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Kirk Durston: Information decrease falsifies essential Darwinian prediction

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From Kirk Durston,

Mounting evidence that the digital information that encodes all of life is steadily degrading, falsifies a key prediction of the theory of neo-Darwinian macroevolution and verifies a prediction of intelligent design science.

Longer:

I was struck, but not surprised, by a statement made a few days ago by Neil Turok, Director of the Perimeter Institute for Theoretical Physics here in Waterloo, Ontario. Speaking of the apparent collapse of evidence for a critical component of the Big Bang theory, he responded, ‘even though hundreds or thousands of people are working on an idea, it may still be wrong.’

His statement is a harbinger of a much greater collapse looming on the scientific horizon, also involving thousands of scientists. There is mounting evidence that most, if not all the key predictions of the neo-Darwinian theory of macroevolution are being consistently falsified by advances in science, several of which I will discuss in later posts. Here, we look at a fundamental prediction Darwinism makes regarding the increase of genetic information.

Computer information is digitally encoded using just two symbols (‘1’ and ‘0’). We now know that the instructions for the full diversity of life, are digitally encoded in the DNA of all living things using a four-symbol alphabet. In more technical terms, this is referred to as functional information.

In the neo-Darwinian scenario for the origin and diversity of life, the digital functional information for life would have had to begin at zero, increase over time to eventually encode the first simple life form, and continue to increase via natural processes to encode the digital information for the full diversity of life.

An essential, falsifiable prediction of Darwinian theory, therefore, is that functional information must, on average, increase over time.

Interestingly enough, a prediction of intelligent design science is quite the opposite. Since information always degrades over time for any storage media and replication system, intelligent design science postulates that the digital information of life was initially downloaded into the genomes of life. It predicts that, on average, genetic information is steadily being corrupted by natural processes. The beauty of these two mutually incompatible predictions in science is that the falsification of one entails verification of the other. So, which prediction does science falsify, and which one does science verify? More.

Actually, it no longer matters whether Darwinian evolution has any relationship to fact. Airheads believe it, judges enforce it, union teachers spout it, students know they had better absorb it—a combo like that doesn’t need facts or evidence, and is in fact hostile to them. They are unwelcome intruders into a System That Works for its proponents.

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125 Replies to “Kirk Durston: Information decrease falsifies essential Darwinian prediction

  1. 1
    Mung says:

    Durston writes:

    Computer information is digitally encoded using just two symbols (‘1’ and ‘0’). We now know that the instructions for the full diversity of life, are digitally encoded in the DNA of all living things using a four-symbol alphabet. In more technical terms, this is referred to as functional information.

    Actually we do not know this.

    Not only do we not know this, we actually have good reason to believe it is factually false.

    And if this is not true, then it seems to me that Durston’s entire argument here fails due to it’s basis in a single faulty premise.

  2. 2
    Mapou says:

    Mung @1, what are you, the infallible Pope of genetics? Provide evidence for your assertions. They look false from my vantage point.

  3. 3
    Mung says:

    For goodness sake Mapou, even the ID literate itself argues (contra Darwinism) that all the information isn’t in the DNA. You just don’t get to have it both ways.

    Intelligent Design asserts that all the information is in the DNA. You’re willing to defend that claim?

    If you absolutely insist I think I can come up with the requested evidence, and I may even spend the time doing so, because I absolutely detest claims made in the name of ID that are not claims entailed by ID.

    Durston:

    Interestingly enough, a prediction of intelligent design science is quite the opposite.

    How so?

  4. 4
    Mapou says:

    Mung,

    Chill, dude. You are dismissing Durston’s argument on a minor technicality. His argument is that information degrades with time. Whether or not all the information that describes an organism is in its genes is really irrelevant. It’s a sure bet that almost all of it is, IMO. But, again, it is irrelevant to his argument that information always degrades over time, wherever it may be stored.

    This being said, I think Durston is essentially correct in saying that the information responsible for the full diversity of life is encoded in DNA.

    PS to News: That first link to Durston seems incorrect.

  5. 5
    55rebel says:

    “They are unwelcome intruders into a System That Works for its proponents.”

    Indeed, its “proponents” (pushers) being… the puppet Masters of this ‘God’ called: the STATE.

    Have you ever submit an application (prayer) to it?
    …ikr?

  6. 6
    Mung says:

    Mapou, I am pleased to see that you agree with me that Durston’s premise is false.

    Your answer is that it doesn’t matter because we can replace it with a different premise, which I find rather odd.

    I’ll await Durston’s modified argument.

    Meanwhile, there is the still the question of whether the information in the DNA (or wherever else you imagine it exists) is complete or incomplete.

    If organisms manage to develop in the absence of complete information specifying their development his argument is still in trouble.

    The argument that information must degrade and that this is somehow relevant is based upon the unstated but assumed premise that the information is complete.

    But again, we have little reason to believe this is true and good reason to believe that it is not.

  7. 7
    Mapou says:

    Mung, stop being so anal retentive. It smacks of autism or something. Durston’s premise is that the information that describes an organism is encoded somewhere (almost all of it is in DNA but who cares?) and that it degrades over time. This is a fact. Darwinists insist that information increases over time and that this increase is reflected in the full diversity of the lifeforms that we observe, which is false. Durston is not making an argument that others have not made.

  8. 8
    Mung says:

    Mapou: Durston’s premise is that the information that describes an organism is encoded somewhere

    We have good reason to believe that this is either false or untestable. Encoded in the mind of God? Then how could it degrade?

    People make decisions all the time in the absence of complete information. Organisms cannot do this because they are machines? Walk me through the logic please.

  9. 9
    Roy says:

    Ok, so he’s not only ignored the effects of natural selection on a Malthusian population, he’s extrapolated from short term measurements on a handful of species over a few decades to a global long-term average for the entire flora and fauna of Earth over 4 billion years.

    Not convincing.

  10. 10
    55rebel says:

    The question is…

    Given the ’empirical’ evidence, via the “scientific method” (something Darwinist wouldn’t, or couldn’t employ, to support their theories, and/or these “Billions” of years they keep pulling out of their asses), what is the overall accumulative effect of mutations to DNA, RNA or WEA (whatEver A?)’ to a living organism? Are they useful, or are they detrimental?

    In my humble opinion? I think that this is a… No-brainer.

    Of course, that’s if this technology doesn’t have the ability to self-correct over time. Which there is actually evidence for, BTW. Read this somewhere….on the internet! 😛

  11. 11
    butifnot says:

    Roy, natural selection is a process of removal, elimination, culling. Wholesale removal of individuals and the information they contain. Not creating anything, eliminating things. Trivial, self evident and powerless. All observation shows corruption and degradation, not a few species. A process supposedly responsible for the entire biosphere, should be exploding with examples of increasing information and complexity. Not conjecture of a upward march through unobservable eons, but observation of the underlying mechanism – ‘genetics’. Yet mutations (information corruption) are overwhelmingly detrimental, and even when beneficial, involve loss.

  12. 12
    harry says:

    Hello Mung,

    Actually we do not know this.

