Intelligent Design

Biologos, Venema and the Scientific Imagination

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Denis Venema wants to explain evolution to evangelical Christians because he doesn’t think it is understand sufficiently. But he asks us to use our imagination and avoids a carefully modelled defence of evolution. If that is the best Darwinists can do then is it any wonder that many of us reject it? See:
Venema Understanding Evolution: An Introduction to Populations and Speciation

Firstly, Venema follows the common evolutionary practice of presenting evidence for evolution by focussing upon the micro changes and then extrapolating without evidence to the macro evolutionary scale by assuming it happens by similar means. But the micro changes, such as that of his exampled stickleback fish, are simply uncontested even by young earth creationists, but what is contested is the belief that we can move from the small to the big without developing and modelling a credible pathway. Time and again evolutionists fail to deal with the problems, but simply make the switch from small to big thinking the flaws in their reasoning will not be noticed.

Venema though asks us to use our imagination to understand evolution. I find that wholly inadequate scientifically, especially when we can model such claims mathematically. And I wonder why such imaginary thinking has a right to be called science. He does though present claims that can be questioned scientifically; for instance believing that humanity evolved within a population size of roughly 10,000 people. So how should we model these claims?

Assuming 20 years for a generation and 6 million years from an ape-like ancestor to mankind would give 300,000 generations to achieve an evolutionary progression from an ape-like ancestor to man. As an aside, in that time only 3 billion individuals would have lived and died, a smaller number than the present human population alive today. Does he really expect us to believe that man could have arisen in so small a number of ancestors? Presumably we can look at the incidence of beneficial mutations in the present human population and ask whether sufficient beneficial mutations would have arisen and be compounded through 300,000 generations. I am afraid it doesn’t look good for evolution.

So down to modelling; we are led to believe that there is 1 percent difference between ape and man in the 3 billion base pairs of DNA, and if we use unrealistic assumptions then we might assume only 10 percent of DNA is coded with the rest considered ‘junk.’ But even 1 percent of 300 million is 3 million nucleotide differences between ape and man.

So we have to find 3 million base-pair beneficial mutational changes in 300,000 generations, or 10 per generation, both found and fixed in the population per generation. Is that possible? I challenge anyone to tell me it is adequate from what we know about the way the present day human population finds and fixes beneficial mutations, even for instance on a small island community of 10,000 people. It comes up against a number of problems.

Problem1. Haldane’s dilemma as discussed by ReMines in The Biotic Message and Sandford in Genetic Entropy (Refs below) (One might have thought these books would be at the top of Venema’s reading list considering his position). Anyway, as a simple overview of the claims of these books, in order for beneficial mutations to be fixed in the population we would need to pay a cost in terms of survivability of the mutated offspring against the un-mutated ones. Haldane thought it as high as 30 to 1, and higher vertebrates cannot hope to pay that cost. Haldane thought a cost of 0.1 per generation might be affordable and that it would take 300 generations to fix 1 beneficial mutation in a population. Venema’s population might then fix 1000 beneficial mutations in 6 million years; a little short of the 3 million required. 

Problem 2. We may also ask whether beneficial mutations actually provide any selective advantage to an organism. Sandford for instance has pointed out that beneficial mutations, when they rarely occur, are virtually invisible at the level of the phenotype anyway and so even Haldane’s 0.1 per generation looks unlikely.           

Problem 3. Harmful mutations are far more common than beneficial ones, perhaps as high as 1000 to 1. In order to weed out the harmful mutations evolution would have to proceed at a very slow rate indeed so that error catastrophe doesn’t occur in the population; a problem known today where small inbreeding populations are often on the verge of extinction. Furthermore, small populations do not have sufficient resources to find the necessary beneficial mutations, even though it makes it easier to spread the mutations that do occur through a population. A large population is more likely to find beneficial mutations, but work against their spread through the population due to the size.   

 So in summary, I would challenge Venema to respond seriously to the questions raised by Sandford and ReMine.

Sources: Walter ReMine’s The Biotic Message, St Paul, Minnesota: St Paul’s Science, pp. 208-236. Sanford, J (2005) Genetic Entropy and the Mystery of the Genome, New York: Elim Publ, especially pp.159-160, Haldane JBS (1957) ‘The Cost of Natural Selection,’ J. Genetics 55:511-24.

85 Replies to “Biologos, Venema and the Scientific Imagination

  1. 1
    DrREC says:

    I chuckled at this one. You lead with:”Denis Venema wants to explain evolution to evangelical Christians because he doesn’t think it is understand sufficiently” and as if to prove his point, you proceed to butcher the topic.

    Your assumptions:
    1) 10 percent of DNA is coded with the rest considered ‘junk.’ (way high)
    2) 3 million base-pair beneficial mutational changes (Beneficial???)

    Could you explain your logic on these mutations ALL being beneficial? Really, I’m curious. Do you think only beneficial mutations can fix?

    In contrast to your approach, let’s just take the simplest route, and say that on average, the across the genome mutations are neutral. Under neutral selection, the rate of fixation for a mutation not subject to selection is the rate of introduction of such mutations. A low estimate is ~1.1×10?8 per site per generation. Times 3 billion sites, 300,000 generations, 2 lineages, we’re at 19.8 million, or 1.51%.

    Not bad. Of course, functional sites show purifying selection, so fewer mutations get fixed there then elsewhere, and open reading frames end up showing ~99.5%+ identity-that is, about 30% of human and chimp proteins having identical amino acid sequences, and the remainder having one or two differences. Are even all these beneficial? Probably not. Some of those tested seem to do little functionally. Many are nearly synonymous, substituting a very similar amino acid.

    By the way, this difference is only about 10 times the difference between any two humans, if I recall correctly.

    Haldane’s dilemma has been dealt with extensively elsewhere.

  2. 2
    bornagain77 says:

    Instead of DrREC’s grossly misleading hypothetical scenarios for the neo-Darwinian evolution of humans, let’s look at some actual evidence and see what reality itself is telling us about the plausibility of neo-Darwinian evolution of humans. First no neo-Darwinists seems be able to show me ANY beneficial mutations, in humans (or anything else for that matter), that will withstand scrutiny, (Lactase persistence, and Himilaya high altitude/low oxygen tolerance mutations, in humans, both fail scrutiny for functional information generation, much less can the mutations be claimed as purely random mutations and not, in fact, be claimed as ‘calculated’ mutations), Yet the evidence for detrimental mutations in humans is simply overwhelming:

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57 By John C. Avise
    Excerpt: “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.”

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

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.biobase-internation.....mddatabase

    I really question their use of the word ‘celebrating’. Using real world parameters, here is the correct model for what is actually going on with genomes:

    Evolution Vs Genetic Entropy – video
    http://www.metacafe.com/watch/4028086/

    Genetic Entropy vs. Evolution – The Stark Reality – video
    http://vimeo.com/24870022

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net
    http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf

    Here is a pretty accurate measure for the detrimental mutation rate in humans.

    We Are All Mutants: First Direct Whole-Genome Measure of Human Mutation Predicts 60 New Mutations in Each of Us – June 2011
    http://www.sciencedaily.com/re.....012758.htm

    This ‘slightly detrimental’ mutation rate of 60, per generation is far greater than even what neo-Darwinists agree is a acceptable mutation rate for an organism:

    Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction
    Excerpt: Shakhnovich’s group found that for most organisms, including viruses and bacteria, an organism’s rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.
    http://www.sciencedaily.com/re.....172753.htm

    etc.. etc.. etc..

  3. 3
    bornagain77 says:

    To show how grossly misleading neo-Darwinists can be about population genetics, on the web and to the general public, here is the neo-Darwinists very own population genetics model applied to the hypothetical scenario for whale evolution;

    Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology – video
    http://www.metacafe.com/watch/4165203

    referenced paper in preceding video:

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.
    http://www.discovery.org/a/9461

    Moreover, despite what DrREC, and other neo-Darwinists on the web may say, the fact that there are severe problems in the mathematical population genetics model of neo-Darwinists is readily admitted by many of the population geneticists themselves:

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

    But, of personal note, when considering the multiple overlapping layers of coding in the genome,,,

    Scientists Discover Parallel Codes In Genes
    Excerpt: Their work,,, shows that the genetic code — used by organisms as diverse as reef coral, termites, and humans — is nearly optimal for encoding signals of any length in parallel to sequences that code for proteins.
    http://www.sciencedaily.com/re.....230116.htm

    There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
    Dr. John Sanford; Genetic Entropy 2005

    DNA – Evolution Vs. Polyfuctionality – video
    http://www.metacafe.com/watch/4614519

    Scientists Map All Mammalian Gene Interactions – August 2010
    Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome.
    http://www.sciencedaily.com/re.....142044.htm

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.
    http://www.sciencedaily.com/re.....142957.htm

    ,,,I simply find that it is beyond ludicrous to even begin to entertain the thought that this level of unmatched functional integrated information was put together by mutations filtered by differential death. But alas, as Dr. Hunter says, ,,, Religion drives science and it matters!

  4. 4
    bornagain77 says:

    Moreover, neo-Darwinism is simply at a complete loss to explain the beauty of this:

    Standing Ovation! Jackie Evancho WOW’s Audience! – Inspirational Videos
    http://www.godtube.com/watch/?v=KK67Y7NX

  5. 5
    JDH says:

    If it’s one thing I hate with a passion its the low probability but great amount of time argument. If everyone is honest we will realize that this is a very difficult problem where small mistakes in measured rates have great consequences.

    Two examples from basic math

    The harmonic sequence
    1/1 + 1/2 + 1/3 + 1/4 …. so many terms , but each gets smaller. What is the answer? – it never stops growing and can be shown to be infinite ( or more technically, non-convergent.(

    A power series

    9/10 + 9/10^2 + 9 /10^3 + 9/10^4… This again has an infinite number of terms, but it not only converges but has a recognizable answer. It is the number that is usually written 1. ( one ).

    In order to make real quantitative arguments about probabilities or sequences involving a large number of trials with small probability, you have to know the detailed quantities to incredible precision. Hand waving arguments which move from micro evolution to macro evolution are just so much garbage.

  6. 6
    Mytheos says:

    Initially it may have seemed the more “scientific” option to be a naturalist. However as soon as the naturalist endeavors to defend their belief they are constantly defying “science” at every turn.
    How can a “scientist” look at a whole system that is slowly by short and sure steps degrading, go and tell the world that it is evolving?
    Imagination is key I suspect.

