  115. 115
    Barry Arrington says:

    rvb8 @ 110:

    “We do not accept the supernatural because we can’t test for that.”

    Please describe how one would test the hypothesis that all that exists is natural.

    Doh!

  116. 116
    PaV says:

    Bob O’H:

    It is now common for articles to say that “de novo” genes come from non-coding DNA. This is simply a way of saying that it comes from DNA that is not annotated since translation of the DNA would produce amino acid products that would likely have been annotated by now.

    Having thought over the reality that “de novo” genes seem to come from NC DNA, coupled to the fact that scientists have a hard time wrapping their minds around how these “new” genes can be ‘functional,’ i.e., what happens that allows these new genes to incorporate themselves into the overall functioning of the cell/organism, it strikes me that the best explanation for this–and this comes from an ID perspective which looks at these types of dilemmas as an engineering type problem—would be that these “de novo” genes are simply ‘genes’ that have been stored away for future use; a kind of back-up ‘drive’ for the genome, and so, they have essential markings for insertion into existing cellular machinery, or, that transposons, e.g., provide the added needed machinery.

    The whole idea of “frame shifts,” then, can possibly be viewed as a way of ‘storing’ this information in the DNA in a hidden manner: i.e., another layer of information storage.

    However, if we can, at long last, get back to the seminal paper in this discussion, then if “de novo” genes are nothing but ‘un-hiding’ ‘hidden genes,’ then the “information” is already there, and the machinery of the cell simply ‘finds’ it. But, ‘gene loss’ involves a complete loss of information in many cases, and, we’re told, this leads to speciation.

    What is obvious here is that this is the complete opposite of the Darwinian/neo-Darwinian narrative.

    OTOH, this fits in quite nicely with the ID conception of “front-loading,” a concept that has been talked about for twenty years.

    The war is over: we won!

  117. 117
    Axel says:

    @Alicia #71

    ‘let’s say take the number of things we have at least a partial explanation for in evolutionary biology, now take 1% of that, and that’s the number of things that if we had absolutely no explanation for or completely went against everything we know, then I would begin to question evolution.’

    ‘… at least a partial explanation…’?

    But that is like the children’s game of pinning the tail on the donkey, isn’t it ? Groping about in the dark, blindfolded, looking to establish coherence and intelligibility. You know, it just takes a single false assumption to end up in Bedlam, as the economist J M Keynes put it, in a review of one of Hayek’s ‘oeuvres’.

    However, when each fork in the road can lead closer and closer to the madhouse… it’s really not good – no less in science than in theology or any other discipline.

  118. 118
    PaV says:

    Just as an update, it really shouldn’t be (at least for the time-being) a “we won”; it should be “James Shapiro’s NGE” has won.

  119. 119
    Bob O'H says:

    PaV – yes, getting back to the original paper, how important is gene loss in evolution, as compared to (say) gene gain? I don’t think any evolutionary biologist would object to the idea that genes can be lost. But it could only rarely be important, or (speculatively) the function of the gene could have been taken over by another gene, in which case this doesn’t do much to support your case. So, you’re going to have to do more before declaring victory. After all, you can’t declare victory in a war just because you killed one of the enemy.

    Incidentally, as you’ve brought up front-loading, how does front-loading theory view genetic entropy?

  120. 120
    PaV says:

    Bob O’H:

    Front-loading and genetic entropy are hand-and-glove. Unless there is “front-loading,” the genome cannot afford entropy (loss of information).

  121. 121
    Bob O'H says:

    PaV – but genetic entropy degrades genetic information. So how are front-loaded genes prevented from being degraded?

  122. 122
    PaV says:

    Bob:

    If one is willing to look at things intuitively, one will see that we’re moving in the direction of greater and greater gene processing capacities. wd400 consistently takes the position that everything a cell does, it does because of what is contained in the genome. IOW, it’s all coded in. But the problem with this position, of course, is that there are no intermediates between rocks and bacteria, nor between prokaryotes and eukaryotes. So, then, if all of this functioning is simply part and parcel of what cells do, then how did this process come about? Where did all the DNA genes and RNA genes come from? What gave rise to them?

    There are no answers to these questions. And then there’s the Cambrian explosion.

    This is all ground we’ve covered before; but, it tells me that sooner, rather than later, biology will be forced, little-by-little, the more far-reaching theses of Darwinism. In fact, as we know, this process is now taking place with the MS being reevaluated.

    Intuition, seeing and penetrating the essence of realities more powerfully than simple logic, should suggest, even now, that Darwinism is a failed attempt at explaining biological origins. (Even plain and simple “adaptation” looks to be the work of the inner resources cells possess)

    The handwriting is on the wall, so to speak.

    I can’t help but think of the time I was in a library and opened a reference book on the history of science. The most remarkable revelation was concerning the shift from the Ptolemaic view to that of Copernicus: the so-called “Copernican Revolution.”

    Well, this “revolution” took right around 100 years. You have to admit, that was some kind of ‘slow’ revolution!

    I hope the shift away from Darwinism happens a little bit faster.

  123. 123
    PaV says:

    Bob O’H:

    Front-loaded genes are NOT prevented from becoming degraded. And “speciation” would be the result of this ‘degradation.’ You see why this fits in so well with the paper cited in the OP.

    This view—per Denton, a’one-time’ front-loading brought about completely by the ‘nature’ of the natural order—requires that each of the major “explosions” of forms (including the mammalian explosion) a kind of infusion of information would take place. From there, information decreases, and species increase.

  124. 124
    Bob O'H says:

    PaV – but if front-loaded genes are being degraded, how come they are still functional? Or are only some functional when they are needed?

    I don’t see how you can have it both ways – genes laying around inactive, and genetic entropy happening, but then when these genes are needed, they are fully functional. I assume I’m missing something here, so it might help if you fleshed out your model more fully. Intuition is great, but it’s only a starting point.

    (and having asked you to flesh out your theory, I have to apologise in advance if I don’t reply after this evening – I’m off to Seattle for a conference).

  125. 125
    bill cole says:

    Hi Bob

    PaV – yes, getting back to the original paper, how important is gene loss in evolution, as compared to (say) gene gain? I don’t think any evolutionary biologist would object to the idea that genes can be lost. But it could only rarely be important, or (speculatively) the function of the gene could have been taken over by another gene, in which case this doesn’t do much to support your case.

    I made the cell phone analogy to demonstrate how unlikely adding information to a sequence is. It turns out that an op on our discussion was written at the skeptical zone. Sequences ( phone numbers, the english language, DNA, Proteins) are great for creating diversity but they break down with random change. Evolutionary biologists like Michael Lynch have tried to model adaptions mathematically and the results have been long times and large populations with adaptions requiring only a few changes. This is because the genome is a sequence.

  126. 126
    PaV says:

    Bob:

    Genetic entropy, as it is presented by John Sanford, has more to do with degradation of information in general. That would be the general model. NS would be seen as part of the correction process. Fred Hoyle concluded as much.

    However, the kind of genetic entropy I’m referring to would involve speciation events associated with the continual loss of gene function, and even the loss of genes themselves. But this is more peripheral to the ID perspective. (More on that later.)

    Gene-centric Darwinism, OTOH, would see gradual gene gain.

    Any notion we have of gene loss/gain is glimpsed only through comparison of the whole genome of related organisms. That’s essentially all we have to look at. Per “front-loading” in the “gene-centric” sense, the more basal organism would be the one which has the least amount of loss. That’s about as much as you can say.

    However, the ID perspective has always understood ‘genes’ as simply the building blocks of organisms, with the blueprint of construction being located somewhere else in the genome—what has been, until now, called non-coding DNA, or, even, “junk-DNA,” and representing the much more important and essential part of what an organism is.