    There is functional information that is not in the coding regions of DNA. (Google up the ENCODE project.) There is probably functional information necessary for the development of life that does not not reside in DNA at all. The coding regions of DNA contain functional information that is essentially the digitally stored assembly instructions for the protein machines within the cell that enable metabolism and reproduction. Where the information resides that directs the construction of overall body plans hasn’t been nailed down yet as far as I know.

    The “alphabet” is not the A,C,G and T values, one of which resides in each unit of DNA memory. It is an amino acid alphabet, each letter of which consists of a series of three values (a codon), each of which is either A,C,G or T. This is like computer memory where each letter of the English alphabet is represented (in ASCII) by a unique series of seven 0 and 1 memory unit values. DNA uses a twenty character amino acid alphabet.

    Also, just as computer memory can contain representations of lots of things besides the tokens of which an alphabet consists, the non coding regions of DNA probably contain much functional information that we just have deciphered yet, but is probably just as organized and ordered as the regions of DNA memory that code for protein machines.

  13. 13
    bornagain77 says:

    a few notes on information loss;
    Michael Behe surveyed the last four decades of laboratory evolution experiments and found:

    “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.
    http://behe.uncommondescent.co.....evolution/

    For you tech geeks, here is a more detailed analysis of Behe’s work:

    Biological Information – Loss-of-Function Mutations by Paul Giem 2015 – video
    (Behe – Loss of function mutations are far more likely to fix in a population than gain of function mutations)
    https://www.youtube.com/watch?v=hzD3hhvepK8&index=20&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ

    Interestingly, the gain of function mutations listed by Behe in his paper all involve ‘compensatory mutations’ that are implemented by the programming in the cell.
    Compensatory mutations are ‘directed’ mutations, as opposed to purely random mutations, which compensate for the deletion and/or loss of a gene and/or protein.
    Yet, compensatory mutations have never been shown to surpass wild type bacteria in a fitness test.

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    https://www.youtube.com/watch?v=rYaU4moNEBU

    Thus compensatory mutations are not evidence for a gain of functional information over and above what was already present in the cell and/or life.
    In regards to the ‘fitness test’, the following is of related interest”

    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

    “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.”
    http://www.physicsforums.com/s.....p?t=281961

    In reply to a personal e-mail from myself, Dr. Cano commented on the ‘Fitness Test’ on the ancient bacteria that I had asked him about:
    Dr. Cano stated:

    “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    RJ Cano and MK Borucki – Fitness test which compared ancient amber sealed bacteria to its modern day descendants

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.
    To continue on:

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    Excerpt: Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” ,,, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding.
    http://www.trueorigin.org/bacteria01.asp

    (Ancient) Cave bacteria resistant to antibiotics – April 2012
    Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes.
    http://www.scotsman.com/news/h.....1-2229183#

    The consequences of genetic drift for bacterial genome complexity – Howard Ochman – 2009
    Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.
    http://genome.cshlp.org/conten.....091785.109

    Moreover, beneficial, i.e. ‘information building’, mutations may be too rare to actually allow the accurate measurement of just how rare they are:

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

  14. 14
    bornagain77 says:

    ‘Kimura’s Distribution’ is used in the following video to illustrate just how rare ‘truly’ beneficial mutations are. i.e. ‘Truly’ beneficial mutations that build up functional information instead of degrading it in one way or the other to gain a short term fitness advantage:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    https://vimeo.com/91162565

    Genetic deterioration is also well documented in humans in particular. The evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 150,000 mutational disorders in humans.

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

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

    Mutation total (as of June 27, 2015) – 166,768
    http://www.hgmd.cf.ac.uk/ac/

    John Sanford comments on the reality of the situation here,,,

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

    Dr. John Sanford “Genetic Entropy and the Mystery of the Genome” – video
    https://vimeo.com/35088933

    This following study found that the genetic deterioration of humans has happened fairly recently over the past 5,000 to 10,000 years:

    Human Genome in Meltdown – January 11, 2013
    Excerpt: According to a study published Jan. 10 in Nature by geneticists from 4 universities including Harvard, “Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.”,,,:
    “We estimate that approximately 73% of all protein-coding SNVs [single-nucleotide variants] and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000 -10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes.”,,,
    As for advantageous mutations, they provided NO examples,,,
    http://crev.info/2013/01/human-genome-in-meltdown/

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

    Moreover, contrary to what Hitler thought, blond hair, blue eyes, and light skin are actually examples of ‘Devolution’ not ‘Evolution’:

    The Genetics of Blond Hair June 1, 2014
    Excerpt: ,,,When he and his colleagues studied this regulatory DNA in human cells grown in a laboratory dish, they discovered that the blond-generating SNP reduced KITLG activity by only about 20%. Yet that was enough to change the hair color.“This isn’t a ‘turn the switch off,’ ” Kingsley says. “It’s a ‘turn the switch down.’ ”
    “This study provides solid evidence” that this switch regulates the expression of KITLG in developing hair follicles,
    http://news.sciencemag.org/bio.....blond-hair

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

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

  15. 15
    bornagain77 says:

    Measurement for ‘genetic diversity’ also shows a loss of information:

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

    “…but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have…”
    Maciej Marian Giertych – Population Geneticist – member of the European Parliament – EXPELLED
    https://www.youtube.com/watch?v=6z5-15wk1Zk

    The human fossil record agrees with the preceding genetic evidence:

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

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

    Cro Magnon skull shows that our brains have shrunk – Mar 15, 2010 by Lisa Zyga
    Excerpt: Using new technology, researchers have produced a replica of the 28,000-year-old brain and found that it is about 15-20% larger than our brains.
    http://phys.org/news187877156.html

    Are brains shrinking to make us smarter? – February 2011
    Excerpt: Human brains have shrunk over the past 30,000 years,
    http://www.physorg.com/news/20.....arter.html

    Human face has shrunk over the past 10,000 years – November 2005
    Excerpt: Human faces are shrinking by 1%-2% every 1,000 years. What’s more, we are growing less teeth. Ten thousand years ago everyone grew wisdom teeth but now only half of us get them, and other teeth like the lateral incisors have become much smaller. This is evolution in action.”
    http://www.stonepages.com/news.....01604.html

    of related note:

    “Neanderthals are known for their large cranial capacity, which at 1600cc is larger on average than modern humans.”
    http://en.wikipedia.org/wiki/Neanderthal#Anatomy

    Moreover, Dog breeding is shown to be accomplished by the culling of information, not by the generation of new information as is held neo-Darwinists:

    Interview with Wolf-Ekkehard Lönnig – Mar 22, 2014
    Excerpt: Richard Dawkins and many other evolutionary biologists (claim) that dog breeds prove macroevolution. However, virtually all the dog breeds are generated by losses or disturbances of gene functions and/or developmental processes. Moreover, all the three subfamilies of the family of wild dogs (Canidae) appear abruptly in the fossil record.
    http://dippost.com/2014/03/22/.....rd-lonnig/