  7. 7
    Mytheos says:

    One day there was a single celled organism splooshing around all by itself having all sorts of fun. It was the only life in the whole universe. I cant tell you how it got there.
    He was lonely so he turned into two organisms. I cant tell you how. He wished he could turn into a bird and fly in the sky so he did. Don’t worry its not magic coz it took a real long time for him to do it.
    Wow! thank you imagination I now understand the theory of evolution.

  8. 8
    bornagain77 says:

    Semi OT:, In this podcast, Casey Luskin thoroughly debunks the hype surrounding the newest missing link, Australopithecus sediba. Starting a little after the 7:00 minute mark on the podcast, he quotes from several leading paleontologists in the field who express deep skepticism for the grandiose claims being made in media headlines about its status as irrefutable proof of a ‘missing link’ for human evolution:

    Recently Reported Fossil is Old News: Media Hype & the Upcoming Election
    http://intelligentdesign.podom.....6_16-07_00

  9. 9
    DrREC says:

    “much less can the mutations be claimed as purely random mutations and not, in fact, be claimed as ‘calculated’ mutations)”

    Haha…there it is. Show BA77 evidence of a gain-of-information mutation, and guess what, it is designed. How was this detected, how do you discern it from natural processes?

    Doesn’t matter-because design is just something you can tack onto any observation. It is unfalsifiable in this sense. See something evolve-thats just design unfolding.

    Which is fine as a personal belief. It is also more simply called theistic evolution. It isn’t much of a science.

  10. 10
    DrREC says:

    Anyone want to show calculations that the number of mutations between humans and chimps is impossible?

    Anyone want to defend the claim in the original post that there must be a whopping number of beneficial mutations?

  11. 11
    bornagain77 says:

    DrREC actually, to show you for the inflexible/dishonest neo-Darwinian dogmatist that you truly are (which I enjoy doing by the way), here is the clear evidence, in the Himalayan oxygen mutation, that throws up a huge red flag on such mutations being considered truly random mutations, as is required by neo-Darwinism (your religion), and clearly points to the fact that they should in fact be considered ‘designed/calculated’ mutations arising ‘rapidly’ from the regulatory epigentic information controlling the DNA:

    neo-Darwinism presupposes that the ‘beneficial mutations’ which conferred the advantage for Tibetans to live at high altitudes was completely random, yet when looked at from the point of population genetics, the evidence gives every indication that the ‘beneficial mutations’ were not random at all but were in fact ‘programmed’ mutations:

    Another Darwinian “Prediction” Bites the Dust – PaV – August 2010
    Excerpt: this means the probability of all three sites changing “at once” (6.25 X 10^-9)^2 = approx. 4 X 10^-17 specific bp change/ yr. IOW (In Other Words), for that size population, and this is a very reasonable guess for size, it would take almost twice the life of the universe for them to take place “at once”. Thus, the invocation of “randomness” in this whole process is pure nonsense. We’re dealing with some kind of programmed response if, in fact, “polygenic selection” is taking place. And, that, of course, means design.
    http://www.uncommondescent.com.....more-14516

    Further notes:

    Recently new supposedly ‘beneficial mutations’ were found in Tibetans that have allowed them to survive in extremely high altitudes, with less oxygen. Yet once again the new supposedly ‘beneficial mutations’ are actually found to be ‘slightly detrimental’ because they in fact result in a limit on the red cell blood count for Tibetans:

    Tibetans Developed Genes to Help Them Adapt to Life at High Elevations – May 2010
    Excerpt: “What’s unique about Tibetans is they don’t develop high red blood cells counts,”
    http://www.sciencedaily.com/re.....143453.htm

    Yet high red blood cell counts are actually found to be good,,

    Extremely fit individuals may have higher values—significantly more red cells in their bodies and significantly more oxygen-carrying capacity—but still maintain normal hematocrit values.
    http://wiki.medpedia.com/Red_Blood_Cells

    ,,,Thus they were actually incorrect to imply that a limit on red blood cell counts in Tibetans is ‘beneficial’,,, Thus this is clearly another example of a loss of overall functional information, and fitness, for the human genome, since, on the molecular level, nothing was gained but something was lost.

    This following article goes into more detail and points out many other inconsistencies with the Tibetan mutations that evaporate any claim for evidence of a ‘truly’ beneficial mutation:

    Tibetans Evolved Altitude Tolerance in 3,000 Years? – July 2010
    http://www.creationsafaris.com.....#20100703a

  12. 12
    bornagain77 says:

    DrREC, do you want to show ANY evidence that just one gene and/or protein can arise by neo-Darwinian processes?

    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

    “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: – Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.”
    http://www.mendeley.com/resear.....yme-folds/

  13. 13
    DrREC says:

    “DrREC, do you want to show ANY evidence that just one gene and/or protein can arise by neo-Darwinian processes?”

    Recent de novo origin of human protein-coding genes
    http://genome.cshlp.org/conten.....095026.109

    Evolution of novel genes.
    http://www.ncbi.nlm.nih.gov/pubmed/11682312

    Strategy and success for the directed evolution of enzymes.
    http://www.ncbi.nlm.nih.gov/pubmed/21684150
    “……including examples of catalytic activity for which there is no precedent in nature”

  14. 14
    bornagain77 says:

    This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 ‘ORFan’ genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!

    Human Gene Count Tumbles Again – 2008
    Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes. Although this was strong evidence that the sequences were not true protein-coding genes, it was not quite convincing enough to justify their removal from the human gene catalogs. Two other scenarios could, in fact, explain their absence from other mammalian genomes. For instance, the genes could be unique among primates, new inventions that appeared after the divergence of mouse and dog ancestors from primate ancestors. Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes.
    http://www.sciencedaily.com/re.....161406.htm

    The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true.

    This following site has a brief discussion on the biased methodology of the preceding study:
    http://www.uncommondescent.com.....ent-358505

    If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins:

    A survey of orphan enzyme activities
    Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles.
    http://www.biomedcentral.com/1471-2105/8/244

    Dr. Howard Ochman – Dept. of Biochemistry at the University of Arizona
    Excerpt of Proposal: The aims of this proposal are to investigate this enigmatic class of genes by elucidating the source and functions of “ORFans”, i.e., sequences within a genome that encode proteins having no homology (and often no structural similarity) to proteins in any other genome. Moreover, the uniqueness of ORFan genes prohibits use of any of homology-based methods that have traditionally been employed to establish gene function.,,, Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins.
    http://www.uncommondescent.com.....ent-358868

    In fact it turns out that the authors of the ‘kick the ORFans out in the street’ paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore it in favor of their preconceived evolutionary bias:
    http://www.uncommondescent.com.....ent-358547

    Moreover the ‘anomaly’ of unique ORFan genes is found in every new genome sequenced:

    Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references to literature
    http://www.vimeo.com/17135166

    As well, completely contrary to evolutionary thought, these ‘new’ ORFan genes are found to be just as essential as ‘old’ genes for maintaining life:

    Age doesn’t matter: New genes are as essential as ancient ones – December 2010
    Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
    http://www.sciencedaily.com/re.....142523.htm

    New genes in Drosophila quickly become essential. – December 2010
    Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
    http://www.sciencemag.org/cont.....2.abstract

    of related interest:

    Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny – Casey Luskin – June 2011
    Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)
    http://www.evolutionnews.org/2.....47041.html

  15. 15
    bornagain77 says:

    Why DrREC, so all you have to do to prove your point is say that Protein a evolved from protein b??? Why that is just special DrREC! Perhaps you could sooth my doubts and actually physically demonstrate the origination of a new protein from a old protein and establish your theory/religion as at least scientifically plausible???

    Dollo’s law, the symmetry of time, and the edge of evolution – Michael Behe – Oct 2009
    Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,,
    A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses.
    http://www.evolutionnews.org/2.....f_tim.html

    Severe Limits to Darwinian Evolution: – Michael Behe – Oct. 2009
    Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
    http://www.evolutionnews.org/2......html#more

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway – Ann K. Gauger and Douglas D. Axe – April 2011
    Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth.
    http://bio-complexity.org/ojs/.....O-C.2011.1

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed – along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

    “A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble.”
    Problems in Protein Evolution:
    http://www.cs.unc.edu/~plaisted/ce/blocked.html

    Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors – Doug Axe
    Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular.
    http://nsmserver2.fullerton.ed.....lution.pdf

    Darwin’s God: Post Synaptic Proteins Intolerant of Change – December 2010
    Excerpt: Not only is there scant evidence of intermediate designs leading to the known proteins, but the evidence we do have is that these proteins do not tolerate change.
    http://darwins-god.blogspot.co.....nt-of.html

  16. 16
    DrREC says:

    BA77, they aren’t limited in red blood cell production.

    Read the article: “What’s unique about Tibetans is they don’t develop high red blood cells counts”

    Which is a good thing. Google polycythemia and thrombosis if you don’t believe me. Increased blood viscosity risks clots, spleen damage, etc.

    They have heathy hematocrit values–not exactly a loss of information, or deleterious mutation. What is remarkable is they harbor adaptive mutations to a number of genes, that allow them, without cranking out massive numbers of red blood cells, to survive at elevation. These are gain-of-function mutations, despite your blustering otherwise.

    Many more recent publications:
    http://scholar.google.com/scho.....8;as_vis=1

  17. 17
    DrREC says:

    “Why DrREC, so all you have to do to prove your point is say that Protein a evolved from protein b??? Why that is just special DrREC! Perhaps you could sooth my doubts and actually physically demonstrate the origination of a new protein from a old protein and establish your theory/religion as at least scientifically plausible???”

    I’m sorry, I find this rant awfully incoherent, and I don’t understand why my previous references are insufficient to answer your query.

    The first two demonstrate the generation of novel, functional proteins by mutation and recombination of previously non-coding regions. The last demonstrates the directed evolution of novel activities (taking activity/protein a and evolving it into activity/protein b, where b doesn’t exist in nature, by ‘Darwinian’ processes-mutation and recombination acted on by selection.

  18. 18
    bornagain77 says:

    DrREC, you got to be kidding, do you actually think your last paper that you cited is neo-Darwinian in the least. Those guys are using every bit of knowledge and ingenuity they got to ‘intelligently’ direct the experiment. Perhaps you don’t consider the experimenters intelligent since they are merely accidental by-products of Darwinism and thus it is okay for them to interfere with neo-Darwinian processes as much as they wany?? 🙂 But as for myself, I see a very heavy thumb on the scale for your supposed evidence that testifies all the more clearly of the poverty of your evidential base since you have had to resort to such shenanigans!