    Thus, as techniques for faithful sequencing of the ncDNA improve, and they too become “annotated,” then the blueprint of major taxonomic lineages should emerge as the ncDNA is better understood and begins to be correlated with taxonomic groupings.

    So, when ID talks about “front-loading,” it’s not the traditional notion of the gene, per se, that it has in mind. Take, for example, transposons. These little creatures move about in the cell with their powerful machinery. It is entirely possible that they involve, and then un-involve, various gene products as the organisms adapts to its environment. A recent paper has shown that inbred populations that have adopted to their environment show clusters of transposons that have built up. So, transposons, would be something more central to the ID perspective, with the interesting question becoming: what is directing the movement of these transposons. It’s not the genes they activate that is of interest, but the actual genetic machinery at play: what’s driving all of this.

    Yet, even here, this is something more tangential to the more essential view of ID. Our focus would be on the discovery and understanding of basic embryological developmental programs. These ‘programs’ would involve, very likely, ncDNA. Recent studies, e.g., have shown that “pseudo-genes” are very much involved with the development of the brain; what once was considered “junk-DNA”, or ncDNA, seems to play an important role in developoment and speciation. Will this trend continue?

    Assuming it continues, ID predicts discontinuity of these eventually discovered ncDNA ‘programs’ between major lineages. NS, and mating, would correct the genetic entropy involved in these programs, and so we should find a high degree of conservation. These would be some basic expectations.

    Meanwhile, the importance of gene ‘loss’–what we’ve been discussing here—is that it paints a picture of genomic inheritance showing growth in species via “information” loss.

    The ‘build-up’ of bau-plans for the major lineages then becomes very hard to support, and any discovered discontinuity of these plans would require invocation of some other effective agency.

    To me, that’s where science will likely lead, a kind of ‘end-point.’ And then everyone will be free to understand it any way they like. But, neo-Darwinism will have be shown to have failed as an explanation.

    I’m opposed to Darwnism, not so much because of its anti-religious implications, but because it is simply bad science.

    Based on what I’ve seen so far, and especially within the last few years, I’m certainly ready to write its obituary. Perhaps I already have.

    Have a nice conference. Meanwhile, the work of many scientists in the lab leads us forward.

  127. 127
    bill cole says:

    PaV

    I’m opposed to Darwnism, not so much because of its anti-religious implications, but because it is simply bad science.

    I completely agree with you here. The problem is when this theory unwinds to causes that can be tested, what is left? Do we tell everyone we were just kidding there is no theory of evolution? The gap that has formed between real testable science and public perception is enormous.

  128. 128
    harry says:

    PaV @126

    I’m opposed to Darwnism, not so much because of its anti-religious implications, but because it is simply bad science.

    I once accepted theistic evolution, thinking that God’s perfect providence might have arranged for natural selection acting on predestined variations or mutations could have resulted in life as we find it now.

    But after following the debate for years I ended up where you are: Darwinism is simply bad science.

    And it also became clear to me that the notion that inanimate matter somehow mindlessly and accidentally assembled itself into self-replicating, digital information-based nanotechnology the functional complexity of which is light years beyond our own was simply batsh*t crazy.

  129. 129
    bill cole says:

    Harry

    And it also became clear to me that the notion that inanimate matter somehow mindlessly and accidentally assembled itself into self-replicating, digital information-based nanotechnology the functional complexity of which is light years beyond our own was simply batsh*t crazy.

    Exactly, I would not be surprised if neo darwinian theory goes down in history as the worst scientific idea anyone has ever had.

  130. 130
    Origenes says:

    Harry, Bill

    I once thought that the general state of humanity is one of sanity interrupted by short flashes of delirium. Nowadays I hold the opposite view.

  131. 131
    Evolve says:

    ////the notion that inanimate matter somehow mindlessly and accidentally assembled itself into self-replicating, digital information-based nanotechnology the functional complexity of which is light years beyond our own was simply batsh*t crazy.////

    This statement only shows your ignorance and laziness.
    Inanimate matter did not somehow mindlessly assemble into living things. That happened via distinct processes and our challenge is to understand those processes. Instead, what you and your ilk are doing is to resign from the hard work and attribute everything to an imaginary designer for which absolutely no evidence exists.

    “I don’t understand and I cannot imagine how something came about. Therefore God must have done it.” <<< That's your position. But it doesn't work, I'm sorry.

  132. 132
    bornagain77 says:

    The Origin of Life: An Inside Story – March 2016 Lecture with James Tour
    https://www.youtube.com/watch?v=_zQXgJ-dXM4

    Origin of Life: Professor James Tour – May 1, 2016
    Excerpt: “All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated…
    So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal.
    You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.“
    James Tour – leading Chemist
    http://www.uncommondescent.com.....nt-design/

  133. 133
    Evolve says:

    I’m rolling on the floor laughing seeing Pav’s unilateral declaration of victory. What nonsense is that fellow blurting out?

    Gene gain and gene loss are all part of evolution, that’s neither anything new nor beyond the capability of standard evolutionary processes. He talks about frontloading? Mammals evolved from reptiles, who evolved from amphibians, who in turn evolved from fish, which evolved from invertebrates. And there have been multiple events of gene gain and loss all throughout these transitions. Where exactly is the frontloading?

    His statements on de novo genes are nothing more than shifting goalposts. First he claims de novo genes spring out of nowhere hinting that his imaginary designer introduced them. Then when someone pointed out that de novo genes arise from noncoding DNA, he does the classic creationist trick of shifting goalposts. He then starts claiming de novo genes were “hidden” in the genome waiting for the right moment when the designer felt that they were needed.

    Pav’s designer can have it anyways, he’s ultra-flexible. That’s because the deisgner is not only imaginary for which no evidence exists, but also one whose properties, capabilities, limitations and intentions are all unknown. Therefore creationists can spin any scenario to fit their designer! And no one can question it!

    By the way, here’s a good recent review on de novo genes:
    http://www.cell.com/trends/gen.....0034-7.pdf
    They arise when mutations in non-coding DNA introduce binding sites for transcription factors or remove stop codons or join short protogene products into a larger gene. None of these are beyond already known processes and, as such, does not require invoking a designer for explanation – except for creationists.

  134. 134
    Barry Arrington says:

    Evolve @ 131:

    Inanimate matter did not somehow mindlessly assemble into living things.

    But according to the theory you support, it did exactly that. Why do you feel the need to deny that?

  135. 135
    Evolve says:

    No, I already mentioned above that distinct processes were involved, not aimless, mindless assembling as creationists always claim. If we can figure those processes out, we’ll solve the problem. What’s needed is the resolve and commitment, the hard work and dedication to probe the unknown. The creationist attitude of resigning to the easiest answer will take us nowhere. It’s a dead end.

  136. 136
    bornagain77 says:

    Denying the law of biogenesis, i.e. that life always comes from life, is unscientific and is more of a ‘dead end’ than you can possibly imagine right now:

    1. The Law of Biogenesis
    Spontaneous generation (the emergence of life from nonliving matter) has never been observed. All observations have shown that life comes only from life. This has been observed so consistently it is called the law of biogenesis. The theory of evolution conflicts with this scientific law when claiming that life came from nonliving matter through natural processes.a
    Evolutionary scientists reluctantly accept the law of biogenesis.b However, some say that future studies may show how life could come from lifeless matter, despite virtually impossible odds. Others are aware of just how complex life is and the many failed and foolish attempts to explain how life came from nonlife. They duck the question by claiming that their theory of evolution doesn’t begin until the first life somehow arose. Still others say the first life was created, then evolution occurred. All evolutionists recognize that, based on scientific observations, life comes only from life.