  16. 16
    bornagain77 says:

    podcast – On this episode of ID the Future, Casey Luskin talks with geneticist Dr. Wolf-Ekkehard Lönnig about his recent article on the evolution of dogs.
    http://intelligentdesign.podom.....1_14-08_00
    Part 2: Dog Breeds: Proof of Macroevolution?
    http://intelligentdesign.podom.....7_07-08_00

    The Dog Delusion – October 30, 2014
    Excerpt: In his latest book, geneticist Wolf-Ekkehard Lönnig of the Max Planck Institutes in Germany takes on the widespread view that dog breeds prove macroevolution.,,, He shows in great detail that the incredible variety of dog breeds, going back in origin several thousand years ago but especially to the last few centuries, represents no increase in information but rather a decrease or loss of function on the genetic and anatomical levels.
    Michael Behe writes:
    “Dr. Lönnig shows forcefully that one of the chief examples Darwinists rely on to convince the public of macroevolution — the enormous variation in dogs — actually shows the opposite. Extremes in size and anatomy come at the cost of broken genes and poor health. Even several gene duplications were found to interfere strongly with normal growth and development as is also often the case in humans. So where is the evidence for Darwinian evolution now?”
    The science here is indeed solid. Intriguingly, Lönnig’s prediction from 2013 on starch digestion in wolves has already been confirmed in a study published this year.,,,
    http://www.evolutionnews.org/2.....90751.html

    Caveman’s Best Friend, Evolution’s Newest Upset – October 2011
    Excerpt: Our view of domestication as a process has also begun to change, with recent research showing that, in dogs, alterations in only a small number of genes can have large effects in terms of size, shape and behavior.,,, It should be noted that dogs and wolves can interbreed,,,
    http://crev.info/content/20111.....est_friend

    What Darwin Didnt Know – video (21 minute mark,,, jackals, wolves, and huskies were interbred by Russians to be drug sniffing dogs)
    https://www.youtube.com/watch?v=w1fdJJCQOPk

    The overall fossil record supports genetic entropy. In fact, the loss of morphological traits over time, for all organisms found in the fossil record, was/is so consistent that it was made into a ‘scientific law’:

    Dollo’s law and the death and resurrection of genes:
    Excerpt: “As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo’s law, after its propounder, and is taken as a general statement that evolution is irreversible.”
    http://www.pnas.org/content/91.....l.pdf+html

    A general rule of thumb for the ‘Deterioration/Genetic Entropy’ of Dollo’s Law as it applies to the fossil record is found here:

    Dollo’s law and the death and resurrection of genes
    ABSTRACT: Dollo’s law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or “lost” developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints;
    http://www.pnas.org/content/91.....l.pdf+html

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

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

  17. 17
    bornagain77 says:

    The following article is important in that it shows the principle of Genetic Entropy being obeyed in the fossil record by Trilobites, over the 270 million year history of their life on earth (Note: Trilobites abruptly at the base of the Cambrian explosion with no evidence of transmutation from the ‘simple’ creatures that preceded them, nor is there any evidence they ever produced anything else besides other trilobites during the entire time they are found in the fossil record).

    The Cambrian’s Many Forms
    Excerpt: “It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.””From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” – University of Chicago paleontologist Mark Webster; article on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.
    http://www.terradaily.com/repo.....s_999.html

    The following study found, contrary to Darwinian thought, that diversity followed a ‘top down’ pattern of bigger fossils becoming more diverse over time,

    Researchers say larger size is a genuine pattern in evolution, not neutral drift – February 21, 2015
    Excerpt: The research also found that the increase in body size that has occurred since animals first appeared in the fossil record around 550 million years ago is not due to all animal lineages steadily growing bigger, but rather to the diversification of groups of organisms that were already larger than other groups early in the history of animal evolution.
    “That’s also something we didn’t know before,” Payne said. “For reasons that we don’t completely understand, the classes with large body size appear to be the ones that over time have become differentially more diverse.”,,,
    the study included nearly 75 percent of marine fossils (17,000 genera) over the last 542 million years, and,,,
    A pattern soon became apparent: not all classes-groups of related species and genera-of animals trended toward larger size, but those that were bigger tended to become more diverse over time.,,,
    The team found that the neutral drift simulation could not explain the body size trends observed in the fossil record. “The degree of increase in both mean and maximum body size just aren’t well explained by neutral drift,” Heim said.,,,
    http://www.uncommondescent.com.....ral-drift/

    As well, there are strong theoretical reasons for believing that information will be degraded:

    Evolutionary Computing: The Invisible Hand of Intelligence – June 17, 2015
    Excerpt: William Dembski and Robert Marks have shown that no evolutionary algorithm is superior to blind search — unless information is added from an intelligent cause, which means it is not, in the Darwinian sense, an evolutionary algorithm after all. This mathematically proven law, based on the accepted No Free Lunch Theorems, seems to be lost on the champions of evolutionary computing. Researchers keep confusing an evolutionary algorithm (a form of artificial selection) with “natural evolution.” ,,,
    Marks and Dembski account for the invisible hand required in evolutionary computing. The Lab’s website states, “The principal theme of the lab’s research is teasing apart the respective roles of internally generated and externally applied information in the performance of evolutionary systems.” So yes, systems can evolve, but when they appear to solve a problem (such as generating complex specified information or reaching a sufficiently narrow predefined target), intelligence can be shown to be active. Any internally generated information is conserved or degraded by the law of Conservation of Information.,,,
    What Marks and Dembski prove is as scientifically valid and relevant as Gödel’s Incompleteness Theorem in mathematics. You can’t prove a system of mathematics from within the system, and you can’t derive an information-rich pattern from within the pattern.,,,
    http://www.evolutionnews.org/2.....96931.html

    There are many more studies that I could list supporting the overall pattern of deteriorating information that is outlined above, but the main point I want to emphasize is this; Dr. Durston is absolutely correct in his assessment that information degradation is a major failed prediction of Darwinian claims.

    Verse:

    John 1:1-5
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. The light shines in the darkness, and the darkness has not overcome it.

  18. 18
    jerry says:

    There are prominent people in the evolutionary biology mainstream who say just the opposite of what Kirk Durston is saying. They point to new functional proteins/control sequences as the result of the ongoing process of cell division, mutations and recombination. Eventually some of the non coding regions get coded and become functional after substantial modification over time.

    So we should look at how significant their claims are. By the way this is a different from the claim that the genome is deteriorating. This is a theory that says the functionality of a genome will deteriorate out of viability over time independent of whether some new functionality is produced.

    All this is testable with today’s technology and will get easier as the expense of coding genomes gets cheaper. As Durston said, there are thousands working on it. It is just a matter of time before one side or the other is vindicated.

    I suggest that Kirk Durston consult Jurgen Brossius or read what he has proposed and researched.

  19. 19
    jerry says:

    Interestingly enough, a prediction of intelligent design science is quite the opposite. Since information always degrades over time for any storage media and replication system, intelligent design science postulates that the digital information of life was initially downloaded into the genomes of life. It predicts that, on average, genetic information is steadily being corrupted by natural processes. The beauty of these two mutually incompatible predictions in science is that the falsification of one entails verification of the other. So, which prediction does science falsify, and which one does science verify?