  19. 19
    DrREC says:

    ” ‘intelligently’ direct the experiment”

    No, they don’t design the outcome. They generate variation with mutation and recombination, and select for results. How is this not analogous to natural selection?

  20. 20
    bornagain77 says:

    DrREC you claim:

    ‘The first two demonstrate the generation of novel, functional proteins by mutation and recombination of previously non-coding regions.’

    Excuse me, they infer relationship from sequences and definitely do not DEMONSTRATE the novel proteins arising!!!

  21. 21
    bornagain77 says:

    So neo-Darwinian evolution practices,,, Strategy and success for the directed evolution of enzymes

    Calling a AMC Gremlim a formula one race car does not make the it true DrREC, But alas truth is not what you are interested in is it???

  22. 22
    DrREC says:

    LOL, so now we’re down to direct observation, and the rejection of inference.

    Have you observed design, or is it an inference?

  23. 23
    bornagain77 says:

    DrREC, why don’t you use the Lenski Long Term Experiment to DEMONSTRATE what almighty neo-Darwinism can do??? Oh that’s right Lenski’s e-coli support the opposite conclusion!

  24. 24
    DrREC says:

    The query wasn’t limited to natural processes. It was for the origination of a novel protein by ‘Darwinian’ processes. Recombination and mutagenesis coupled with selection made novel proteins.

  25. 25
    bornagain77 says:

    DrREC, you are the one who said DEMONSTRATE, I merely exposed you for being a liar once again to cover up the fact you have ZERO evidence!

  26. 26
    DrREC says:

    But we could do this forever. BA77, regarding the original thread:

    Want to show calculations that the number of observed mutations between humans and chimps is impossible?

    Want to defend the claim in the original post that there must be a whopping number of beneficial mutations?

  27. 27
    DrREC says:

    “DrREC, you are the one who said DEMONSTRATE,”
    “Excuse me, they infer relationship from sequences and definitely do not DEMONSTRATE the novel proteins arising!!!”

    Whatever. Calm down.

    As for the evidence in that paper-why reject the inference. Non-coding sequences in present in other species have a mutation or recombination yielding a functional protein in one. They have been tested for function. Conclusion-evolution of a novel, functional protein.

    You reject this as a inference. Have you observed design, or is it an inference?

  28. 28
    bornagain77 says:

    DrREC, ‘The query wasn’t limited to natural processes.’

    Hmm the exact point being debated wasn’t used. How special!

  29. 29
    bornagain77 says:

    DrREC, you do not seem to grasp the most fundamental point of empirical science. For you to support your delusional claims for neo-Darwinism, you must actually demonstrate the origination of genes and proteins by purely neo-Darwinian processes. You cannot assume the conclusion you want to make in your argument, by merely alluding to sequence similarity. It is the very point being debated and is not satisfied by anything less than a actual demonstration.

  30. 30
    bornagain77 says:

    DrREC, I’ve shown papers (Axe; Behe) that DEMONSTRATE the neo-Darwinian evolution of proteins and genes, that are completely different between chimps and man, is impossible. Whereas you have merely shown a preconceived conclusion imposed on sequence similarity data. As far as science is concerned experiment beats conjecture all the time, thus the burden is on you.

  31. 31
    bornagain77 says:

    DrREC you ask:

    Have you observed design, or is it an inference?

    DrREC, any time you, or anyone else posts a comment, I confidently observe design in action. The reason I can be confident that design is involved is that when you generate the functional information in your comment you post, you have in fact exceeded what is possible for the entire material processes of the universe over the entire history of the universe. Since I know of ZERO instances of neo-Darwinian evolution DEMONSTRATING the generation of that level of functional information, then the inference holds. Whereas you on the other hand are inferring something that has NEVER been demonstrated for neo-Darwinian evolution, must less purely material processes,, namely the generation of a ‘non-trivial’ level of functional information:

    Stephen C. Meyer – The Scientific Basis For the Intelligent Design Inference – video
    http://www.metacafe.com/watch/4104651

    Book Review – Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.
    Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren’t chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.
    So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it’s a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.
    http://www.fourmilab.ch/docume.....k_726.html

    The Capabilities of Chaos and Complexity – David L. Abel – 2009
    Excerpt: “A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Premise One: No materialistic cause of specified complex information is known.
    Conclusion: Therefore, it must arise from some unknown materialistic cause

    On the other hand, Stephen Meyer describes the intelligent design argument as follows:

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

    There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs — intelligent design. We know this from our uniform experience and from the design filter — a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).)

    Of course DrREC, you could deny that you are intelligent and that you really didn’t ‘design’ your comments, but as far as the science is concerned my inference stands firm whereas you have no basis for your sequence similarity inference.

  32. 32
    Prof. FX Gumby says:

    DrREC, you might as well give up the argument. This fool will be satisfied with nothing less than one of his precious youtube videos of a beneficial protein-coding mutation arising in real time, complete with sound effects and laser light shows. On the other hand, he is perfectly willing to accept the slightest hand wave in the direction of divine intervention design.

    I think the operative phrase is “selective hyperskepticism”?

  33. 33
    goodusername says:

    “He does though present claims that can be questioned scientifically; for instance believing that humanity evolved within a population size of roughly 10,000 people. So how should we model these claims?

    Assuming 20 years for a generation and 6 million years from an ape-like ancestor to mankind would give 300,000 generations to achieve an evolutionary progression from an ape-like ancestor to man. As an aside, in that time only 3 billion individuals would have lived and died, a smaller number than the present human population alive today. Does he really expect us to believe that man could have arisen in so small a number of ancestors? ”

    –There were about 1 billion people in 1800. All of those people were dead by 1920, when the world population was 2 billion – and now just about all of those people have died. There’s your previous 3 billion people – just right there. So obviously more than 3 billion people have lived and died in the previous 6 million years.

    Denis Venema wasn’t saying that humans only numbered about 10k throughout our history. He said that humans never numbered LESS than 10k, and he said it in context of explaining that it’s POPULATIONS that evolve, not individuals. And thus his point is that the “first” humans were a population of at least 10k – and so evolution doesn’t claim that there was ever a “first human” or “first pair” of humans. And this was just the initial population size.

    The estimates I usually hear is that pre-agricultural revolution that humans were a roughly stable population of about 1 million, and that over 100 billion humans have lived and died. Those are roughly the numbers mentioned here:
    http://en.wikipedia.org/wiki/W.....ever_lived

  34. 34
    bornagain77 says:

    Prof. FX Gumby, perhaps you can entertain ‘this fool’ with a actual DEMONSTRATION of neo-Darwinian evolution generating genes/proteins, instead of just sequence similarity comparison that presupposes the very thing being asked into its conclusion???. Shoot Prof. FX Gumby, let’s just get all silly, clown-like, foolish and look at the 50,000 generations of e-coli in the Long Term Evolution Experiment of Lenski, which is equivalent to about a million years of supposed Human evolution, since it is the best direct evidence we got for the power of Darwinism, and see what the almighty power of neo-Darwinian evolution has DEMONSTRATED for this fool to behold:

    And the drum-roll please,,,,,,,

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    But that can’t be right Prof. FX Gumby,,, the mutations interfered with each other, preventing further ‘evolution’, so let’s take a closer look,,

    Michael Behe’s Quarterly Review of Biology Paper Critiques Richard Lenski’s E. Coli Evolution Experiments – December 2010
    Excerpt: After reviewing the results of Lenski’s research, Behe concludes that the observed adaptive mutations all entail either loss or modification–but not gain–of Functional Coding ElemenTs (FCTs)
    http://www.evolutionnews.org/2.....41221.html

    Prof. FX Gumby, this is not good for you guys. Perhaps if you insult us fools who question the almighty power of Darwinism a little more, then you can make these consistent types of experimental results magically go away. But then again something tells me this is NEVER going away!

    Dembski and Marks’s work on Conservation of Information;,,,

    LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information
    William A. Dembski and Robert J. Marks II
    http://evoinfo.org/publication.....ation-law/

    ,,,Encoded classical information, such as what we find in computer programs, and yes as we find encoded in DNA, is found to be a subset of ‘transcendent’ quantum information by the following method:,,,

    This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy.
    Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    ,,,And here is the empirical confirmation that quantum information is ‘conserved’;,,,

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

  35. 35
    DrREC says:

    Prof. FX Gumby,

    I wouldn’t be too harsh. I think bornagain77 summarizes the ID position well-no one here seems to ever correct him. His posts are revealing.

    Since functional information DOES increase in directed evolution, natural evolution, and genetic algorithms (even Behe lists “adaptive gain of functional coded elements)” in his latest review, what are we left with?

    BA77 provides the answer–in the face of observations that show the pathways (mutation and recombination) by which the novel activities can about, he sees design.

    This is trick one: “purely neo-Darwinian processes” Purely? How do I prove that? How do I rule out the influence of a designer in human evolution, or my test tube. I can’t. Maybe the designer came in and did something. I can describe the process, the natural process that fully accounts for it. But he sees design, and declares it. No detection, no scientific need to invoke it, but there it is. This makes ID a non-falsifiable equivalent of theistic evolution. See the natural process, study the process, but it must have been guided. What’s the difference?

    Trick two is using the evidence only when it is helpful to ID: “they infer relationship from sequences and definitely do not DEMONSTRATE the novel proteins arising”

    So sequence based-inferences ala the original post, Behe, etc., are fine, but when the evolution of a new gene by comparing humans and chimps is inferred, we must strike it from the record. Very convenient.

    Trick three is resorting to hocus-pocus interpretations of science. The quantum mechanics business is a good laugh. Hey BA77, you never answered my question: does ‘realism’ have the same meaning in quantum mechanics and metaphysics? Until you figure out that one, you’re pretty much embarrassing yourself here.

  36. 36
    bornagain77 says:

    DrREC you state:

    ‘Since functional information DOES increase in directed evolution, natural evolution, and genetic algorithms (even Behe lists “adaptive gain of functional coded elements)” in his latest review, what are we left with?’