    1 John 5:11-12
    And this is that testimony: God has given us eternal life, and this life is in His Son. Whoever has the Son has life; whoever does not have the Son of God does not have life.

  137. 137
    Mung says:

    If we can just figure out how these teleological processes work we’ll be able to rule out teleology!

  138. 138
    magna charta says:

    BA77:

    Denying the law of biogenesis, i.e. that life always comes from life, is unscientific and is more of a ‘dead end’ than you can possibly imagine right now.

    More accurately, physical annimate life has only ever been observed coming from other physical animate life containing similar genetic material. In that case, both a natural cause of the origin of life and a supernatural cause suffer from the same weakness.

  139. 139
    bill cole says:

    Evolve

    By the way, here’s a good recent review on de novo genes:
    http://www.cell.com/trends/gen…..0034-7.pdf
    They arise when mutations in non-coding DNA introduce binding sites for transcription factors or remove stop codons or join short protogene products into a larger gene. None of these are beyond already known processes and, as such, does not require invoking a designer for explanation – except for creationists.

    Can you show any experimental evidence of the origin of a de novo gene? Mathematically sequences degrade with random change. How much time and how large of a population would it take to get a de novo gene of 5 required mutations?

  140. 140
    bornagain77 says:

    Moreover, stubbornly refusing to accept the blatantly obvious fact that life is designed hampers scientific progress, such as was witnessed in the decades long junk DNA fiasco.

    Whereas, honestly admitting that life is designed leads to scientific innovation.

    Don’t believe me? Well, there is a new burgeoning field of Biomimetics that seeks to imitate the design found in life so as to foster innovation in man-made designs, since the design found in life is often times far, far, better than anything man has ever designed thus far.

    Scientists create circuit board modeled on the human brain – April 28, 2014
    Excerpt: Scientists have developed faster, more energy-efficient microchips based on the human brain — 9,000 times faster and using significantly less power than a typical PC.
    http://www.sciencedaily.com/re.....134051.htm

    Uncovering Quantum Secret in Photosynthesis – June 20, 2013
    Excerpt: Photosynthetic organisms, such as plants and some bacteria, have mastered this process: In less than a couple of trillionths of a second, 95 percent of the sunlight they absorb is whisked away to drive the metabolic reactions that provide them with energy. The efficiency of photovoltaic cells currently on the market is around 20 percent.,,,
    http://www.sciencedaily.com/re.....142932.htm

    Mantis Shrimp Stronger than Airplanes – April 21, 2014
    Inspired by mantis shrimp, researchers design composite material stronger than standard used in airplane frames (w/video)
    Excerpt: Inspired by the fist-like club of a mantis shrimp, a team of researchers led by University of California, Riverside, in collaboration with University of Southern California and Purdue University, have developed a design structure for composite materials that is more impact resistant and tougher than the standard used in airplanes.
    “The more we study the club of this tiny crustacean, the more we realize its structure could improve so many things we use every day,”,,
    “Biology has an incredible diversity of species, which can provide us new design cues and synthetic routes to the next generation of advanced materials for light-weight automobiles, aircraft and other structural applications,” Kisailus said.
    http://ucrtoday.ucr.edu/21670

    ‘Unbreakable’ security codes inspired by nature – April 3, 2014
    Excerpt: Dr Stankovski said: “Here we offer a novel encryption scheme derived from biology, radically different from any earlier procedure. Inspired by the time-varying nature of the cardio-respiratory coupling functions recently discovered in humans, we propose a new encryption scheme that is highly resistant to conventional methods of attack.”
    The advantage of this discovery is that it offers an infinite number of choices for the secret encryption key shared between the sender and receiver. This makes it virtually impossible for hackers and eavesdroppers to crack the code.
    The new method is (also) exceptionally resistant to interference from the random fluctuations or “noise” which affects all communications systems.
    It can also transmit several different information streams simultaneously, enabling all the digital devices in the home, for example, to operate on one encryption key instead of dozens of different ones.
    http://www.sciencedaily.com/re.....132111.htm

    As a champion of biomimicry, Benyus has become one of the most important voices in a new wave of designers and engineers inspired by nature. Her most recent project, AskNature, explores what happens if we think of nature by function and looks at what organisms can teach us about design. The website features a search engine that allows users to type in a problem and it yields a solution in the form of a natural phenomena.
    http://www.biomimetic-architec.....ne-benyus/

    “Biomimetics and the Positive Implications for Intelligent Design” – Podcast – September 2011
    http://intelligentdesign.podom.....3_04-07_00

    etc.. etc.. etc…

  141. 141
    Evolve says:

    Here’s one from as far back as 2009. It’s open access I think.

    http://www.sciencedirect.com/s.....2209014754

    They report the origin of a new gene in mouse from an intergenic region. This region is present in rats and even in humans! But, only in the mouse, has it acquired the mutations allowing it to be expressed as a gene.

    In Figure 3, they show a phylogeny illustrating how functional mutations were acquired by various species tested. Humans are the outliers with 4/6 required mutations absent. Next come rats, in whom 2/6 required mutations are absent. Then comes various species of mice, who have either 1/6 required mutations absent or all required mutations present. Thus, even the phylogeny of this new gene matches the general phylogeny of humans, rats and mice!!

    Trying to explain this data from a design perspective will be laborious and contrived (if Pav ever attempts to do that). For example, why would a designer insert this region into humans with 4/6 required mutations absent rendering it non-functional? Why would he insert the same region into rats with more functional sites but still 2/6 missing?
    It makes no sense at all! Only an evolutionary explanation makes any sense here.
    This is why no real scientist will be swayed by the kind of nonsensical victory declaration Pav is making. The data strongly supports evolution.

  142. 142
    bill cole says:

    Hi Evolve

    Results and Discussion
    The role of gene duplications in generating new gene repertoires is well understood [1]. However, every genome harbors also a certain fraction of orphan genes that can not be associated with another known gene. The evolutionary origins of such genes are still rather unclear [2]. Genome comparisons have shown that de novo emergence of genes is possible, although mostly in the context of recruitment of fragments of transposable elements or other genome rearrangements 3, 4, 5, 6, 7 and 8. Also, the taxa analyzed in these studies have comparatively large evolutionary distances, making it difficult to infer the mechanisms of gene emergence.

    Your paper clearly states that it is difficult to infer the mechanisms of gene emergence. This is because the genome is a sequence. Random change rapidly breaks sequences down. Think about making random changes to the direct dial numbers in your cell phone. Will this find friends that are not currently in your direct dial? What it will do is get rid of numbers of people you don’t want to talk to any more. A successful adaption 🙂

  143. 143
    bornagain77 says:

    Perhaps MC would like to explain this without reference to the supernatural?