    This is not true. If the information was downloaded so was the correction mechanism and all the machinery of transcription and translation. This machinery is also part of the ID hypothesis so increases or decreasses in information per se are irrelevant to the ID hypothesis.

    The critical hypothesis is whether the increases in information are possible with this machinery. The evidence is that some but unlikely all the information increases are within the capabilities of these processes.

  20. 20
    bornagain77 says:

    as to:

    “They point to new functional proteins/control sequences as the result of the ongoing process of cell division, mutations and recombination. Eventually some of the non coding regions get coded and become functional after substantial modification over time.”

    That is all ‘just so’ stories on the Darwinist’s part. They have NO empirical evidence that functional information can increase by unguided material processes.

    Disagree? If so, then provide direct empirical evidence to back up their claims and not just sequence comparisons that assume the conclusion into the premise.

    There is a drastic difference between a hypothetical theory as to how something could have possibly happened and established fact as to how it actually did happen!

  21. 21
    bornagain77 says:

    Here are a few more notes that better clarify the ‘top down’ nature of the fossil record:

    Cambrian Explosion Ruins Darwin’s Tree of Life (2 minutes in 24 hour day) – video
    http://www.youtube.com/watch?v=bQKxkUb_AAg

    , as Dr. Wells points out in the preceding video, Darwin predicted that minor differences (diversity) between species would gradually appear first and then the differences would grow larger (disparity) between species as time went on. i.e. universal common descent as depicted in Darwin’s tree of life. What Darwin predicted should be familiar to everyone and is easily represented in the following graph.,,,

    The Theory – Diversity precedes Disparity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/F.gif

    But that ‘tree pattern’ that Darwin predicted is not what is found in the fossil record. The fossil record reveals that disparity (the greatest differences) precedes diversity (the smaller differences), which is the exact opposite pattern for what Darwin’s theory predicted.

    The Actual Fossil Evidence- Disparity precedes Diversity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/G.gif

    Investigating Evolution: The Cambrian Explosion Part 1 – (4:45 minute mark – upside-down fossil record) video
    http://www.youtube.com/watch?v=4DkbmuRhXRY
    Part 2 – video
    http://www.youtube.com/watch?v=iZFM48XIXnk

  22. 22
    bornagain77 says:

    Challenging Fossil of a Little Fish
    Excerpt: "In Chen’s view, his evidence supports a history of life that runs opposite to the standard evolutionary tree diagrams, a progression he calls top-down evolution."
    Jun-Yuan Chen is professor at the Nanjing Institute of Paleontology and Geology
    http://www.fredheeren.com/boston.htm

    Timeline graphic on Cambrian Explosion – 'Darwin's Doubt' (Disparity preceding Diversity) – infographic
    http://www.evolutionnews.org/2.....74341.html

    The Cambrian Explosion – Stephen Meyer and Marcus Ross – video
    Various phylum are discussed in the first part of the video (Top down, disparity preceding diversity, pattern discussed at 33:00 minute mark)
    https://www.youtube.com/watch?v=wLpSb-iDNyw

    “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas."
    James W. Valentine – as quoted from "On the Origin of Phyla: Interviews with James W. Valentine" – (as stated at 1:16:36 mark of video)
    https://www.youtube.com/watch?v=xtdFJXfvlm8&feature=player_detailpage#t=4595

    Erwin and Valentine's The Cambrian Explosion Affirms Major Points in Darwin's Doubt: The Cambrian Enigma Is "Unresolved" – June 26, 2013
    Excerpt: "In other words, the morphological distances — gaps — between body plans of crown phyla were present when body fossils first appeared during the explosion and have been with us ever since. The morphological disparity is so great between most phyla that the homologous reference points or landmarks required for quantitative studies of morphology are absent."
    Erwin and Valentine (p. 340)
    http://www.evolutionnews.org/2.....73671.html

    Moreover, there are ‘yawning chasms’ in the ‘morphological space’ between the phyla which suddenly appeared in the Cambrian Explosion,,,

    “Over the past 150 years or so, paleontologists have found many representatives of the phyla that were well-known in Darwin’s time (by analogy, the equivalent of the three primary colors) and a few completely new forms altogether (by analogy, some other distinct colors such as green and orange, perhaps). And, of course, within these phyla, there is a great deal of variety. Nevertheless, the analogy holds at least insofar as the differences in form between any member of one phylum and any member of another phylum are vast, and paleontologists have utterly failed to find forms that would fill these yawning chasms in what biotechnologists call “morphological space.” In other words, they have failed to find the paleolontogical equivalent of the numerous finely graded intermediate colors (Oedleton blue, dusty rose, gun barrel gray, magenta, etc.) that interior designers covet. Instead, extensive sampling of the fossil record has confirmed a strikingly discontinuous pattern in which representatives of the major phyla stand in stark isolation from members of other phyla, without intermediate forms filling the intervening morphological space.”
    Stephen Meyer – Darwin’s Doubt (p. 70)

    Moreover, this top down pattern in the fossil record, which is the complete opposite pattern as Darwin predicted for the fossil record, is not only found in the Cambrian Explosion, but this ‘top down’, disparity preceding diversity, pattern is found in the fossil record subsequent to the Cambrian explosion as well.

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.”
    TS Kemp – Fossils and Evolution,– Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.”
    Robert L Carroll (born 1938) – vertebrate paleontologist who specialises in Paleozoic and Mesozoic amphibians

    What should be needless to say, this is NOT what Darwin predicted:

  23. 23
    Virgil Cain says:

    Roy, Natural selection is eliminative- eliminating the less fit. It is impotent with respect to universal common descent.

  24. 24
    jerry says:

    Disagree? If so, then provide direct empirical evidence to back up their claims and not just sequence comparisons that assume the conclusion into the premise.

    I suggest you read Jurgen Brosius. He is very vehement on this topic. He is considered one of the top evolutionary biologists in the world.

    My guess is that he overstates what has happened which is why I continually say the proof is in the pudding, that is in the genomes. But until then, both sides are just huffing and puffing.

    By the way, the deterioration of the genome thesis is an YEC argument. Are you defending YEC? It is also an hypothesis that designer did not foresee this and deal with it. Or was the designer inept or wanted it?

  25. 25
    Virgil Cain says:

    We now know that the instructions for the full diversity of life, are digitally encoded in the DNA of all living things using a four-symbol alphabet.

    Not even wrong. However seeing that is what evolutionism requires, perhaps Dr D is talking in that context.