    First, let’s look at your example for ‘directed’ evolution. From their abstract in the paper we find this quote

    Strategy and success for the directed evolution of enzymes.
    Excerpt: The underlying principles that lead to early dead-ends for directed evolution experiments are also discussed along with recent strategies designed to by-pass them.
    http://www.ncbi.nlm.nih.gov/pubmed/21684150

    DrREC, perhaps you find designing strategies to overcome the dead-ends of neo-Darwinian processes to be a purely neo-Darwinian process, but DrREC the last time I checked designing strategies was held to be a intelligent activity. i.e. you are severely begging the question by claiming this paper as proof for what neo-Darwinism can do.,,, DrREC, you then claim ‘natural’ (purely Darwinian) evolution can produce functional information; Well since this is the very point being debated now we are getting somewhere. But alas you have provided no paper showing Darwinian evolution producing any non-trivial functional information (genes and/or proteins) where as I’ve cited Lenski, Behe, and Axe that shows that there are severe limits for what neo-Darwinian processes can do. Thus apparently you think your word that it can happen by purely neo-Darwinian processes is good enough to establish your claim beyond reasonable doubt, but alas I do not trust you. In fact I think neo-Darwinists, by and large, are a very dishonest people! Thus please present the exact empirical evidence instead of just your say so that it is so. You then claim that genetic algorithms, which are designed by humans, can create functional information. But when these man-made genetic algorithms are looked at closely we find:

    LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information
    William A. Dembski and Robert J. Marks II
    Excerpt: Searches that operate by Darwinian selection, for instance, often significantly outperform blind search. But when they do, it is because they exploit information supplied by a fitness function — information that is unavailable to blind search. Searches that have a greater probability of success than blind search do not just magically materialize. They form by some process. According to LCI, any such search-forming process must build into the search at least as much information as the search displays in raising the probability of success.
    Though not denying Darwinian evolution or even limiting its role in the history of life, the Law of Conservation of Information shows that Darwinian evolution is inherently teleological. Moreover, it shows that this teleology can be measured in precise information-theoretic terms.
    http://evoinfo.org/publication.....ation-law/

    Thus DrREC, do you concede the main point of Dembski’s paper, that IF neo-Darwinism could generate functional information in life, (which no empirical demonstration has been forthcoming by neo-Darwinists that it can do as such, which is the main point being debated by the way), that that gain in functional information would have to be the result of Intelligent Design built into nature??? Then DrREC, you have the sheer audacity to actually cite Behe’s latest paper as proof for neo-Darwinian evolution. I think Eric Anderson addressed this quite well on Gil’s post:

    DrRec: “Even Behe lists multiple “adaptive gain of functional coded elements” in his latest review*.”

    This is not the first time you have put forward this red herring, so I believe it is high time to weigh in and put a stop to your misreading of the situation.

    Behe has, for some time, and as further illustrated in the paper you cited, been looking for what he calls the “edge of evolution” or the boundary where traditional evolutionary mechanisms can actually do something. Behe goes through many examples of mutations and tries to categorize them to see what lesson can be learned. While there are a small handful of what could be viewed as “gain of function” mutations, the takeaway from Behe’s careful review is most decidedly *not* that natural processes can readily come up with new informational structures.

    Further, even in those cases where there is arguably a gain of function, Behe shows that such “gain” almost inevitably results from the breakage of an existing part or system. Indeed, a large part of the point of Behe’s paper is to propose what he calls the “First Rule of Adaptive Evolution,” namely that in particular circumstances a fitness advantage can sometimes be gained by breaking or blunting a functional coded element.

    The strong takeaway from all this is that (i) naturalistic processes are terrible at producing information gain (indeed, we’re still waiting for a decent example of information gain beyond the absolutely trivial), and (ii) even in those cases where a survival advantage has been conferred by a mutation, it is typically the result of breaking or blunting an existing functional element, not from creating some new informational element.

    You then go on to state I’m being unreasonable in my view of the evidence for discounting your ‘strategies for success’ paper, which clearly, as illustrated earlier, is ‘designed’ to overcome neo-Darwinian dead-ends. But alas DrREC, why do you want this paper to count for neo-Darwinism so badly when, clearly, to reasonable people, it does not count as a purely neo-Darwinian process? It is because, as empirically DEMONSTRATED with Lenski’s e-coli and Behe’s malaria and HIV, you have no evidence, whatsoever, that purely neo-Darwinian processes can do anything beyond the utterly trivial as far as generating functional information above and beyond what is already present in life!!! You then gripe about my discounting of the sequence similarity evidence you cited as ‘proof’ of neo-Darwinism, which once again clearly shows that you have no grasp, whatsoever, of the most fundamental precepts of empirical science, for clearly you have not DEMONSTRATED that proteins can change from one remote island of functionality to another remote island of functionality by neo-Darwinian means, but have merely asserted the very point being questioned does not have to be demonstrated. i.e. neo-Darwinists need to show the step by step amino acid substitution process by which proteins make these universe wide leaps to different islands of functionality (Axe; 2004) without ending in failure for the functionality of the protein!!!

  37. 37
    bornagain77 says:

    DrREC, You then go on to have a ‘good laugh’ at this ‘quantum mechanics business’. But alas the last laugh is on you for quantum mechanics, due to recent breakthroughs in science, has falsified the ‘reductive’ materialistic theory of neo-Darwinism:

    Falsification of neo-Darwinism by quantum mechanics;

    First, Here is the falsification of local realism (reductive materialism).

    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:

    The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    And yet, quantum entanglement, which rigorously falsified local realism (reductive materialism) as the complete description of reality, is now found in molecular biology on a massive scale!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself
    not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!
    ,,,To refute this falsification of neo-Darwinism, one must falsify Alain Aspect, and company’s, falsification of local realism (reductive materialism)!

    To dovetail into Dembski and Marks’s work on Conservation of Information;,,,

    LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information
    William A. Dembski and Robert J. Marks II
    http://evoinfo.org/publication.....ation-law/

    ,,,Encoded classical information, such as what we find in computer programs, and yes as we find encoded in DNA, is found to be a subset of ‘transcendent’ quantum information by the following method:,,,

    This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy.
    Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    ,,,And here is the empirical confirmation that quantum information is ‘conserved’;,,,

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    DrREC, I actually had a neo-Darwinists tell me the other day that none of the preceding evidence matters to neo-Darwinism for neo-Darwinism does not care about material particles or quantum entanglement/information, but only cares about how species change over time. To which, it may surprise you to find, that I whole-heartily agreed with him. For I told him that, as far as I could see, neo-Darwinism has nothing, whatsoever, to do with how reality is constructed at all!!

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007

  38. 38
    bornagain77 says:

    DrREC, here is some more that ‘quantum business’ for you to get a ‘good laugh’ with:

    Information? What Is It Really? Professor Andy McIntosh – Video
    http://www.metacafe.com/watch/4739025/

    As Professor McIntosh points out in the preceding video, information is a very elusive entity to nail down, for though we can write it down, encode it, and transfer the information from one material medium to another completely different material medium, the information never changes its meaning though the material mediums, on which the information is stored, are completely different upon the information’s transfer.,,, It is also interesting to note that a Compact Disc crammed with information on it weighs exactly the same as a CD with no information on it whatsoever.,, i.e. Information, from our everyday experience, gives every indication of being completely transcendent of any material basis. i.e. Information gives every indication of being ‘real’ and yet it also gives every indication of being transcendent of time and space though it may be stored on various material mediums. Moreover, although our everyday experience gives us a very enigmatic picture of ‘information’, breakthroughs in quantum mechanics have given us a more complete picture of ‘information’ and its place (prominence) in the overall structure of reality; Anton Zeilinger, a leading researcher in Quantum mechanics, gives a brief outline, of how quantum entanglement/information is extended to allow quantum teleportation, in this following video;

    Quantum Entanglement and Teleportation – Anton Zeilinger – video
    http://www.metacafe.com/watch/5705317/

    And quantum teleporation shows that atoms, which are suppose to be the basis from which functional information ‘emerges’ in the neo-Darwinian framework, are now shown to be, in fact, reducible to the functional information that the atoms are suppose to be the basis of!

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    i.e. It is impossible for quantum information/entanglement to ever ‘emerge’ from any material basis of atoms when atoms are now shown to reduce to a transcendent basis of quantum information in the first place!!! But alas DrREC, I’m fairly certain that none of these insurmountable problems for the reductive materialistic framework of neo-Darwinism presented by quantum mechanics matters to you, and that you will have another ‘good laugh’ at all that ‘quantum business’. But, if you do do as such, then to me it just demonstrates once again your intellectual dishonesty to the facts and your dogmatic belief in neo-Darwinism no matter what the evidence says to the contrary;

  39. 39
    bornagain77 says:

    Further note:

    Quantum entanglement is shown to be related to ‘functional information’ by the following evidence;

    Quantum Entanglement and Information
    Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems.
    http://plato.stanford.edu/entries/qt-entangle/

    Quantum Computing in DNA – Stuart Hameroff
    Excerpt: Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist).
    Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement.
    http://www.quantumconsciousnes.....InDNA.html

    Indeed the ‘quantum computation’ that is accomplished by the quantum entanglement within DNA is very impressive (and drastically surpasses, by many, many, orders of magnitude, anything man has accomplished in his efforts at quantum computation):

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

  40. 40
    Joseph says:

    There still isn’t any genetic evidence that demonstrates the changes required (from chimp to human) are even possible.

    So you have to start there. Good luck…

  41. 41
    Joseph says:

    DrREC:

    Recent de novo origin of human protein-coding genes
    http://genome.cshlp.org/conten.....095026.109

    Nope, nothing about Darwinian processes there- just question-begging.

    Not one link supports the claim that Darwinian processes didit. Strange…

  42. 42
    Joseph says:

    DrREC,

    All you are doing is engaging in question-begging- Just how was it determined that gene duplication and recombination are ‘Darwinian’ processes?

    Do you realize that ID is not anti-evolution? Or do you really think your ignorance refutes ID?

  43. 43
    Stu7 says:

    Would the Darwinists among us care to comment on the points BA77 highlighted relating to Lenski’s 50,000 generation e. coli experiments, which would equate to about 1 million years of human evolution.

    In particular the points raised in comment 12.1. Quite revealing in it’s findings, but perhaps I’m missing something.

  44. 44

    Well, a quick comments from me:

    ba77 wrote:

    Shoot Prof. FX Gumby, let’s just get all silly, clown-like, foolish and look at the 50,000 generations of e-coli in the Long Term Evolution Experiment of Lenski, which is equivalent to about a million years of supposed Human evolution

    It isn’t “equivalent to about a million years of supposed Human evolution” because bacteria are cloning species, not sexually reproducing species. This makes a huge difference.

    It’s not the only problem with ba77’s point, but it’s an especially glaring one.

  45. 45

    Actually, there’s a sense in which bacteria aren’t “species” at all. They aren’t by most definitions.