    There is fairly strong evidence that photosynthesis goes all the way back to the first life:

    When did oxygenic photosynthesis evolve? – Roger Buick – 2008
    Excerpt:,, U–Pb data from ca 3.8?Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.
    http://rstb.royalsocietypublis...../2731.long

    Yet photosynthesis is dependent on quantum coherence for photon transfer

    Quantum Mechanics Explains Efficiency of Photosynthesis – Jan. 9, 2014
    Excerpt: Previous experiments suggest that energy is transferred in a wave-like manner, exploiting quantum phenomena, but crucially, a non-classical explanation could not be conclusively proved as the phenomena identified could equally be described using classical physics.,,,
    Now, a team at UCL have attempted to identify features in these biological systems which can only be predicted by quantum physics, and for which no classical analogues exist.
    ,,,said Alexandra Olaya-Castro (UCL Physics & Astronomy), supervisor and co-author of the research. “We found that the properties of some of the chromophore vibrations that assist energy transfer during photosynthesis can never be described with classical laws, and moreover, this non-classical behaviour enhances the efficiency of the energy transfer.”,,,
    Other biomolecular processes such as the transfer of electrons within macromolecules (like in reaction centres in photosynthetic systems), the structural change of a chromophore upon absorption of photons (like in vision processes) or the recognition of a molecule by another (as in olfaction processes), are influenced by specific vibrational motions. The results of this research therefore suggest that a closer examination of the vibrational dynamics involved in these processes could provide other biological prototypes exploiting truly non-classical phenomena,,
    http://www.sciencedaily.com/re.....092008.htm

    To be clear, quantum coherence, like quantum entanglement, is a ‘non-local’, beyond space and time, effect

    Coherence and nonlocality
    Usually quantum nonlocality is discussed in terms of correlated multiparticle systems such as those discussed by John Bell in his famous 1964 theorem and then later clarified by GHZ, David Mermin and others.
    But more striking and significant is the qualitative nonlocal phenomena associated with coherent states,,,,
    In fact, theoretically these two kinds of nonlocality have precisely the same basis: the unmeasured singlet state uncovered by EPR is a coherent ‘pure state’ despite its spacial extension, and when the parts are realized in a measurement (a la Bell) this coherence is harvested or cashed in.
    Whereas the “EPR” connections are ephemeral and fragile, some forms of nonlocal coherence are robust.
    http://www.nonlocal.com/hbar/n.....rence.html

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    As a Theist, I have a beyond space and time cause to appeal to explain non-local photosynthesis, whereas the materialist has none to appeal to.

  144. 144
    bill cole says:

    Hi Art

    Hmmm…

    If gene duplication doesn’t add information, then the duplicates have no information. But if a duplicate is lost, then information is lost.

    That’s some sort of funny math there.

    If I duplicate a phone number in the direct dial of my cell phone have I added information? Perhaps, but I have not added a new contact which would indeed be new information.

  145. 145
    Dr JDD says:

    Evolve @141:

    Let’s take a step back a second. Like most naturalists, there is a clear misinterpretation of what I consider to be the standard model that most ID proponents take. You, like others, fall into the trap of believing that anyone who supports ID or does not subscribe to naturalistic evolution is a purist and simplistic creationist. This is a complete fallacy and a misunderstanding of the common position (I hasten to add, even one held by most YECs).

    It is not black and white, it is not evolution or no evolution at all. I think PaV has been demonstrating this the whole thread here. Most IDers fully accept that evolution of sorts does occur. What is contested is to ability to direct molecules to man or create new meaningful information from no information. That is the whole point of this thread. Do you really think even YECs would say that God created antibiotic resistant bacteria? Of course not – microevolution is a fully embraced phenomenon but that is selection acting on existing information.

    So with that in mind, on to your cited example of the pldi gene in mice. This is certainly an interesting case but there are a number of things that need to be studied further. Firstly, it is surprising how this is what you reference to support your case given how so many of the naturalists around here downplay the importance of lncRNAs. This does appear to be, by all means a non-protein coding sequence. That does in fact raise the question of the fact so many lncRNAs are being described these days, and outside the normal expected gene start consensus sequence sites, as to how much work has been performed to demonstrate that the region is not functional in humans or other species that lack these particular mutations described to give pldi it’s mouse specific initiation sites?

    Secondly, why if this is not an important region in humans, does this portion of sequence appear to be under “purifying selection”? In this study:

    The de novo sequence origin of two long non-coding genes from an inter-genic region
    Yulin Dai et al

    They state:

    In Pldi region, reduced polymorphism has been detected in specific mouse lineage, which suggests the present of purifying selection. Nevertheless, we found in our data that partial Pldi-Ak158810 sequence is conserved in all mammalians. It raises the possibility that purifying selection may be acquired in partial Pldi-Ak158810 region much earlier than the gene birth.

    So why in the world would purifying selection occur on a sequence that has no function, pre “gene-birth”? What selective advantage is gained by having a non-functional region present that would mean less drift would occur in this region? How does RM+NS account for that observation?

    Further, the authors state:

    We checked factors that could be responsible to the early fixation. Our calculation of substitution rate change shows that the inversed Ak158810 exon 1 was prone to decreasing the evolutional ability after inversion event, relative to surrounding genes (Table ?(Table33 & Additional File 7). This trend may represent for an increasing natural selection [25-27]. We also checked DNA modification of the region in human. A series significant signals of demethylation in CpGs are highly correlated with the conserved inversed element, CE1 (Figure ?(Figure66 & Additional File 3) using Encode browser [28], CE1 is overlapped with the promoter region of Pldi ‘s antisense gene, Ak158810, and the promoter sequence in mouse was found with low DNA methylations [21]. Furthermore, from the transcription factor binding site conserved tracks in UCSC, we find this CE1 homologue site is a potential transcription factor binding site of Chx10 conserved in both human and mouse (Figure ?(Figure6)6) [24]. This binding site exists both in human and mouse. According to these observations, we suggested in species other than mouse, partial region of Pldi-Ak158810 loci could not be simply recognized as “non-functional” before the birth of Pldi.

    So there is perceived to be function in this region. What is that function? No one knows but the point is this is not a useless stretch of DNA that a gene popped into existence from.

    So going back to my original point, and more pertinently PaV’s point, nothing here is inconsistent with a front loading event. In fact, quite the opposite. Whilst this paper is interesting (and I’m sure not the first time you have brought this up), it is certainly not inconsistent with what is being discussed in this thread.

    Personally, I suspect this is much more complex than we realise. I also think that you can look at things the other way around – genetic loss in a number of organisms (weak spots, susceptible to viral endomucleases and other similar phenomenon). Emergence of sequence is one explanation but disappearance is another to consider (except it is ruled out as it does not fir within the naturalistic evolutionary paradigm). I am not saying this has occurred here,but it is worth considering in general.

  146. 146
    magna charta says:

    BA77:

    To be clear, quantum coherence, like quantum entanglement, is a ‘non-local’, beyond space and time, effect.

    Here, I fixed that for you:

    To be clear, quantum coherence, like quantum entanglement, is a ‘non-local’, beyond space and time, natural effect

    As a Theist, I have a beyond space and time cause to appeal to explain non-local photosynthesis, whereas the materialist has none to appeal to

    That would certainly explain why all of the scientists studying quantum physics are theists.

    Correct me if I am mistaken, but are you now breaking the cardinal ID rule and proposing a mechanism for turning design into reality? That would certainly be something that could be researched and tested.

  147. 147
    Origenes says:

    Evolve: Inanimate matter did not somehow mindlessly assemble into living things.

    Barry: But according to the theory you support, it did exactly that. Why do you feel the need to deny that?

    Evolve: No, I already mentioned above that distinct processes were involved, not aimless, mindless assembling as creationists always claim.

    In what sense is inanimate matter “not aimless” and “not mindless”? Does inanimate matter have life in mind?

  148. 148
    bornagain77 says:

    MC, redefining ‘natural’ to include beyond space-time matter-energy effects, is a disingenuous ploy. By your new definition of ‘natural’ the Big Bang itself is now itself to be classified a ‘natural’ event since it also cannot be explained by within space-time matter-energy events.