  26. 26
    bornagain77 says:

    jerry, the only huffing and puffing belongs, as usual, to the Darwinian position. Moreover, you did not, and cannot, cite any actual real time empirical evidence to back up your/their specific claim as to the generation of functional information by unguided material processes, whereas I can readily back up my claim that it cannot happen that way:

    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/

    Michael Behe finds Loss of Function Mutations Challenge the Darwinian Model – Casey Luskin – August 24, 2013
    Excerpt: “Because of the many ways in which a gene can be altered to lose function, the LOF mutation would have a rate several orders of magnitude greater than that of the GOF mutation for the duplicated gene.”
    http://www.evolutionnews.org/2.....75591.html

    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/

    Douglas Axe and Ann Gauger Argue that Design Best Explains New Biological Information – Casey Luskin August 26, 2013
    Excerpt: Axe and Gauger observe that “The most widely accepted explanation for the origin of new enzymes is gene duplication and recruitment.” However, they cite experimental work showing that a duplicate gene is much more likely to be silenced (because of the costly resources expended in transcribing and translating it) than it is to acquire a new function.
    http://www.evolutionnews.org/2.....75601.html

    Biologic Institute’s Groundbreaking Peer-Reviewed Science Has Now Demonstrated the Implausibility of Evolving New Proteins – Casey Luskin January 22, 2015
    Excerpt: one of their citations makes a compelling case that the gene duplication step poses a major obstacle to gene recruitment via gene duplication and mutation. They cite a paper from PLOS Genetics, “The Extinction Dynamics of Bacterial Pseudogenes,” which notes:
    In bacteria, however, pseudogenes are deleted rapidly from genomes, suggesting that their presence is somehow deleterious. The distribution of pseudogenes among sequenced strains of Salmonella indicates that removal of many of these apparently functionless regions is attributable to their deleterious effects in cell fitness, suggesting that a sizeable fraction of pseudogenes are under selection.
    It concludes, “Although pseudogenes have long been considered the paradigm of neutral evolution, the distribution of pseudogenes among Salmonella strains indicates that removal of many of these apparently functionless regions is attributable to positive selection.”
    Don’t miss the profound importance of this. What it means is that there is very likely a fitness cost associated with carrying an extra, useless copy of a gene, and therefore it can be advantageous to delete duplicate version. This has major implications for the co-option model of protein evolution, because it shows that producing a new protein does not involve “neutral evolution,” but rather requires steps that very likely will impose a deleterious effect upon the organism.
    http://www.evolutionnews.org/2.....92941.html

    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

    This following articles will give you a primer on how far off the mark Darwinists are from having any actual empirical support for their ‘ahem’ theory as to unguided material processes generating functional information:

    Hopeless Matzke – David Berlinski & Tyler Hampton (Refutation of all popular examples purporting to show the origination of new information by Darwinian processes) – August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

    Can Random Mutations Create New Complex Features? A Response to TalkOrigins – Casey Luskin June 22, 2012
    Excerpt: the (talkorigins) page suggests searching for “gene duplication” on PubMed to find “more than 3000 references” on the topic. These papers, we’re meant to assume, show how evolutionary mechanisms can create new information. But a survey of major review articles on gene duplication I published here on ENV in 2010 revealed that the studies never established that mutations could have produced the complex features in question. After taking a close look at this literature, I found:
    The NCSE’s (and Judge Jones’s) citation bluffs have not explained how neo-Darwinian mechanisms produce new functional biological information. Instead, the mechanisms invoked in these papers are vague and hypothetical at best:
    *exons may have been “recruited” or “donated” from other genes (and in some cases from an “unknown source”);
    *there were vague appeals to “extensive refashioning of the genome”;
    *mutations were said to cause “fortuitous juxtaposition of suitable sequences” in a gene-promoting region that therefore “did not really ‘evolve'”;
    *researchers assumed “radical change in the structure” due to “rapid, adaptive evolution” and claimed that “positive selection has played an important role in the evolution” of the gene, even though the function of the gene was unknown;
    *genes were purportedly “cobbled together from DNA of no related function (or no function at all)”;
    *the “creation” of new exons “from a unique noncoding genomic sequence that fortuitously evolved” was assumed, not demonstrated;
    *we were given alternatives that promoter regions arose from a “random genomic sequence that happens to be similar to a promoter sequence,” or that the gene arose because it was inserted by pure chance right next to a functional promoter.
    *explanations went little further than invoking “the chimeric fusion of two genes” based solely on sequence similarity;
    *when no source material is recognizable, we’re told that “genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors” because they are simply “hypermutable”;
    *we even saw “a striking case of convergent evolution” of “near-identical” proteins.
    To reiterate, in no case were the odds of these unlikely events taking place actually calculated. Incredibly, natural selection was repeatedly invoked in instances where the investigators did not know the function of the gene being studied and thus could not possibly have identified any functional advantages gained through the mutations being invoked. In the case where multiple mutational steps were involved, no tests were done of the functional viability of the alleged intermediate stages. These papers offer vague stories but not viable, plausibly demonstrated explanations for the origin of new genetic information.
    I haven’t gone through all “3000 references” cited by TalkOrigins. Neither, in all likelihood, has the author of the TalkOrigins page. But my strong suspicion is that if you went through many of those pages, you’d reach the same conclusion.
    This 3000-unnamed-paper citation bluff — and much other material on this TalkOrigins page, are not to be taken seriously.
    http://www.evolutionnews.org/2.....61221.html

    etc.. etc..

  27. 27
    REC says:

    What is the ID position on where the “instructions for the full diversity of life” reside?

  28. 28
    Mapou says:

    REC:

    What is the ID position on where the “instructions for the full diversity of life” reside?

    The genome holds > 99% of the information an organism carry, IMO. But the environment and epigenetics will contribute information content that is not inherited. It is obvious that the genes do not code for the knowledge you acquire in life. Your knowledge of English, for example, is not in your genes but the ability to learn to speak a language is.

  29. 29
    Virgil Cain says:

    REC:

    What is the ID position on where the “instructions for the full diversity of life” reside?

    It isn’t the DNA.

  30. 30
    jerry says:


    What is the ID position on where the “instructions for the full diversity of life” reside?

    Meyer indicates there may be a sophisticated information system in the cell wall of the egg and that there are other molecules outside the nucleus that control cell division. Somewhere along the line the cells acquire information that tells them what type of cell to become. Right now no one has a clue.

  31. 31
    jerry says:

    BA,

    I suggest you look up Jurgen Brosius.

    I am in a car on my iPhone and don’t have access to all the links. He is the most cocky one there is about this topic.

  32. 32
    bornagain77 says:

    jerry, I’m more that willing to wait until you personally can back up your claims for unguided material processes generating functional information.

    I’m certainly not going to go through hundreds of papers looking for one that you may or may not think makes your case for you!.

    You find one real time experiment that you think best makes your case for an increase of functional information of a gene/protein by unguided material processes, cite it, and we’ll take it from there OK?

  33. 33
  34. 34
    bornagain77 says:

    Jerry as to your claim that:

    “which is why I continually say the proof is in the pudding, that is in the genomes.”

    You might want to read my response to your falsification threshold that I posted yesterday.

    http://www.uncommondescent.com.....ent-569958

  35. 35
    bornagain77 says:

    Jerry, I don’t want you to crash your car, and I don’t want you to cite hundreds of papers like you just did and expect me to go through them all and find the experiment that you think makes your case for Darwinian evolution.

    So when you get in a safe place. Find the best experimental evidence that you think shows functional information for a gene/protein being generated in real time by unguided material processes, and then cite it.

  36. 36
    Seversky says:

    To start with, I think that using the word “information” as if it is describing a property of the genome could be misleading.