  46. 46
    Petrushka says:

    I’ve shown papers (Axe; Behe) that DEMONSTRATE the neo-Darwinian evolution of proteins and genes, that are completely different between chimps and man, is impossible.

    I’m unable to find Axe or Behe mentioning the evolution from ape to man being impossible.

    Are you quoting them or making an inference?

  47. 47
    DrREC says:

    “Just how was it determined that gene duplication and recombination are ‘Darwinian’ processes?”

    I really now don’t know how much extra meaning you’ve loaded into ‘Darwinian’ but mutation, gene duplication and recombination are well-examined natural processes.

    Are you trying to say I can’t prove they are natural, that perhaps a designer is using them in executing designs?

    Fine. I can’t falsify that. Keep it as a personal belief. This leads me to the answer of your second question. I do NOT think ID is anti-evolution. I think it has degraded to theistic evolution.

  48. 48

    Well, no, ba77, and Lenski himself doesn’t think so.

  49. 49
    Joseph says:

    DrREC:

    I really now don’t know how much extra meaning you’ve loaded into ‘Darwinian’ but mutation, gene duplication and recombination are well-examined natural processes.

    Design is a natural process too- a well-examined natural process.

    But anyway you don’t have any evidence taht gene duplication and recombination are blind, undirected chemical processes- ie darwinian processes.

    As for ID and theistic evolution- well ID is nothing like TE.

  50. 50
    bornagain77 says:

    Well by golly Elizabeth, if bacteria have nothing to do with human evolution then I guess the entire Random Mutation and Natural Selection process itself has absolutely nothing to with Human Evolution either!!!! Too bad I know your playbook Elizabeth,,,, i.e. neo-Darwinian tactic #5, when faced with clear evidence that severely contradicts neo-Darwinism, deny that the clear evidence has anything whatsoever to do with evolution.

    Dr. Behe states in The Edge of Evolution on page 135:

    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.”

    That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....26651.html

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....26281.html

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2....._edge.html

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.

    Elizabeth, you have to be completely blind, or hopelessly dishonest, to not see HUGE problems for neo-Darwinism in this evidence.

    Further notes:

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial microbial. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;
    http://www.thefreelibrary.com/.....a014909330

  51. 51
    Joseph says:

    I’m unable to find Axe or Behe mentioning the evolution from ape to man being impossible.

    Nice non-sequitur. You do realize that ID is not anti-evolution…

  52. 52
    Joseph says:

    It isn’t “equivalent to about a million years of supposed Human evolution” because bacteria are cloning species, not sexually reproducing species. This makes a huge difference.

    Yes it does make a huge difference and that difference argues against universal common descent as sexual reproduction put an end to it.

  53. 53
    bornagain77 says:

    Well Elizabeth, since I’m more interested in what the e-coli experiment actually says, than what Lenski personal opinion is, I think I will follow the evidence and not a dogmatic personal opinion of a scientists that refuses to acknowledge the clear implications of the evidence, even when that evidence is right before their very eyes. In fact, this experiment kills two birds with one stone, 1. It demonstrates the extreme difficultly, faced by neo-Darwinian processes, to locate random mutations that will actually work together to build functional complexity/information, i.e. to actually evolve something,,, and 2. it demonstrates the extreme blindness that Darwinists have to any results that contradict their deeply held beliefs in neo-darwinism, even when those findings are wrought by their very own hands.

  54. 54

    Well by golly Elizabeth, if bacteria have nothing to do with human evolution then I guess the entire Random Mutation and Natural Selection process itself has absolutely nothing to with Human Evolution either!

    Not at all, ba77, but sexual reproduction provides a very different and much more efficient mechanism for propagating potentially useful alleles through a population, because DNA sequences can “travel” independently.

    However, rather than bother to find out whether I might have a point here, you cast aspersions on my motives.

    I suggest you find out a bit more about how alleles propagate through sexually reproducing populations before you generalise findings from bacterial studies to humans, or even to fruitflies,and certainly before you accuse the people who take issue with your conclusions of “blindness”.

  55. 55

    No, it doesn’t “argue against common descent” (or at least you aren’t making the argument that it does).

  56. 56
    bornagain77 says:

    Elizabeth you state:

    certainly before you accuse the people who take issue with your conclusions of “blindness”.

    You are right, it is a extremely bad insult to people who are actually blind to compare them to the dogmatic neo-Darwinists whose ‘blindness’ is, as far as I can tell, a matter of personal religious preference rather something beyond their control, thus my apologies to all actually blind people reading this! 🙂
    Of note:

    Blind Woman Can See During Near Death Experience (NDE) – Pim von Lommel – video
    http://www.metacafe.com/watch/3994599/

    Kenneth Ring and Sharon Cooper (1997) conducted a study of 31 blind people, many of who reported vision during their Near Death Experiences (NDEs). 21 of these people had had an NDE while the remaining 10 had had an out-of-body experience (OBE), but no NDE. It was found that in the NDE sample, about half had been blind from birth. (of note: This ‘anomaly’ is also found for deaf people who can hear sound during their Near Death Experiences(NDEs).)
    http://findarticles.com/p/arti....._65076875/

    The Scientific Evidence for Near Death Experiences – Dr Jeffery Long – Melvin Morse M.D. – video
    http://www.metacafe.com/watch/4454627

    coast to coast – Blind since birth – Vicki’s NDE
    http://www.youtube.com/watch?v=e65KhcCS5-Y

  57. 57

    So I take it you are going to find out why sexual reproduction makes a difference to the rate of adaptation in terms of generations?

  58. 58
    bornagain77 says:

    Elizabeth you also state:

    I suggest you find out a bit more about how alleles propagate through sexually reproducing populations before you generalise findings from bacterial studies to humans, or even to fruitflies,

    Well Elizabeth since you seem to think you have population genetics all figured out, I suggest you apply for the job at Oxford University to straighten the problems of population genetics out;

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

    as to

    how alleles propagate through sexually reproducing populations

    It seems even population geneticists themselves admit to the severe deficiency of neo-Darwinian mechanisms to account for such:

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.
    http://www.discovery.org/a/9461

    Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology – video
    http://www.metacafe.com/watch/4165203

    But alas Elizabeth, this is merely mathematical models, so let’s look at the ‘real’ world, at the experiments on fruit flies (something you accused me of ignorance on), and see if we can find evidence for ‘alleles propagating’;

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    But hey Elizabeth, you say that sexual reproduction solves all this, whereas I, nor apparently population geneticists or experimental biologists, can find any evidence that it does anything of the sort. But just curious Elizabeth, can you please tell me, in purely neo-Darwinian terms, how sexual reproduction came to be in the first place???

    The machinery for recombination is part of the chromosome structure
    Excerpt: “The more we learn about meiosis, the more mysterious it becomes”, says Franz Klein from the Department for Chromosome Biology of the University of Vienna. “It is surprising that maternal and paternal chromosomes find each other at all. Because at the time of interaction all chromosomes have generated a sister and are tightly connected with her like a Siamese twin.
    http://www.physorg.com/news/20.....osome.html

    Shoot Elizabeth, can you please give me a clear neo-Darwiniam pathway as to how self-replication started in the first place???

    Astonishing Molecular Machines – Drew Berry
    http://www.metacafe.com/w/6861283

    Dividing Cells ‘Feel’ Their Way Out Of Warp
    “What we found is an exquisitely tuned mechanosensory system that keeps the cells shipshape so they can divide properly,” – Douglas N. Robinson, Ph.D.
    http://www.sciencedaily.com/re.....142402.htm

    Shoot Elizabeth, can you give me a clear neo-Darwian pathway as to how ANY molecular machine whatsoever came to be???

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    The following expert doesn’t even hide his very unscientific preconceived philosophical bias against intelligent design,,,

    ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,

    Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,

    ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
    Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
    *Professor Emeritus of Biochemistry, Colorado State University, USA

    Michael Behe – No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
    http://www.metacafe.com/watch/5302950/

    “The response I have received from repeating Behe’s claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.”
    David Ray Griffin – retired professor of philosophy of religion and theology

    Molecular Biology Animations – Demo Reel
    http://www.metacafe.com/w/5915291/

    Thus apparently Elizabeth, neo-Darwinists have ZERO evidence for the claims you are making. The sheer poverty of evidence for such sweeping claims as to how life came to be on Earth, should stop neo-darwinism dead in its tracks, but alas, as Dr. Hunter says, its not about the science, it’s about Religion;

    Religion drives science and it matters!

  59. 59
    Petrushka says:

    I’m interested in how the slow change in some bacteria comports with ba77’s views on genetic entropy.

    Does the designer arbitrarily prevent prevent change, or does he only do this for spore-forming bacteria?

  60. 60
    Joseph says:

    Yes, it does. Ya see with sexual reproduction even the most beneficial mutation may not even make it to the next generation as only 1/2 of each parent’s genome makes it. And it doesn’t have to be the 1/2 with the beneficial mutation.

    As geneticist Giuseppe Sermonti said:

    Sexuality has brought joy to the world, to the world of the wild beasts, and to the world of flowers, but it has brought an end to evolution. In the lineages of living beings, whenever absent-minded Venus has taken the upper hand, forms have forgotten to make progress. It is only the husbandman that has improved strains, and he has done so by bullying, enslaving, and segregating. All these methods, of course, have made for sad, alienated animals, but they have not resulted in new species. Left to themselves, domesticated breeds would either die out or revert to the wild state—scarcely a commendable model for nature’s progress.

    (snip a few paragraphs on peppered moths)

    Natural Selection, which indeed occurs in nature (as Bishop Wilberforce, too, was perfectly aware), mainly has the effect of maintaining equilibrium and stability. It eliminates all those that dare depart from the type—the eccentrics and the adventurers and the marginal sort. It is ever adjusting populations, but it does so in each case by bringing them back to the norm. We read in the textbooks that, when environmental conditions change, the selection process may produce a shift in a population’s mean values, by a process known as adaptation. If the climate turns very cold, the cold-adapted beings are favored relative to others.; if it becomes windy, the wind blows away those that are most exposed; if an illness breaks out, those in questionable health will be lost. But all these artful guiles serve their purpose only until the clouds blow away. The species, in fact, is an organic entity, a typical form, which may deviate only to return to the furrow of its destiny; it may wander from the band only to find its proper place by returning to the gang.

    Everything that disassembles, upsets proportions or becomes distorted in any way is sooner or later brought back to the type. There has been a tendency to confuse fleeting adjustments with grand destinies, minor shrewdness with signs of the times.