    No less than Einstein himself considered non-local quantum entanglement to be ‘spooky action at a distance’, and sought a materialistic explanation to circumvent it:

    Einstein wouldn’t like it: New test proves universe is “spooky” – Oct 21, 2015
    Excerpt: Eighty years after the physicist (Einstein) dismissed as “spooky” the idea that simply observing one particle could instantly change another far-away object, Dutch scientists said on Wednesday they had proved decisively that the effect was real.
    Writing in the journal Nature, researchers detailed an experiment showing how two electrons at separate locations 1.3 km (0.8 mile) apart on the Delft University of Technology campus demonstrated a clear, invisible and instantaneous connection.
    Importantly, the new study closed loopholes in earlier tests that had left some doubt as to whether the eerie connection predicted by quantum theory was real or not.
    Einstein famously insisted in a 1935 scientific paper that what he called “spooky action at a distance” had to be wrong and there must be undiscovered properties of particles to explain such counter-intuitive behavior.
    The idea certainly confounds our day-to-day experience of the world, where change only appears to occur through local interactions. But in recent decades scientific evidence has been building that particles can indeed become “entangled”, so that no matter how far apart they are, they will always be connected.
    The Delft experiment is conclusive because, for the first time, scientists have closed two potential loopholes at once.
    The first suggests that particles could somehow synchronize behavior ahead of time, while the second implies that testing might detect only a subset of prepared entangled pairs.
    To prove their case, the team led by Delft professor Ronald Hanson used two diamonds containing tiny traps for electrons with a magnetic property called spin and measured all entangled pairs across 1.3 km separating two laboratories.
    The experiment effectively closes a chapter in an 80-year scientific debate,
    http://www.reuters.com/article.....GQ20151021

    Quantum “Spookiness” Passes Toughest Test Yet – August 28, 2015
    Excerpt: It’s a bad day both for Albert Einstein and for hackers. The most rigorous test of quantum theory ever carried out has confirmed that the ‘spooky action at a distance’ that the German physicist famously hated — in which manipulating one object instantaneously seems to affect another, far away one — is an inherent part of the quantum world.,,,
    Moreover, the experiment closed both loopholes at once: because the electrons were easy to monitor, the detection loophole was not an issue, and they were separated far enough apart to close the communication loophole, too.
    “It is a truly ingenious and beautiful experiment,” says Anton Zeilinger, a physicist at the Vienna Centre for Quantum Science and Technology.
    http://www.scientificamerican......-test-yet/

    Quantum Entanglement is simply completely incompatible with the reductive materialism that Darwinian evolution itself is built upon.

    A few supplemental notes:

    Molecular Biology – 19th Century Materialism meets 21st Century Quantum Mechanics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1141908409155424/?type=2&theater

    Einstein vs. “The Now” of Philosophers and Quantum Mechanics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1129789497033982/?type=2&theater

  149. 149
    magna charta says:

    BA77:

    MC, redefining ‘natural’ to include beyond space-time matter-energy effects, is a disingenuous ploy. By your new definition the Big Bang itself is now to be classified a ‘natural’ event.

    Nobody is redefining “natural”. Quantum physics is just helping us better understand what “natural” is. Just as classical physics and chemistry did before that. With regard to the Big Bang, that question is still to be answered. But my money is on natural. Remember, natural doesn’t have to be common place. Which in some instances is a good thing for life on earth. If super novae, a natural occurrence, were far more common than they are, it is unlikely that life as we know it could get established.

    No less than Einstein himself considered non-local quantum entanglement to be ‘spooky action at a distance’, and sought a materialistic explanation

    And Newton believed in God. Even the most intelligent people are sometimes wrong.

  150. 150
    bornagain77 says:

    magna charta,

    “Nobody is redefining “natural”. Quantum physics is just helping us better understand what “natural” is.”

    So the word ‘natural’ has a fluid definition that is subject to change whenever experimental outcomes conflict with the present definition of the word ‘natural’?

    Well by golly, how could I have been so dense as to think you were disingenuously redefining the word ‘natural’ so as to prevent falsification of the naturalistic/materialistic worldview? Thanks for clearing that up. (snark off)

  151. 151
    magna charta says:

    BA77:

    So the word ‘natural’ has a fluid definition that is subject to change whenever experimental outcomes conflict with the present definition of the word ‘natural’

    No. But knowledge of a phenomenon previously ascribed to the supernatural can result in it being re-classified as natural. There are many things we consider natural today that were considered supernatural in the past. I would provide examples but you obviously are far more proficient at Google than I am.

    Well by golly, how could I have been so dense…

    I have often wondered that about you. 🙂

  152. 152
    bornagain77 says:

    “But knowledge of a phenomenon previously ascribed to the supernatural can result in it being re-classified as natural”

    But never the other way round?

    Well by golly, that is some set up you got there.

    Of course others not so enamored with your one sided redefinition of natural to include beyond space-time matter-energy events might suggest the game is rigged towards ‘naturalism’.

    Question, in your scheme of naming all experimental outcomes as ‘natural’, could God himself someday be classified as ‘natural’ in your scheme of redefining all beyond space-time matter-energy things as ‘natural’? If not why not?

    as to:

    ” There are many things we consider natural today that were considered supernatural in the past.”

    do you think of a atom as ‘natural’?

    Science vs God: Bryan Enderle at TEDxUCDavis – video (how much empty space is in the atom is at the beginning of the video)
    http://www.youtube.com/watch?v=sn7YQOzNuSc

    “As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter.”
    Max Planck – The main originator of Quantum Theory – Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944) (from Archiv zur Geschichte der Max-Planck-Gesellschaft, Abt. Va, Rep. 11 Planck, Nr. 1797)(Of Note: Max Planck was a devoted Christian from early life)

  153. 153
    magna charta says:

    BA77:

    But never the other way round?

    I don’t see why not.

    Question, in your scheme of naming all experimental outcomes as ‘natural’, could God himself someday be classified as ‘natural’ in your scheme of redefining all beyond space-time matter-energy things as ‘natural’? If not why not?

    First, we don’t know that entanglement is beyond space time matter energy things. but that is beside the point. The God you believe in wouldn’t be considered natural. Because, as far as I know, it can’t be affected, other than by getting angry or happy, by any natural physical actions. However, i can’t speak for all gods.

    do you think of a atom as ‘natural’?

    Yes.

  154. 154
    bornagain77 says:

    “First, we don’t know that entanglement is beyond space time matter energy things.”

    Actually all experimental and mathematical evidence we currently have, some of which was already referenced, disconfirms any materialistic, within space-time matter-energy, interpretation of quantum entanglement

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”

    This is a well known scientific fact. For you to deny the current state of affairs in quantum mechanics reveals either a irrational bias against the implications, or a profound ignorance of the current state of quantum mechanics. Perhaps both.

    As to you arbitrarily excluding God from your definition of the word natural, yet readily including ‘spooky’ quantum entanglement within you definition of natural, even though Einstein himself fought against quantum non-locality since it went against his naturalistic assumptions, reveals your irrational bias against God.

    Moreover, I guess reality not existing until we look at it is also to be considered ‘natural’ in your forever flexible definition of the ‘word’ natural?

    New Mind-blowing Experiment Confirms That Reality Doesn’t Exist If You Are Not Looking at It – June 3, 2015
    Excerpt: The results of the Australian scientists’ experiment, which were published in the journal Nature Physics, show that this choice is determined by the way the object is measured, which is in accordance with what quantum theory predicts.
    “It proves that measurement is everything. At the quantum level, reality does not exist if you are not looking at it,” said lead researcher Dr. Andrew Truscott in a press release.,,,
    “The atoms did not travel from A to B. It was only when they were measured at the end of the journey that their wave-like or particle-like behavior was brought into existence,” he said.
    Thus, this experiment adds to the validity of the quantum theory and provides new evidence to the idea that reality doesn’t exist without an observer.
    http://themindunleashed.org/20.....at-it.html

    Of related note:

    Double Slit, Quantum-Electrodynamics, and Christian Theism – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1127450170601248/?type=2&theater

    Perhaps you can forgive me MC when, if you continue to pester me with such irrational reasoning, I will ask the admin of UD to remove you for trollish behavior?