    In popular usage, “information” refers to something like what we are exchanging through these comments. It is transferring meaningful data from the mind of one intelligent agent to another through the medium of a shared language, although the process of being informed occurs at the recipient’s end. I am informed if you tell me something I didn’t know before. You are not informed by telling me something you already knew.

    This doesn’t mean you can’t use the word “information” to label what happens in the genome – you can use whatever word you like – but if you are going to call it “information” you have an obligation to provide the specialized definition you are using in this context to avoid any confusion. Because what happens in the genome is not what is happening here. As far as we can tell, there are no intelligent agents talking to each other using a language made up of four chemical bases, saying things like “This is an arm. Grow it here!”

    As for the so-called degradation of genetic information, who gets to decide whether a mutation is detrimental or beneficial? In the classic illustration, a mutation which causes a brown bear to grow a white coat could put it at a disadvantage if it lived in a landscape that was mostly brown and green. The unfortunate individual could been seen more easily by prey compared with his brown fellows and would have a harder time surviving and raising offspring. A white coat in predominantly snow-covered terrain, on the other hand, could give him an advantage over other brown bears. Same mutation, in one situation detrimental, in another beneficial. The environment decides.

    Current thinking holds that the majority of mutations are neutral or nearly neutral in effect. A smaller number are detrimental – there are more ways for something to go wrong than than go right – and a much smaller number still are beneficial.

    So why don’t the greater number of harmful mutations simply swamp the good ones and cause species to go extinct?

    Simple answer one, if they were to happen at such a rate that the species couldn’t cope with, then that’s exactly what would happen. There are no guarantees under evolution. We could go extinct just as easily as the next species if things went wrong.

    Simple answer two, detrimental mutations are harmful, by definition, because they impair the capacity to survive in a given environment. Those so afflicted, in the words of the philosopher W V O Quine in another context, “ have a pathetic but praiseworthy tendency to die before reproducing their kind”. In other words, natural selection tends to filter out the harmful mutations and only the beneficial are left. If you want to put it in information terms, harmful information has been lost and good information has replaced it. What’s the big deal about losing bad information?

  37. 37
    Virgil Cain says:

    Umm, Seversky, Crick is the one who discussed information with respect to biology.

  38. 38
    Mapou says:

    So, Virgil Cain, where is the information that is responsible for the full diversity of life, if it’s not in DNA according to you? Enquiring minds and all that.

  39. 39
    harry says:

    harry @12

    … the non coding regions of DNA probably contain much functional information that we just have deciphered yet, but is probably just as organized and ordered as the regions of DNA memory that code for protein machines.

    Should have been

    … the non coding regions of DNA probably contain much functional information that we just have NOT deciphered yet, but is probably just as organized and ordered as the regions of DNA memory that code for protein machines.

  40. 40
    Mung says:

    Seversky, I can’t really think of any good reason to think that humans are so utterly different from other living organisms that they are the only ones capable of storing, communicating and transferring information. Can you?

    Oh, and the nucleic acids are symbols which just might give us pause and lead us to think there is language involved within the cell as well as outside.

    Or are you a dualist?

  41. 41
    Virgil Cain says:

    Hi Mapou- Please check out the following from Dr Denton. Also read “Why is a Fly Not a Horse?” by geneticist Giuseppe Sermonti. And finally read what Dr Wells has to say about it.

    First Dr Denton in his chapter from “Dissent from Darwin”:

    To understand the challenge to the “superwatch” model by the erosion of the gene-centric view of nature, it is necessary to recall August Weismann’s seminal insight more than a century ago regarding the need for genetic determinants to specify organic form. As Weismann saw so clearly, in order to account for the unerring transmission through time with precise reduplication, for each generation of “complex contingent assemblages of matter” (superwatches), it is necessary to propose the existence of stable abstract genetic blueprints or programs in the genes- he called them “determinants”- sequestered safely in the germ plasm, away from the ever varying and destabilizing influences of the extra-genetic environment.

    Such carefully isolated determinants would theoretically be capable of reliably transmitting contingent order through time and specifying it reliably each generation. Thus, the modern “gene-centric” view of life was born, and with it the heroic twentieth century effort to identify Weismann’s determinants, supposed to be capable of reliably specifying in precise detail all the contingent order of the phenotype. Weismann was correct in this: the contingent view of form and indeed the entire mechanistic conception of life- the superwatch model- is critically dependent on showing that all or at least the vast majority of organic form is specified in precise detail in the genes.

    Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes as Weismann’s “unambiguous bearers of information” or view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a small fraction of all known genes, such as the developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene

    Now a snippet from Sermonti,Chapter VI “Why is a Fly not a horse?” (same as the book’s title)

    ”The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”

    Do computer application programs make the computer? Does the OS make the computer? Does the combination of all programs make the computer?

    We can figure out where the software is by synthesizing an organism one piece at a time. Venter did the DNA so we can cross that off.

  42. 42
    bornagain77 says:

    Virgil Cain, here are a few more notes to go with yours that show ‘form’ is not reducible to DNA:

    The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism – Michael J. Denton – 2013
    Excerpt: Cell form ,,,Karsenti comments that despite the attraction of the (genetic) blueprint model there are no “simple linear chains of causal events that link genes to phenotypes” [77: p. 255]. And wherever there is no simple linear causal chain linking genes with phenotypes,,,—at any level in the organic hierarchy, from cells to body plans—the resulting form is bound to be to a degree epigenetic and emergent, and cannot be inferred from even the most exhaustive analysis of the genes.,,,
    To this author’s knowledge, to date the form of no individual cell has been shown to be specified in detail in a genomic blueprint. As mentioned above, between genes and mature cell form there is a complex hierarchy of self-organization and emergent phenomena, rendering cell form profoundly epigenetic.
    http://bio-complexity.org/ojs/.....O-C.2013.3

    Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA – 2014 – Jonathan Wells
    Excerpt Page 11: Most proteins are not completely specified by DNA sequences:
    The central dogma (which here includes Crick’s sequence hypothesis) claims that (1) DNA specifies RNA and (2) RNA specifies protein. Yet this claim fails at both steps, because most RNAs are not uniquely specified by DNA sequences, and many proteins are not uniquely specified by RNAs—either in their amino acid sequences or in their final folded forms. After transcription, RNAs from many eukaryotic genes undergo alternative splicing. Recent studies estimate that transcripts from approximately 95% of multi-exon human genes are spliced in more than one way [289?291]. By intervening between transcription and translation, alternative splicing generates RNAs with sequences that differ from DNA sequences [292]. The differences are functionally significant.,,,
    Page 12
    In addition to alternative splicing, many metazoan transcripts undergo RNA editing, which can (a) modify cytidine to uridine; (b) modify adenosine to inosine; or (c) insert additional nucleotides. Several recent analyses have demonstrated extensive RNA editing in the human transcriptome [303?305]. The editing of an mRNA often alters the amino acid sequence of the encoded protein so that it differs from the sequence predicted by the DNA [306,307].
    References:
    289. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476. doi: 10.1038/nature07509
    290. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-1415. doi: 10.1038/ng.259
    291. Barash Y, Calarco JA, Gao W, Pan Q, Wang X, et al. (2010) Deciphering the splicing code. Nature 465:53-59. doi: 10.1038/nature09000
    292. Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, et al. (2013) Alternative splicing: A pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 14:153-165. doi: 10.1038/nrm3525
    303. Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, et al. (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30:253-260. doi: 10.1038/nbt.2122
    304. Bahn JH, Lee JH, Li G, Greer C, Peng G, et al. (2012) Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res 22:142-150. doi: 10.1101/gr.124107.111
    305. Sakurai M, Ueda H, Yano T, Okada S, Terajima H (2014) A biochemical landscape of A-to-I RNA editing in the human brain transcriptome. Genome Res (January 9, 2014). doi: 10.1101/gr.162537.113
    306. Brennicke A, Marchfelder A, Binder S (1999) RNA editing. FEMS Microbiol Rev 23:297-316. doi: 10.1111/j.1574-6976.1999.tb00401.x
    307. Eisenberg E, Li JB, Levanon EY (2010) Sequence based identification of RNA editing sites. RNA Biol 7:248-252. doi: 10.4161/rna.7.2.11565
    http://bio-complexity.org/ojs/.....O-C.2014.2