    It is true that species may lose something on the way—the mole its eyes, say, and the succulent plant its leaves, never to recover them again. But here we are dealing with unhappy, mutilated species, at the margins of their area of distribution—the extreme and the specialized. These are species with no future; they are not pioneers, but prisoners in nature’s penitentiary.

  61. 61
    bornagain77 says:

    Semi OT; Casey Luskin’s excellent follow up article debunking Australopithecus sediba’s exalted status, in mainstream media, as a missing link;

    Australopithecus sediba: The Hype-Cycle Starts Again – Casey Luskin – September 2011
    Excerpt: So leading paleoanthropologists like Bernard Wood, Donald Johanson, Fred Spoor, Ian Tattersal, and Tim White aren’t convinced that Au. sediba was a human ancestor, but the media believes it’s perfectly acceptable to promote the opposite view to the public.

    A final problem with the claims being made about Au. sediba is related the paleoanthropologist who found the fossils himself. Science reports that he formerly had a career as a TV news producer and has a tendency to overstate his findings:,,,
    http://www.evolutionnews.org/2.....50831.html

  62. 62
    Joseph says:

    Sexual reproduction will only slow the rate, if not kill it.

  63. 63

    Well, Sermonti has ignored drift.

  64. 64
    bornagain77 says:

    as to:

    Well, Sermonti has ignored drift.

    to which it can only be observed

    Well, Elizabeth has ignored reality.

  65. 65

    To which I could observe: nope, Joseph and ba77 are ignoring reality.

    But it wouldn’t get us very far, would it?

    I suggest both of you read a little more widely on the population genetics of sexually reproducing populations.

  66. 66
    bornagain77 says:

    Well Elizabeth since you claim you are NOT ignoring reality, let’s just conduct a little experiment and observe, once again, just a little bit about how reality is actually constructed, and how it relates to life, and how it falsifies the materialistic framework of neo-Darwinism, and see if you will ignore how reality is constructed, once again, just so as to preserve your blind faith in your atheistic form of neo-Darwinism; i.e. your chosen religion!

    First, as to ‘spatial relations’ of reality, I noticed that in this following video, on the optical effects for a observer approaching the speed of light, that the 3- Spatial Dimensions, we currently live in, ‘folded and collapsed’ into a tunnel shape, around the direction of travel, as the observer approached the constant of the speed of light.,,,

    Traveling At The Speed Of Light – Optical Effects – video
    http://www.metacafe.com/watch/5733303/

    Here is the interactive website, put together by two Australian University Physics professors, which is directly related to the preceding video, which has a link to the relativistic math on it at the bottom of the page;

    Seeing Relativity
    http://www.anu.edu.au/Physics/Searle/

    Please note the ‘light at the end of the tunnel’, at the 3:22 minute mark of the preceding video, which uncannily matches very many of the Judeo-Christian Near Death Experience testimonies of western cultures;

    The NDE and the Tunnel – Kevin Williams’ research conclusions
    Excerpt: I started to move toward the light. The way I moved, the physics, was completely different than it is here on Earth. It was something I had never felt before and never felt since. It was a whole different sensation of motion. I obviously wasn’t walking or skipping or crawling. I was not floating. I was flowing. I was flowing toward the light. I was accelerating and I knew I was accelerating, but then again, I didn’t really feel the acceleration. I just knew I was accelerating toward the light. Again, the physics was different – the physics of motion of time, space, travel. It was completely different in that tunnel, than it is here on Earth. I came out into the light and when I came out into the light, I realized that I was in heaven.(Barbara Springer)

    Near Death Experience – The Tunnel – video
    http://www.vimeo.com/29021432

    Near Death Experience – The Tunnel, The Light, The Life Review – video
    http://www.metacafe.com/watch/4200200/

    Also of related note to how the 3-Dimension world folds and collapses into a tunnel shape, as the ‘higher dimension’ of the speed of light is approached, is the ‘eternality of time’ revealed by the time dilation of special relativity.

    “I’ve just developed a new theory of eternity.”
    Albert Einstein – The Einstein Factor – Reader’s Digest

    “The laws of relativity have changed timeless existence from a theological claim to a physical reality. Light, you see, is outside of time, a fact of nature proven in thousands of experiments at hundreds of universities. I don’t pretend to know how tomorrow can exist simultaneously with today and yesterday. But at the speed of light they actually and rigorously do. Time does not pass.”
    Richard Swenson – More Than Meets The Eye, Chpt. 12

    This higher dimension, ‘eternal’, inference for the time framework of light is warranted because light is not ‘frozen within time’ yet it is shown that time, as we understand it, does not pass for light.

    Experimental confirmation of Time Dilation
    http://en.wikipedia.org/wiki/T.....nfirmation

    But since the material particles, of the person’s body who is having a Near Death Experience, are clearly ‘staying behind’ as the person is having the Near Death Experience, then, of course, the consciousness of the person must be based on something other than the material particles of the body. Something that must be transcendent of the material realm. (Also of interest to this, as the Cern Particle Accelerator readily testifies, it is not ‘natural’ for material particles to approach the speed of light and, indeed, takes a massive amount of energy for even sub-atomic particles to closely approach the speed of light.) This transcendent something, on which human consciousness must actually be based, instead of ’emerging’ from the material particles, is found to be ‘quantum information’. Transcendent Quantum Information is now shown, empirically, to be foundational to the human body here:

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini & Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73
    Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
    http://www.scimednet.org/quant.....d-protein/

    Quantum states in proteins and protein assemblies:
    The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI
    Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign.
    http://www.tony5m17h.net/SHJTQprotein.pdf

    Myosin Coherence
    Excerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects.
    http://www.energetic-medicine......Page1.html

  67. 67
    bornagain77 says:

    Whereas, quantum information is strongly implicated in human consciousness here:

    Quantum Coherence and Consciousness – Scientific Proof of ‘Mind’ – video
    http://www.metacafe.com/watch/6266865/

    Particular quote of note from preceding video;

    “Wolf Singer Director of the Max Planck Institute for Brain Research (Frankfurt) has found evidence of simultaneous oscillations in separate areas of the cortex, accurately synchronized in phase as well as frequency. He suggests that the oscillations are synchronized from some common source, but the actual source has never been located.”
    James J. Hurtak, Ph.D.

    Corroborating experimental evidence here:

    Brain ‘entanglement’ could explain memories – January 2010
    Excerpt: In both cases, the researchers noticed that the voltage of the electrical signal in groups of neurons separated by up to 10 millimetres sometimes rose and fell with exactly the same rhythm. These patterns of activity, dubbed “coherence potentials”, often started in one set of neurons, only to be mimicked or “cloned” by others milliseconds later. They were also much more complicated than the simple phase-locked oscillations and always matched each other in amplitude as well as in frequency. (Perfect clones) “The precision with which these new sites pick up on the activity of the initiating group is quite astounding – they are perfect clones,” says Plen
    http://www.uncommondescent.com.....ent-399098

    And quantum information is conclusively shown to be transcendent of any material basis here:

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    This following study adds to Alain Aspect’s work in Quantum Mechanics and solidly refutes the ‘hidden variable’ argument that has been used by materialists to try to get around the Theistic implications of the instantaneous ‘spooky action at a distance’ found in quantum mechanics.

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    This following video reveals just how downright ‘spooky’ (to use Einstein’s description) quantum entanglement is:

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182

    And quantum information is shown to be ‘conserved’ here;

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    Of related note; I really enjoyed Michael Egnor’s essay on how consciousness is not reducible to matter;

    The Mind and Materialist Superstition – Six “conditions of mind” that are irreconcilable with materialism:
    http://www.evolutionnews.org/2.....super.html

    more notes of interest:

    Quantum mind–body problem
    Parallels between quantum mechanics and mind/body dualism were first drawn by the founders of quantum mechanics including Erwin Schrödinger, Werner Heisenberg, Wolfgang Pauli, Niels Bohr, and Eugene Wigner – Wikipedia

    “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.” Eugene Wigner (1902 -1995) from his collection of essays “Symmetries and Reflections – Scientific Essays”; Eugene Wigner laid the foundation for the theory of symmetries in quantum mechanics, for which he received the Nobel Prize in Physics in 1963.

    The Unbearable Wholeness of Beings – Steve Talbott
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    http://www.thenewatlantis.com/.....-of-beings

    Can a Computer Think? – Michael Egnor
    Excerpt: The Turing test isn’t a test of a computer. Computers can’t take tests, because computers can’t think. The Turing test is a test of us. If a computer “passes” it, we fail it. We fail because of our hubris, a delusion that seems to be something original in us. The Turing test is a test of whether human beings have succumbed to the astonishingly naive hubris that we can create souls.

    Breathtaking Performance Of Agnus Dei From Child Singer – Music Videos
    http://www.godtube.com/watch/?v=K7WZYPNX

  68. 68
    bornagain77 says:

    Whereas, quantum information is strongly implicated in human consciousness here:

    Quantum Coherence and Consciousness – Scientific Proof of ‘Mind’ – video
    http://www.metacafe.com/watch/6266865/

    Particular quote of note from preceding video;

    “Wolf Singer Director of the Max Planck Institute for Brain Research (Frankfurt) has found evidence of simultaneous oscillations in separate areas of the cortex, accurately synchronized in phase as well as frequency. He suggests that the oscillations are synchronized from some common source, but the actual source has never been located.”
    James J. Hurtak, Ph.D.

    Corroborating experimental evidence here:

    Brain ‘entanglement’ could explain memories – January 2010
    Excerpt: In both cases, the researchers noticed that the voltage of the electrical signal in groups of neurons separated by up to 10 millimetres sometimes rose and fell with exactly the same rhythm. These patterns of activity, dubbed “coherence potentials”, often started in one set of neurons, only to be mimicked or “cloned” by others milliseconds later. They were also much more complicated than the simple phase-locked oscillations and always matched each other in amplitude as well as in frequency. (Perfect clones) “The precision with which these new sites pick up on the activity of the initiating group is quite astounding – they are perfect clones,” says Plen
    http://www.uncommondescent.com.....ent-399098

    And quantum information is conclusively shown to be transcendent of any material basis here:

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    This following study adds to Alain Aspect’s work in Quantum Mechanics and solidly refutes the ‘hidden variable’ argument that has been used by materialists to try to get around the Theistic implications of the instantaneous ‘spooky action at a distance’ found in quantum mechanics.