    Verse:

    Romans 1:20
    For since the creation of the world God’s invisible qualities, His eternal power and divine nature, have been clearly seen, being understood from His workmanship, so that men are without excuse.

  155. 155
    magna charta says:

    BA77:

    Actually all experimental and mathematical evidence we currently have, some of which was already referenced, disconfirms any materialistic, within space-time matter-energy, interpretation of quantum entanglement

    The point I was trying to make is that we only know about these effects by measuring physical parts of the universe. If these effects are caused by the physical parts, then they are not supernatural. If they are caused by the unknown and unknowable that is outside of time space matter energy, then it is supernatural. And we don’t know one way or the other.

    Perhaps you can forgive me MC when, if you continue to pester me with such irrational reasoning, I will ask the admin of UD to remove you for trollish behavior?

    If that is going to be your response to every difficult question that I ask you, maybe you should go ahead and do that. But all onlookers can readily see that I have not been trollish. But it is your call. I can live with whatever you decide and wish you well either way.

  156. 156
    Querius says:

    Bornagain noted:

    . . . could God himself someday be classified as ‘natural’ in your scheme of redefining all beyond space-time matter-energy things as ‘natural’?

    No, because anything outside of our universe, especially what created our universe, is considered, by definition, supernatural.

    For example, that’s why the multiverse is considered supernatural. No, wait. That would be natural too.

    Ok, let’s try again.

    Anything outside the universe that’s natural that could have caused our natural universe, is natural. Naturally.

    And the difference between a hypothetical God making the Big Bang happen and Nature making the Big Bang happen naturally, is that Nature did it by accident!

    We now know it was an accident because accidents are Natural and God is not natural, so it must have been Nature, which proves that God can’t exist because he didn’t to anything.

    So, given an infinite amount of Time, you get an infinite amount of Chance. And an infinite amount Chance can result in anything or everything including the Space, (local) Time, Energy, and Mass of our universe.

    So you see, bornagain77, it all makes sense to those who refuse to accept the evidence screaming in their face. 😉

    -Q

  157. 157
    bornagain77 says:

    So Q, are you basically saying that his explanation just ain’t natural?

    🙂

  158. 158
    PaV says:

    magna charta:

    Quantum mechanics helps us understand the physical world, yes; however, it also has an ‘underbelly’; viz, the Copenhagen interpretation, which is, itself, based on positivist thinking, a brand of philosophy.

    Entanglement, and with it non-locality, something first pointed to by Schrodinger, ( no fan of the Copenhagen Interpretation) is not well understood. The ultimate foundation of entanglement could wind up having a seemingly supernatural cause.

    But here’s the problem: if we search “matter” for answers, we may, or may not, get them. If we search our “minds” for answers, again, we may, or may not get the answers. Yet, to perceive that something is an “answer,” itself requires the functioning of the ‘mind.’ So, it all boils down to this: what is the origin of the mind?

    Is the mind completely “natural”? Does QM describe it?

    How would you answer these types of questions?

  159. 159
    bornagain77 says:

    Of note:

    “If you go back and look at the premises which underlie materialism, They are all presumptions that were made back in the 17th and 18th century. Those (presumptions) are: reality, locality, causality, continuity, and determinism. All of those concepts were assumed to be self evident. And all of them have been disproved by quantum theory. The last one to fall was locality. (John Bell’s theory of non-locality disproved locality, which has now been proven I think 11 times in 11 different experiments throughout the world.),,, Anyone who says, “Well, I want to believe materialism and I don’t want to believe quantum physics.” Okay then, get rid of your cell phone, along with anything you have with a transistor in it. Get rid of your MRIs, get rid of all those things. Because quantum electro-dynamics is the theory which allows those things. It is the most proven theory in all of science.”
    Dr. Alan Hugenot – Hugenot holds a doctorate of science in mechanical engineering, and has had a successful career in marine engineering, serving on committees that write the ship-building standards for the United States. He studied physics and mechanical engineering at the Oregon Institute of Technology.
    quote taken from 16:35 minute mark of interview
    http://www.skeptiko.com/276-al.....-research/

    Double Slit, Quantum-Electrodynamics, and Christian Theism – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1127450170601248/?type=2&theater

    On The Comparison Of Quantum and Relativity Theories – Sachs – 1986
    Excerpt: quantum theory entails an irreducible subjective element in its conceptual basis. In contrast, the theory of relativity when fully exploited, is based on a totally objective view.
    http://books.google.com/books?.....38;f=false

    Does Quantum Physics Make it Easier to Believe in God? Stephen M. Barr – July 10, 2012
    Excerpt: Couldn’t an inanimate physical device (say, a Geiger counter) carry out a “measurement” (minus the ‘observer’ in quantum mechanics)? That would run into the very problem pointed out by von Neumann: If the “observer” were just a purely physical entity, such as a Geiger counter, one could in principle write down a bigger wavefunction that described not only the thing being measured but also the observer. And, when calculated with the Schrödinger equation, that bigger wave function would not jump! Again: as long as only purely physical entities are involved, they are governed by an equation that says that the probabilities don’t jump.
    That’s why, when Peierls was asked whether a machine could be an “observer,” he said no, explaining that “the quantum mechanical description is in terms of knowledge, and knowledge requires somebody who knows.” Not a purely physical thing, but a mind.
    https://www.bigquestionsonline.com/content/does-quantum-physics-make-it-easier-believe-god

  160. 160
    Evolve says:

    JDD,

    ///Like most naturalists, there is a clear misinterpretation of what I consider to be the standard model that most ID proponents take.///

    Not right. Although short on time, I follow creationist literature whenever I get a chance and so I’m very familiar with your false claim that microevolution can happen, but macroevolution cannot. This has been debunked ad infinitum. If microevolution can happen, then no barriers exist to prevent macroevolutionary change. I can do no better than what TalkOrigins has said on the subject years ago:
    http://www.talkorigins.org/indexcc/CB/CB902.html

    ///What is contested is ability to direct molecules to man or create new meaningful information from no information///

    Another typical creationist catchphrase: “molecules into man”!
    No, molecules did not turn into man one fine morning as you imply. Molecules did not randomly assemble, either, just as mountains were not produced by random piling up of rocks and rubble. Distinct geological processes produced mountains. Likewise, distinct biochemical processes produced life as well.
    It took hundreds of millions of years (not overnight) for the first life to emerge, which alone shows the rarity of the event.
    And then there was an even longer, much more arduous journey to get anywhere close to man. This too involved myriad chemical and biological processes.

    By the way, nobody intended to create man in the first place.
    And nobody intended to create meaningful information either. You’re caught up in this perpetual teleological thinking: Somebody wanted to create living things, so he made information for it. Much like how somebody wanted to create a computer, so he wrote software for it.

    But this kind of reasoning is unwarranted. Computer software can neither come about by itself nor chemically interact. On the other hand, a random sequence of nucleotides coming about by chance can turn into a gene if it can successfully interact with its surrounding molecules. That’s all that’s needed. Life is just a cascade of chemical reactions at the fundamental level. With a mutation here or there, the DNA strand can now maybe interact more strongly with more molecules. Then the reactions are much more efficient and it gets selected for naturally.

    What we call “information” in life for convenience is nothing like man-made information. Life’s “information” actually is just a 3D molecular structure that engages efficiently in one or more chemical interactions. For example, the TATA Box is a DNA sequence to which transcription factors bind, facilitating the decoding of a gene. Why does the TATA box recruit transcription factors? The T-A-T-A bases impart a specific 3D structure that makes interaction with proteins easier. Molecular Biologists can fiddle around with bases to make such interactions weaker or stronger, thereby altering gene expression entirely.