    In Embryo Development, Non-DNA Information Is at Least as Important as DNA – Jonathan Wells – May 2012
    Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns.
    http://www.evolutionnews.org/2.....60031.html

    “Live memory” of the cell, the other hereditary memory of living systems – 2005
    Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.
    http://www.ncbi.nlm.nih.gov/pubmed/15888340

    podcast – Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 – Bioelectric code
    http://intelligentdesign.podom.....5_52-07_00

    Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011
    Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo.
    http://www.evolutionnews.org/2.....54071.html

    The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern – July 2011
    Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, “When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,”,,, “We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”,,,
    http://www.physorg.com/news/20.....-seen.html

    Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015
    Excerpt: humans have a “few thousand” different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,,
    The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It’s called genomic mosaicism.
    In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,,
    ,,,(then) “genomic equivalence” — the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA — became the accepted view.
    I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common.
    I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It’s the organism controlling the DNA, not the DNA controlling the organism.
    http://www.evolutionnews.org/2.....93851.html

    Extreme Genome Repair – 2009
    Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,,
    http://www.ncbi.nlm.nih.gov/pm.....MC3319128/

  43. 43
    Mapou says:

    Virgil Cain,

    I read your reply and I still see no reason to believe that genes are not the primary cause of the full diversity of lifeforms on earth. Even if environmental pressure modifies an organism (adaptation via epigenetics) in a way that changes the form and fitness of its offsprings, the new information that is inherited by the offsprings is still in the genes.

    Your software/hardware metaphor either went over my head or it’s inappropriate. The medium in which the information is stored and interpreted is irrelevant. What’s important if whether the information can be used by some “bootstrapping” mechanism to build, not only the organism, but a major portion of the mechanism itself.

    One more thing, why is this issue important to IDists?

  44. 44
    Virgil Cain says:

    Building materials influence what type of building you can build. They do not determine the building.

  45. 45
    Silver Asiatic says:

    where is the information that is responsible for the full diversity of life, if it’s not in DNA

    Where is the information difference between human and chimp? Is it in the 1% difference in DNA?

  46. 46
    Mung says:

    SA, I am going to go with a no on that one. 🙂

  47. 47
    Mung says:

    Mapou, I personally don’t think this is an argument for intelligent design.

    It might be an argument for young earth creationism, or what Salvador has taken to calling “young life.”

    I have no idea though what Durston’s position is on the age of the earth.

  48. 48
    Mapou says:

    Well, ladies and gentlemen. I’m not convinced at all by the arguments I have seen so far. I see no reason to change my mind that genes (DNA) are the primary determinants of the wide ranging diversity of life on earth.

    One more thing. I put YEC in the same crap basket as Darwinism. I’m just voicing an opinion, BTW. So don’t get bent out of shape.

  49. 49
    jerry says:

    where is the information that is responsible for the full diversity of life, if it’s not in DNA

    As I said earlier, Meyer thinks it is in the egg cell wall. See Ch 14 of his book, Darwin’s Doubt, especially the Sugar Code.

    Biologists know of an additional source of epigenetic information stored in the arrangement of sugar molecules on the exterior surface of the cell membrane. Sugars can be attached to the lipid molecules that make up the membrane itself (in which case they are called “glycolipids”), or they can be attached to the proteins embedded in the membrane (in which case they are called “glycoproteins”). Since simple sugars can be combined in many more ways than amino acids, which make up proteins, the resulting cell surface patterns can be enormously complex. As biologist Ronald Schnaar explains, “Each [sugar] building block can assume several different positions. It is as if an A could serve as four different letters, depending on whether it was standing upright, turned upside down, or laid on either of its sides. In fact, seven simple sugars can be rearranged to form hundreds of thousands of unique words, most of which have no more than five letters.”

    There is a lot more there on other epigenetic information.

    Where is the information difference between human and chimp? Is it in the 1% difference in DNA?

    Most of the difference are in control mechanisms that affect expression of proteins in the brain. See Wilcox

    http://www.asa3.org/ASA/meetin.....Wilcox.pdf

    for a discussion. From Wilcox

    We and chimps share 96% to 99% of our protein coding sequences. Why are we different? Not the 1.5% of our genome that codes for proteins but the 98.5% that controls their production. Literally, no other primate lineage has evolved as fast as our lineage has during the last 1.5 million years, and it’s all due to unique changes in our control genome.

  50. 50
    jerry says:

    BA,

    Here is a thread from last year which has information about Brosius, including more links to his ideas.

    http://www.uncommondescent.com.....-in-rooms/

    Here is a major review (just abstract and footnotes)

    http://www.bioone.org/doi/abs/.....2.0.CO%3B2

    I have the full pdf and this was a chapter in a book about macro evolution by Vrba which I also have. You might be able to get it from your library if they have JSTOR service.

    You will notice that I do not believe he has really solved the problem but points to a few coding areas that have come into being through the exaptation of mutated DNA sequences. He is a major player and not a clown like Coyne or PZ Myers.

    Brosius came up because of Allen MacNeil over 6 years ago. He pointed out Vrba’s book as a discussion of macro-evolution and Brosius was given the honor of authoring a long introduction in the book. He had been a co-author with Stephen Gould and his ideas provides some basis for punctuated equilibrium because they hypothesize a sudden appearance of genes.

  51. 51
    bornagain77 says:

    jerry, please cite the specific experimental data requested of a single gene and/or protein being generated by unguided material processes in real time.

    You made the claim. YOU need to support it with real time evidence! It is not up to me to dig through your myriad of links to try to find some evidence for a gene/protein being generated by unguided material processes when I KNOW for a fact that the evidence does not exist!

    You are more than welcome to try to prove me, Durston, Behe, Meyer, Axe, Gauger, Luskin, Sanford, etc.. etc.. wrong.

  52. 52
    jerry says:

    jerry, please cite the specific experimental data requested of a single gene and/or protein being generated by unguided material processes in real time.