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    This following video reveals just how downright ‘spooky’ (to use Einstein’s description) quantum entanglement is:

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182

    And quantum information is shown to be ‘conserved’ here;

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    Of related note; I really enjoyed Michael Egnor’s essay on how consciousness is not reducible to matter;

    The Mind and Materialist Superstition – Six “conditions of mind” that are irreconcilable with materialism:
    http://www.evolutionnews.org/2.....super.html

    more notes of interest:

    Quantum mind–body problem
    Parallels between quantum mechanics and mind/body dualism were first drawn by the founders of quantum mechanics including Erwin Schrödinger, Werner Heisenberg, Wolfgang Pauli, Niels Bohr, and Eugene Wigner – Wikipedia

    “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.” Eugene Wigner (1902 -1995) from his collection of essays “Symmetries and Reflections – Scientific Essays”; Eugene Wigner laid the foundation for the theory of symmetries in quantum mechanics, for which he received the Nobel Prize in Physics in 1963.

    The Unbearable Wholeness of Beings – Steve Talbott
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.

    Can a Computer Think? – Michael Egnor
    Excerpt: The Turing test isn’t a test of a computer. Computers can’t take tests, because computers can’t think. The Turing test is a test of us. If a computer “passes” it, we fail it. We fail because of our hubris, a delusion that seems to be something original in us. The Turing test is a test of whether human beings have succumbed to the astonishingly naive hubris that we can create souls.

    Breathtaking Performance Of Agnus Dei From Child Singer – Music Videos
    http://www.godtube.com/watch/?v=K7WZYPNX

  69. 69
    bornagain77 says:

    whoops wrong spot:

    Whereas, quantum information is strongly implicated in human consciousness here:

    Quantum Coherence and Consciousness – Scientific Proof of ‘Mind’ – video
    http://www.metacafe.com/watch/6266865/

    Particular quote of note from preceding video;

    “Wolf Singer Director of the Max Planck Institute for Brain Research (Frankfurt) has found evidence of simultaneous oscillations in separate areas of the cortex, accurately synchronized in phase as well as frequency. He suggests that the oscillations are synchronized from some common source, but the actual source has never been located.”
    James J. Hurtak, Ph.D.

    Corroborating experimental evidence here:

    Brain ‘entanglement’ could explain memories – January 2010
    Excerpt: In both cases, the researchers noticed that the voltage of the electrical signal in groups of neurons separated by up to 10 millimetres sometimes rose and fell with exactly the same rhythm. These patterns of activity, dubbed “coherence potentials”, often started in one set of neurons, only to be mimicked or “cloned” by others milliseconds later. They were also much more complicated than the simple phase-locked oscillations and always matched each other in amplitude as well as in frequency. (Perfect clones) “The precision with which these new sites pick up on the activity of the initiating group is quite astounding – they are perfect clones,” says Plen
    http://www.uncommondescent.com.....ent-399098

    And quantum information is conclusively shown to be transcendent of any material basis here:

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    This following study adds to Alain Aspect’s work in Quantum Mechanics and solidly refutes the ‘hidden variable’ argument that has been used by materialists to try to get around the Theistic implications of the instantaneous ‘spooky action at a distance’ found in quantum mechanics.

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    This following video reveals just how downright ‘spooky’ (to use Einstein’s description) quantum entanglement is:

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182

    And quantum information is shown to be ‘conserved’ here;

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    Of related note; I really enjoyed Michael Egnor’s essay on how consciousness is not reducible to matter;

    The Mind and Materialist Superstition – Six “conditions of mind” that are irreconcilable with materialism:
    http://www.evolutionnews.org/2.....super.html

    more notes of interest:

    Quantum mind–body problem
    Parallels between quantum mechanics and mind/body dualism were first drawn by the founders of quantum mechanics including Erwin Schrödinger, Werner Heisenberg, Wolfgang Pauli, Niels Bohr, and Eugene Wigner – Wikipedia

    “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.” Eugene Wigner (1902 -1995) from his collection of essays “Symmetries and Reflections – Scientific Essays”; Eugene Wigner laid the foundation for the theory of symmetries in quantum mechanics, for which he received the Nobel Prize in Physics in 1963.

    The Unbearable Wholeness of Beings – Steve Talbott
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.

    Can a Computer Think? – Michael Egnor
    Excerpt: The Turing test isn’t a test of a computer. Computers can’t take tests, because computers can’t think. The Turing test is a test of us. If a computer “passes” it, we fail it. We fail because of our hubris, a delusion that seems to be something original in us. The Turing test is a test of whether human beings have succumbed to the astonishingly naive hubris that we can create souls.

    Breathtaking Performance Of Agnus Dei From Child Singer – Music Videos
    http://www.godtube.com/watch/?v=K7WZYPNX

  70. 70
    Timaeus says:

    Elizabeth Liddle (16.1.2.1.2):

    You wrote:

    “Well, Sermonti has ignored drift.”

    Anything is possible. But here is some biographical background on Sermonti:

    “Born in Rome, graduated in agriculture and genetics, he entered the Superior Institute of Health in 1950, founding a department of Microbiological Genetics. He became professor of genetics at the University of Camerino, then at the University of Palermo in 1965, and finally moved to the University of Perugia in 1970, where he is presently emeritus professor and where he manages the Genetics Institute of the University from 1974. From 1970-1971 he presided over the Associazione Genetica Italiana.[1] He is the discoverer of the genetic parasexual recombination in antibiotic-producing Penicillium and Streptomyces. He was vice-president of the XIV International Congress of Genetics held in Moscow and he was appointed as president of the International Committee of the Working Group on Genetics of Industrial Microorganisms.”

    It would appear to me that Sermonti’s background in genetics is extensive, and likely more extensive than your own. How probable is it that he has “ignored drift”? Isn’t it more likely that he is well aware of drift, but does not believe that it can accomplish what it is said to accomplish in standard neo-Darwinism? And if someone with this level of expertise in a field which is not your own holds an opinion different from your own, wouldn’t it make more sense for you to inquire into the basis of his judgment than to dismiss his view with a comment that implies that he is either (a) ignorant of the basic facts in his field or (b) unusually careless in his reasoning?

  71. 71
    DrREC says:

    BA77 and Joseph,

    You two have a special hypocrisy in your use of evidence.

    Designed experiments are out, oh, except when they are done by your side. For example, how many time have you cited Gauger’s Biocomplexity paper? Maybe you should write her, and tell her a directed evolution (however poorly designed) experiment has no bearing on evolution.

    Oh, and ‘sequence comparisons’ mean nothing, except say, in the original post, or when Behe uses them to estimate the rate of evolution,for example, in Malarial resistance. He not only uses them, and must presume methodological naturalism. Suppose a designer continually reverted the mutations, meaning the rate of evolution was much greater but washed out by design. Behe has to assume that didn’t happen.

    You see the issue. You try to dispense with evolutionary lab experiments and sequence comparison then in the very next breath, cite ID evidence that uses these very methods.

    Problem?

  72. 72
    DrREC says:

    Joseph,

    “you don’t have any evidence taht gene duplication and recombination are blind, undirected chemical processes”

    I don’t know what you mean by this. We can perform several types of recombination in a test tube, with purified components, like any other chemical reaction.

    Gene duplication has understood physical mechanisms accounting for it.

    Do you not know how these processes work, or are you saying there is a chance a designer is pulling the strings?

  73. 73
    bornagain77 says:

    DrREC, despite what you may think of my ‘hypocritical’ standard for science, the standard for empirical science is brutally unchanging in its threshold of satisfaction and requires nothing less than a actual empirical DEMONSTRATION for what you are claiming, and in such resolute firmness empirical science is the very antithesis of hypocrisy!!!. You claim that sequence comparisons prove protein evolution from one remote island of functionality to the next remote island of functionality is true for neo-darwinian evolution. Yet, when I point out that you have not actually changed any functional protein to any other functional protein, by Darwinian means (Lenski, Behe, Axe) you claim that you don’t need to demonstrate as such and that sequence comparisons are all fine and well. Well, I’m sorry to hurt your feelings DrREC, but it is not me that requires that this extremely trivial threshold to be met (actually you would have to actually demonstrate Body Plan morphogenesis as well, to satisfy empirical science, but that is digressing), it is empirical science itself that demands you actually demonstrate what you say can be done, by neo-Darwinian means, to actually BE DONE by neo-Darwinian means. And as previously referenced here:

    http://www.uncommondescent.com.....ent-399693

    There is actual, and ample, DEMONSTRATED empirical evidence that severely questions the legitimacy of your claims!!!

  74. 74
    bornagain77 says:

    DrREC, gene duplication suffers from the same lack of empirical support as you claim for protein evolution does:

    Is gene duplication a viable explanation for the origination of biological information and complexity? – December 2010 –
    Excerpt: The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case. Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms. © 2010 Wiley Periodicals, Inc. Complexity, 2011
    http://onlinelibrary.wiley.com.....5/abstract

    Evolution by Gene Duplication Falsified – December 2010
    Excerpt: The various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original.
    http://www.creationsafaris.com.....#20110103a

    The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations Douglas D. Axe*
    Excerpt: In particular, I use an explicit model of a structured bacterial population, similar to the island model of Maruyama and Kimura, to examine the limits on complex adaptations during the evolution of paralogous genes—genes related by duplication of an ancestral gene. Although substantial functional innovation is thought to be possible within paralogous families, the tight limits on the value of d found here (d ? 2 for the maladaptive case, and d ? 6 for the neutral case) mean that the mutational jumps in this process cannot have been very large.
    http://bio-complexity.org/ojs/.....O-C.2010.4

    An Insurmountable Problem for Darwinian Evolution – Gene Duplication – And Minor Transformation of Protein Function – May 2011
    http://intelligentdesign.podom.....1_43-07_00

    Michael Behe Hasn’t Been Refuted on the Flagellum!
    Excerpt: Douglas Axe of the Biologic Institute showed in one recent paper in the journal Bio-complexity that the model of gene duplication and recruitment only works if very few changes are required to acquire novel selectable utility or neo-functionalization. If a duplicated gene is neutral (in terms of its cost to the organism), then the maximum number of mutations that a novel innovation in a bacterial population can require is up to six. If the duplicated gene has a slightly negative fitness cost, the maximum number drops to two or fewer (not inclusive of the duplication itself).
    http://www.evolutionnews.org/2.....44801.html

    The GS (genetic selection) Principle – David L. Abel – 2009
    Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.”
    http://www.scitopics.com/The_G.....ciple.html

    Genome truncation vs mutational opportunity: can new genes arise via gene duplication?—Part 1 – Royal Truman and Peter Borger
    Conclusions: Various evolutionary scenarios were examined by varying parameters such as prokaryote population size, mutational rate, generation times, proportion of population with additional genes, number of duplicate genes and selectivity coefficient favouring genome truncation. Assuming mutations on a duplicate are harmless would permit these to accumulate, but in reality natural selection would systematically remove the descendents of duplication events, drastically limiting both the total number and variety of mutants. Duplicate genes would be created, accumulate at most a very small number of mutations, and then go extinct, again and again. The number of distinct mutational variants generated would be far too small to explain the origin of novel cellular functions. All scenarios using prokaryote populations failed to generate enough mutation to produce novel genes. The most promising approach assumes huge populations would be involved, although subsequently surviving and fixing would now become exceedingly unlikely. Preventing novel gene families from developing denies
    nature the necessary infrastructure to produce complex new features. This finding contradicts what is being claimed by evolutionary biologists, which therefore invites other explanations as to the source of genetic complexity to be considered.
    http://creation.com/images/pdf.....99-110.pdf

  75. 75
    DrREC says:

    Well, that was some non-answer.