  161. 161
    Evolve says:

    ///so many of the naturalists around here downplay the importance of lncRNAs///

    No naturalist who knows what he’s talking about will downplay lncRNAs or any non-coding RNAs for that matter. They’re all important. However, creationists tend to over-hype such RNAs produced from non-protein coding regions of the genome. The reason is obvious, they want to prove that Junk DNA does not exist. But even if you take all non-coding RNAs discovered till date and liberally allow for hundreds, or even thousands, more to be discovered in the future, that still won’t invalidate Junk DNA! Because all those functional RNAs will still only constitute a fraction of the genome.

  162. 162
    bornagain77 says:

    Evolve claims:

    If microevolution can happen, then no barriers exist to prevent macroevolutionary change. I can do no better than what TalkOrigins has said on the subject years ago:

    Here is a detailed refutation, by Casey Luskin, to TalkOrigins severely misleading site on the claimed evidence for observed macro-evolution (speciation);

    Specious Speciation: The Myth of Observed Large-Scale Evolutionary Change – Casey Luskin – January 2012 – article
    http://www.evolutionnews.org/2.....55281.html

    Here is part 2 of a podcast exposing the Talk Origin’s speciation FAQ as a ‘literature bluff’

    Talk Origins Speciation FAQ, pt. 2: Lack of Evidence for Big Claims – Casey Luskin – podcast
    http://intelligentdesign.podom.....9_41-08_00

    Evolve then claimed:

    It took hundreds of millions of years (not overnight) for the first life to emerge, which alone shows the rarity of the event.

    And yet, despite the fact that nobody has a clue how Life can possibly originate naturalisticly (James Tour; An Inside Story – 2016), we have evidence of life suddenly appearing on Earth immediately following the late heavy bombardment

    Isotopic Evidence For Life Immediately Following Late Bombardment – Graph
    http://cdn.physorg.com/newman/.....bitofc.jpg

    Dr. Hugh Ross – Origin Of Life Paradox (No prebiotic chemical signatures)- video (40:10 minute mark)
    https://www.youtube.com/watch?feature=player_detailpage&v=UPvO2EkiLls#t=2410

    “We get that evidence from looking at carbon 12 to carbon 13 analysis. And it tells us that in Earth’s oldest (sedimentary) rock, which dates at 3.80 billion years ago, we find an abundance for the carbon signature of living systems. Namely, that life prefers carbon 12. And so if you see a higher ratio of carbon 12 to carbon 13 that means that carbon has been processed by life. And it is that kind of evidence that tells us that life has been abundant on earth as far back as 3.80 billion years ago (when water was first present on earth).,,, And that same carbon 12 to carbon 13 analysis tells us that planet earth, over it entire 4.5662 billion year history has never had prebiotics. Prebiotics would have a higher ratio of carbon 13 to carbon 12. All the carbonaceous material, we see in the entire geological record of the earth, has the signature of being post-biotic not pre-biotic. Which means planet earth never had a primordial soup. And the origin of life on earth took place in a geological instant” (as soon as it was possible for life to exist on earth).
    – Hugh Ross – quote as stated in preceding video at 40:10 mark

    Origins of Life – Hugh Ross – video (7:00 minute mark: late heavy bombardment and extremely early origin of life, 19:00 minute mark: diversity of first life, 21:00 minute mark no life from Mars, 24:00 minute mark: no sugars or complex amino acids in space, 27:00 minute mark: impossibility of transporting complex organic molecules to earth on comets, 31:00 minute mark: chemists at a OOL convention each defending various origin of life scenarios and humorously debunking each other’s models) – video
    https://www.youtube.com/watch?v=VTI5mEiz4O0

    Evolve then claims:

    And then there was an even longer, much more arduous journey to get anywhere close to man.

    And yet

    Anthropic Principle: A Precise Plan for Humanity By Hugh Ross
    Excerpt: Brandon Carter, the British mathematician who coined the term “anthropic principle” (1974), noted the strange inequity of a universe that spends about 15 billion years “preparing” for the existence of a creature that has the potential to survive no more than 10 million years (optimistically).,, Carter and (later) astrophysicists John Barrow and Frank Tipler demonstrated that the inequality exists for virtually any conceivable intelligent species under any conceivable life-support conditions. Roughly 15 billion years represents a minimum preparation time for advanced life: 11 billion toward formation of a stable planetary system, one with the right chemical and physical conditions for primitive life, and four billion more years toward preparation of a planet within that system, one richly layered with the biodeposits necessary for civilized intelligent life. Even this long time and convergence of “just right” conditions reflect miraculous efficiency.
    Moreover the physical and biological conditions necessary to support an intelligent civilized species do not last indefinitely. They are subject to continuous change: the Sun continues to brighten, Earth’s rotation period lengthens, Earth’s plate tectonic activity declines, and Earth’s atmospheric composition varies. In just 10 million years or less, Earth will lose its ability to sustain human life. In fact, this estimate of the human habitability time window may be grossly optimistic. In all likelihood, a nearby supernova eruption, a climatic perturbation, a social or environmental upheaval, or the genetic accumulation of negative mutations will doom the species to extinction sometime sooner than twenty thousand years from now.
    http://christiangodblog.blogsp.....chive.html

    Life and Earth History Reveal God’s Miraculous Preparation for Humans – Hugh Ross, PhD – video (2014)
    https://www.youtube.com/watch?v=n2Y496NYnm8

  163. 163
    bornagain77 says:

    Evolve then claims:

    By the way, nobody intended to create man in the first place.
    And nobody intended to create meaningful information either.

    And yet,

    I hold, from the scientific evidence itself, that the Theist is more than justified for his belief that he is ‘made in the image’ of God and that the atheist is, once again, left with deep unanswered questions that go completely contrary to his materialistic assumptions.
    http://www.uncommondescent.com.....ent-611511

    Evolve then claims:

    a random sequence of nucleotides coming about by chance can turn into a gene if it can successfully interact with its surrounding molecules.

    And yet, the chances of a protein developing a new protein/protein binding site so as to ‘interact with its surrounding molecules’ is 1 in 10^20 (Behe; White).

    Michael Behe – Observed (1 in 10^20) Edge of Evolution – video – Lecture delivered in April 2015 at Colorado School of Mines
    25:56 minute quote – “This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not.”
    https://www.youtube.com/watch?v=9svV8wNUqvA

    Evolve then claims:

    What we call “information” in life for convenience is nothing like man-made information.

    And yet:

    Information Theory, Evolution, and the Origin of Life – Hubert P. Yockey, 2005
    Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.”
    http://www.cambridge.org/catal.....038;ss=exc

    Complex grammar of the genomic language – November 9, 2015
    Excerpt: The ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher –,,,
    ,,, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to.
    Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.
    http://www.sciencedaily.com/re.....140252.htm

    Evolve claims:

    No naturalist who knows what he’s talking about will downplay lncRNAs or any non-coding RNAs for that matter. They’re all important.

    Apparently hardcore Darwinian biologists have no clue what they are talking about since they still vehemently defend junk DNA:

    Why Are Biologists Lashing Out Against Empirically Verified Research Results? – Casey Luskin July 13, 2015
    Excerpt: Evolutionists Strike Back
    Darwin defenders weren’t going to take ENCODE’s data sitting down.,,,
    How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm–and by personally attacking, (i.e. ad hominem), those who challenge their position.,,,
    http://www.evolutionnews.org/2.....97561.html

    UCLA Scientists Find 3000 New Genes in “Junk DNA” of Immune Stem Cells – October 28, 2015
    Excerpt: Not Junk After All
    Now back to “Junk DNA”… scientists thought that because this mass of DNA sequences was never turned into protein, it served no purpose. It turns out that they couldn’t be farther from the facts.,,,
    Using sequencing technology and bioinformatics, they mapped the RNA landscape (known as the transcriptome) of rare stem cells isolated from human bone marrow (hematopoietic stem cells) and the thymus (lymphoid progenitor cells). They identified over 9000 genes that produced lncRNAs that were important for moderating various stages of immune cell development. Of this number, over 3000 were genes whose lncRNAs hadn’t been found before.,,,
    If the pace keeps up, the term “Junk DNA” will need to be retired to the junk yard.
    http://blog.cirm.ca.gov/2015/1.....tem-cells/

  164. 164
    Querius says:

    How about an experiment that even evolutionists can do if they don’t chicken out?