    Are experimental evolution approaches valid, or do you want to write a letter to Bio-complexity?

    Are sequence comparisons valid, or do you disavow the original post and Behe’s analyses contributing to the edge of evolution, etc.?

    You can’t reject the evidence I provided, and accept those.

  76. 76
    Petrushka says:

    Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences with their modern relatives.
    Vreeland RH, Rosenzweig WD, Lowenstein T, Satterfield C, Ventosa A.
    Source
    Department of Biology, West Chester University, West Chester, PA 19383, USA. rvreeland@wcupa.edu
    Abstract
    The isolation of living microorganisms from primary 250-million-year-old (MYA) salt crystals has been questioned by several researchers. The most intense discussion has arisen from questions about the texture and age of the crystals used, the ability of organisms to survive 250 million years when exposed to environmental factors such as radiation and the close similarity between 16S rRNA sequences in the Permian and modern microbes. The data in this manuscript are not meant to provide support for the antiquity of the isolated bacterial strains. Rather, the data presents several comparisons between the Permian microbes and other isolates to which they appear related. The analyses include whole cell fatty acid profiling, DNA-DNA hybridizations, ribotyping, and random amplified polymorphic DNA amplification (RAPD). These data show that the Permian strains, studied here, differ significantly from their more modern relatives. These differences are accumulating in both phenotypic and molecular areas of the cells. At the fatty acid level the differences are approaching but have not reached separate species status. At the molecular level the variation appears to be distributed across the genome and within the gene regions flanking the highly conserved 16S rRNA itself. The data show that these bacteria are not identical and help to rule out questions of contamination by putatively modern strains.

  77. 77
    bornagain77 says:

    DrREC, this following evidence is actual empirical evidence from the lab, and the best models we have, not sequence comparison from the imagination of neo-Darwinists as your evidence is:

    Dollo’s law, the symmetry of time, and the edge of evolution – Michael Behe – Oct 2009
    Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,,
    A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses.
    http://www.evolutionnews.org/2.....f_tim.html

    Severe Limits to Darwinian Evolution: – Michael Behe – Oct. 2009
    Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
    http://www.evolutionnews.org/2......html#more

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway – Ann K. Gauger and Douglas D. Axe – April 2011
    Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth.
    http://bio-complexity.org/ojs/.....O-C.2011.1

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed – along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

    “A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble.”
    Problems in Protein Evolution:
    http://www.cs.unc.edu/~plaisted/ce/blocked.html

    Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors – Doug Axe
    Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular.
    http://nsmserver2.fullerton.ed.....lution.pdf

    Darwin’s God: Post Synaptic Proteins Intolerant of Change – December 2010
    Excerpt: Not only is there scant evidence of intermediate designs leading to the known proteins, but the evidence we do have is that these proteins do not tolerate change.
    http://darwins-god.blogspot.co.....nt-of.html

  78. 78
    Joseph says:

    DrREC:

    You two have a special hypocrisy in your use of evidence.

    Nice false accusation.

    Designed experiments are out, oh, except when they are done by your side.

    I never said nor implied such a thing. However your position doesn’t have any experiments that support its grand claims.

  79. 79
    Joseph says:

    “you don’t have any evidence taht gene duplication and recombination are blind, undirected chemical processes”

    DrREC:

    I don’t know what you mean by this. We can perform several types of recombination in a test tube, with purified components, like any other chemical reaction.

    Gene duplication has understood physical mechanisms accounting for it.

    Do you not know how these processes work, or are you saying there is a chance a designer is pulling the strings?

    Computers run via understood physical mechanisms, as do automobiles. And no need for the designers to pull the strings in either case.

    PROGRAMMING DrREC- gene duplications are directed by the internal programming of the organism/ cell.

  80. 80
    DrREC says:

    “PROGRAMMING DrREC- gene duplications are directed by the internal programming of the organism/ cell.”

    Really?

    In a simple cell like E. coli, known to have gene duplications-

    1) Where does the ‘internal programming’ to determine what gene to duplicate and the mechanism to do that exist? Which genes are involved?

    2) If this is part of the cell’s programming, why isn’t it deterministic? Why doesn’t the whole population execute the program at once? Can you present evidence for such? I’ve never heard of such an observation.

    3) How are unused ‘programs’ to emerge later maintained in the face of genetic entropy? Without purifying selection, information is lost.

  81. 81
    DrREC says:

    BA,

    You ask for evidence which I provide. You accuse it of just being inference from sequence alignments and designed experiments. I point out the hypocrisy of you citing data using that very same methodology. To refute this point, you list articles that use the same methodology!

    Unbelievable.

  82. 82
    bornagain77 says:

    DrREC, you cite gene duplication in bacteria as ‘proof’ for neo-Darwinism, well let’s see what the real world empirical science says about the gene duplication scenario in bacteria and not what your imagination is saying is happening:

    This following paper clearly reveals that there is a ‘cost’ to duplicate genes that further precludes the scenario from being plausible:

    Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model
    Excerpt: In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. http://www.springerlink.com/co.....4014664w8/

    This recent paper also found the gene duplication scenario to be highly implausible:

    The Extinction Dynamics of Bacterial Pseudogenes – Kuo and Ochman – August 2010
    Excerpt: “Because all bacterial groups, as well as those Archaea examined, display a mutational pattern that is biased towards deletions and their haploid genomes would be more susceptible to dominant-negative effects that pseudogenes might impart, it is likely that the process of adaptive removal of pseudogenes is pervasive among prokaryotes.”
    http://www.evolutionnews.org/2.....37581.html

    Thus once again the ‘real’ evidence argues forcefully against what you imagine to be possible. Moreover Lenski’s Long Term e-coli shows that even ‘simple’ point mutations interfere with each other, preventing the ‘building’ of functional complexity/information. ,,, Perhaps if you click your heals three times you shall wake up DrREC??? 🙂

  83. 83
    bornagain77 says:

    DrREC, it certainly is not ‘the very same’ methodology, since sequence comparisons of proteins of different functions are not a actual demonstration that a functional protein can evolve into another functional protein!!! Exactly how does you just SAYING sequence A evolved into sequence B help you overcome the EXPERIMENTAL evidence that finds severe thermodynamic stability for any given functional protein, plus experimental evidence for extreme rarity for ‘islands of functionality’ of functional proteins, and the obvious observation that this calls into question the very claim you are making??? i.e. You have no experimental support for your position but merely the assertion that it is so!!! This ‘sequence comparison’ of yours is not even close to satisfying the demands of empirical science DrREC!!! Whereas the observation of rarity of functional proteins comes directly from what the empirical science is telling us, not from what we ‘wish’ the rarity, or non-rarity, to be!!!

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    Moreover, your cited ‘designed’ experiment, which developed several ‘strategies’ for overcoming the many ‘dead ends’ of protein evolution, that they themselves readily acknowledge to be prevalent, is a complete joke for you to use as proof of the ability of proteins to ‘naturally evolve’ as far as empirical science is concerned, for it is precisely those many ‘naturally occurring’ dead ends for protein evolution, that they readily acknowledge and are clearly ‘designing strategies’ to overcome, that is the very question under debate!!! i.e. Can neo-Darwinism, and only neo-Darwinism, traverse the chasms of non-functionality between proteins???

    further notes:

    Quantum Entanglement falsified the reductive materialistic framework upon which neo-Darwinism happens to be built;

    Quantum Entanglement – The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    And yet quantum entanglement, which falsified the reductive materialistic framework upon which neo-Darwinism is built, is found to be within molecular biology, on a massive scale, especially including proteins.

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini & Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73
    Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
    http://www.scimednet.org/quant.....d-protein/

    Quantum states in proteins and protein assemblies:
    The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI
    Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign.
    http://www.tony5m17h.net/SHJTQprotein.pdf

    Moreover, quantum information is found to be ‘conserved’:

    Quantum no-hiding theorem experimentally confirmed for first time – March 2011
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.
    http://www.physorg.com/news/20.....tally.html

    Quantum no-deleting theorem
    Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist.
    http://en.wikipedia.org/wiki/Q.....onsequence

    So basically DrREC, for you to cling to neo-Darwinism, in spite of what the empirical science is telling us, you end up being completely detached from how reality is actually constructed;

    Tori Amos – Cornflake Girl [UK Version] (HD Official Video)
    http://www.youtube.com/watch?v=4oWSGcRrauA

  84. 84
    Joseph says:

    “PROGRAMMING DrREC- gene duplications are directed by the internal programming of the organism/ cell.”

    DrREC:

    Really?

    Yes, the alternative of stuff just happens cannot be tested and therefor is unscientific.

    1) Where does the ‘internal programming’ to determine what gene to duplicate and the mechanism to do that exist? Which genes are involved?

    Internal means inside of the organism. cell, just as I stated.

    2) If this is part of the cell’s programming, why isn’t it deterministic? Why doesn’t the whole population execute the program at once? Can you present evidence for such? I’ve never heard of such an observation.

    Why would it be deterministic? Why would the whole population execute the same program at once? Haven’t you ever heard of different people searching for a different solution to the same problem? The evidence for programming is in the way the cells transcribe, translate- well just about everything they do.

    Again what is the alternative besides “it just does” these things?

    3) How are unused ‘programs’ to emerge later maintained in the face of genetic entropy? Without purifying selection, information is lost.

    Who said they are maintained?

  85. 85
    Petrushka says:

    And yet, in the course of ten years, a tiny population of bacteria evolved a new protein function requiring three independent mutations.

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