    Take some non-motile bacteria in an environment favoring motility and expose them to massive quantities of ionizing radiation through enough generations to simulate millions of years of evolution.

    If the bacteria are able to evolve cilia, flagella, propellers, or jet engines, you will have provided direct evidence. You will win the argument and become rich and famous!!

    And if they don’t evolve . . . 😮

    -Q

  165. 165
    bornagain77 says:

    As to Behe’s ‘observed’ 1 in 10^20 ‘Edge of Evolution’

    Michael Behe – Observed (1 in 10^20) Edge of Evolution – video – Lecture delivered in April 2015 at Colorado School of Mines
    25:56 minute quote – “This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not.”
    https://www.youtube.com/watch?v=9svV8wNUqvA

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    – Michael Behe – The Edge of Evolution – page 146

    This finding is far more problematic than many people realize. Although many people have been misled to believe that Chimps and Humans are virtually identical, due to genetic similarity alone, yet due to alternative splicing, the protein-protein interaction profiles are vastly different between chimps and humans

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013
    Excerpt: Although humans and chimpanzees share,, similar genomes, previous studies have shown that the species evolved major differences in mRNA (messenger RNA) expression levels.,,,
    http://www.sciencedaily.com/re.....144632.htm

    Frequent Alternative Splicing of Human Genes – 1999
    Excerpt: Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes.
    http://www.ncbi.nlm.nih.gov/pm.....PMC310997/

    Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing – 2016
    In Brief
    Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,
    Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013).
    http://iakouchevalab.ucsd.edu/.....M_2016.pdf

    Thus since alternatively splicing is very different between even humans and chimps, and alternative splicing produces proteins that behave as if encoded by distinct genes rather than as minor variants of each other and alternative splicing also produces strikingly different interaction profiles for proteins, and yet the ‘observed’ Edge of Evolution for Darwinian processes to generate a new protein/protein binding site are only 1 in 10^20, then we are more than justified to conclude that humans did not evolve from apes.

    In fact, since humans possess a distinct alternative splicing code, we are more than justified to believe that humans were created distinctly:

    An easy way of understanding why a unique code, such as the unique alternative splicing code that humans have, will never evolve in a gradual bottom up Darwinian fashion is elucidated by Dawkins himself:

    Venter vs. Dawkins on the Tree of Life – and Another Dawkins Whopper – March 2011
    Excerpt:,,, But first, let’s look at the reason Dawkins gives for why the code must be universal:
    “The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.” (2009, p. 409-10)
    http://www.evolutionnews.org/2.....44681.html

    In other words, a unique and new code, since the entire context of the code matters, must be implemented ‘top down’, all at once, in order to avoid ‘catastrophic effects’

  166. 166
    bill cole says:

    Hi Evolve

    But this kind of reasoning is unwarranted. Computer software can neither come about by itself nor chemically interact. On the other hand, a random sequence of nucleotides coming about by chance can turn into a gene if it can successfully interact with its surrounding molecules. That’s all that’s needed. Life is just a cascade of chemical reactions at the fundamental level. With a mutation here or there, the DNA strand can now maybe interact more strongly with more molecules. Then the reactions are much more efficient and it gets selected for naturally.

    This statement tells me you don’t understand how many ways a sequence of nucleotides can be arranged, for an average protein coding gene for just exons 4^1500. This number is larger than all the matter in the universe measured in atoms. There is no experimental evidence that more than a few adaptions have occurred in nature. This is due to the almost infinite ways to arrange nucleotides.

  167. 167
    bornagain77 says:

    Of semi related note:

    Can DNA become the future of digital storage? Microsoft is betting on it – Aaron Krumins – May 2, 2016
    Excerpt: Microsoft announced a partnership with the San Francisco-based Twist Bioscience, which will provide the long oligonucleotides used for synthetic DNA storage. As part of the deal, Microsoft will purchase 10 million strands of such DNA, in what augurs to be the first phase of their DNA storage ambitions.,,,
    Not only is DNA remarkably effective at retrieving and copying data, it’s extremely efficient in scale. It’s estimated that a diploid cell in the human contains about 1.5 gigabytes of information, which it can store and retrieve with frightening accuracy. At 1.5GB per cell, the cells in your hand could provide a storage medium bigger than the largest mechanical hard drive in existence.
    http://www.extremetech.com/ext.....ting-on-it

    Information Storage in DNA by Wyss Institute – video
    https://vimeo.com/47615970
    Quote from preceding video:
    “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
    Sriram Kosuri PhD. – Wyss Institute

    Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA – January 29, 2013
    Excerpt: researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, UK, report online today in Nature that they’ve improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.,,,
    http://www.evolutionnews.org/2.....68641.html

    Storing information in DNA – Test-tube data – Jan 26th 2013
    Excerpt: Dr Goldman’s new scheme is significant in several ways. He and his team have managed to set a record (739.3 kilobytes) for the amount of unique information encoded. But it has been designed to do far more than that. It should, think the researchers, be easily capable of swallowing the roughly 3 zettabytes (a zettabyte is one billion trillion or 10²¹ bytes) of digital data thought presently to exist in the world and still have room for plenty more.
    http://www.economist.com/news/.....d-magnetic

  168. 168
    arunrama2019 says:

    To- evolution scientists. Dear ladies and gentlemen. I am not a scientists like you but I can understand the fundamental aspect of science. there are four fallacies in yur conception of evolution.

    Firstly. Darwin’s theory of evolution speaks about macro evolution and yu are speaking about micro evolution in other words some small changes within the species. Just like there are different varieties of dogs. There may be small or big dogs with different colors still they are dogs and are limited to its particular size.
    Secondly- mutation in literal sense means changes or modifications and you people say such changes happens by various adaptive pressures and nature selects the protein and arranges in its particular sequence. Here Darwin himself has confessed that nature does not works randomly rather it “Selects”. This means that Darwin himself cannot explain the diversification of species without the idea of intelligent design or Selector.
    Thirdly, you did not answer how the first self replicating cell came in to existence from inorganic matter by gradual steps of changes from a prebiotic soup.
    Fourthly, DNA, RNA, Proteins and amino acids are all organic “Matter”. This means that it is just like an inorganic “Matter” like a thousands of spare parts of a car. Which themselves has no intelligence or energy to precisely assemble itself to make up a suffisticated car.

    You people speak about a species gets adapted to such environment or circumstances and passes on its higher traits to its off springs. Here there is common misunderstanding. A species which lives in antartic ocean like polar bear or penguin when migrated to tropical countries cannot survive the hot climatic conditions rather it dies quickly before it gets adapted to that environment and passes on its higher traits to its offsprings. Even assuming that evolution from simple to complex forms to happen in randomness there must be Constant Favorable conditions for a positive multiple mutations and any unfavorable conditions will result in the destruction of positive mutations quickly. And life from simple forms to complex forms from single cell to humans becomes highly impossible. . as per the second laws of thermo dynamics such random energy destroys the molecules quickly and does not creates.

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