    I gave you a reference for a review article. In it he discusses his ideas and lists his research. Pick one. Several look good for what he says.

    Brosius, J. 1991. Retroposons—seeds of evolution. Science 251:753.
    Brosius, J. 1999a. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107:209–238.
    Brosius, J. 1999b. Many G-protein-coupled receptors are encoded by retrogenes. Trends in Genetics 15:304–305.
    Brosius, J. 1999c. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115–134.
    Brosius, J. 1999d. Transmutation of tRNA over time. Nature Genetics 22:8–9.
    Brosius, J. 2001. tRNAs in the spotlight during protein biosynthesis. Trends in Biochemical Sciences 26:653–656.
    Brosius, J. 2003a. The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118:99–116.
    Brosius, J. 2003c. Gene duplication and other evolutionary strategies: from the RNA world to the future. Journal of Structural and Functional Genomics 3:1–17.
    Brosius, J. 2005a. Echoes from the past—are we still in an RNP world? Cytogenetic and Genome Research (in press).
    Brosius, J. 2005b. Waste not, want not—transcript excess in multicellular Eukaryotes. Trends in Genetics 21:287–288.
    Brosius, J. and S. J. Gould. 1992. On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA.”. Proceedings of the National Academy of Sciences USA 89:10706–10710. CrossRef, PubMed
    Brosius, J. and H. Tiedge. 1995. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 11:163–179.
    Brosius, J. and H. Tiedge. 2004. RNomenclature. RNA Biology 1:81–83.

    From the footnotes of his review

    An extension of Wally Gilbert’s metaphor “exons in a sea of introns” (Gilbert 1978). Functional nuons are islands in a sea of nonfunctional (nonaptive) sequences. Nevertheless, any of those sequences has the potential to be exapted into novel functions
    (Brosius and Gould 1992; Balakirev and Ayala 2003).

    Balakirev, E. S. and F. J. Ayala. 2003. Pseudogenes: are they “junk” or functional DNA? Annual Review of Genetics 37:123–151.

    While “plate tectonics,” or exon shuffling, occasionally leads to rearrangements of existing functional nuons (Gilbert 1978), retroposition, the major force in the plasticity of genomes, which in our analogy is more akin to volcanic eruptions, frequently creates new nuons. Initially, most nuons (islands) are barren (nonfunctional, nonaptive) but have the potential to be fertilized by some microevolutionary base changes or short indels and exapted as functional nuons. Nonfunctional nuons erode over time and the islands disappear in the sea of anonymous sequences. An interesting example is the recruitment of part of an Alu retronuon as an alternative exon in an isoform of the cytokine tumor necrosis factor receptor. Insertion of the Alu element occurred after Anthropoidea split from prosimians and a subsequent point mutation generated an ATG start codon. This base substitution alone, however, was not sufficient for exaptation of the Alu element as a protein-coding exon, as this sequence is nonaptive (not used as part of an alternative mRNA) in Platyrrhini. Only two additional small changes in the lineage leading to Catarrhini including apes, a C?T transition to generate a GT 5? splice site and a 7-bp deletion to provide translation into the next exon in the correct reading frame, led to generation and exaptation of this alternative exon (Singer et al. 2004).

    Singer, S. S., D. N. Männel, T. Hehlgans, J. Brosius, and J. Schmitz. 2004. From “junk” to gene: curriculum vitae of a primate receptor isoform gene. Journal of Molecular Biology 341:883–886.

    —————————

    You are more than welcome to try to prove me, Behe, Meyer, Axe, Guager, Luskin, Sanford, etc.. etc.. wrong.

    You completely misunderstand what is happening here. I am not trying to prove you wrong. I am saying that one of the most prestigious researchers today in evolutionary biology says that new information is no big deal. As such he carries a lot more weight with the scientific community than you and all the others combined. And because of this his ideas should be examined.

    I have never endorsed Brosius, just the opposite. But he has never been dealt with.

  53. 53
    bornagain77 says:

    Jerry, do you actually believe, in all the links you cited, that he has ANY real time experimental evidence showing unguided material processes generating a single gene/protein? If so, I have a bridge for you!

    You asked me to pick one. OK how about the this one?:

    Gene duplication and other evolutionary strategies: from the RNA world to the future – 2003
    Abstract
    Beginning with a hypothetical RNA world, it is apparent that many evolutionary transitions led to the complexity of extant species. The duplication of genetic material is rooted in the RNA world. One of two major routes of gene amplification, retroposition, originated from mechanisms that facilitated the transition to DNA as hereditary material. Even in modern genomes the process of retroposition leads to genetic novelties including the duplication of protein and RNA coding genes, as well as regulatory elements and their juxtapositon. We examine whether and to what extent known evolutionary principles can be applied to an RNA-based world. We conclude that the major basic Neo-Darwinian principles that include amplification, variation and selection already governed evolution in the RNA and RNP worlds. In this hypothetical RNA world there were few restrictions on the exchange of genetic material and principles that acted as borders at later stages, such as Weismann’s Barrier, the Central Dogma of Molecular Biology, or the Darwinian Threshold were absent or rudimentary. RNA was more than a gene: it had a dual role harboring, genotypic and phenotypic capabilities, often in the same molecule. Nuons, any discrete nucleic acid sequences, were selected on an individual basis as well as in groups. The performance and success of an individual nuon was markedly dependent on the type of other nuons in a given cell. In the RNA world the transition may already have begun towards the linkage of nuons to yield a composite linear RNA genome, an arrangement necessitating the origin of RNA processing. A concatenated genome may have curbed unlimited exchange of genetic material; concomitantly, selfish nuons were more difficult to purge. A linked genome may also have constituted the beginning of the phenotype/genotype separation. This division of tasks was expanded when templated protein biosynthesis led to the RNP world, and more so when DNA took over as genetic material. The aforementioned barriers and thresholds increased and the significance and extent of horizontal gene transfer fluctuated over major evolutionary transitions. At the dawn of the most recent transformation, a fast evolutionary transition that we will be witnessing in our life times, a form of Lamarckism is raising its head.
    http://link.springer.com/artic.....2627311114

    All I see is one big romp through imagination, (i.e. just so stories), with no empirical support whatsoever.

    Remember I said

    Disagree? If so, then provide direct empirical evidence to back up their claims and not just sequence comparisons that assume the conclusion into the premise.

    and then you said

    “I suggest you read Jurgen Brosius.”

    and, after you asked me to ‘pick one’ of his papers, I am still waiting for that real time empirical evidence that you insinuated existed in his writings.

    i.e. The emperor Brosius has no clothes on!

  54. 54
    Mapou says:

    Jerry @49,

    I don’t get it. You are insinuating something that is simply not there. I don’t see any evidence where Meyer claims that the information that is responsible for the full diversity of life on earth is in the egg cell wall. You’re making this up, IMO.

    In fact, it’s a good bet that the proteins that make up the cell wall are manufactured according to genetic information prescribed in the gene, just like every other protein.

  55. 55
    bornagain77 says:

    New tools developed to unveil mystery of the ‘glycome’ – June 10, 2012
    Excerpt: One of the Least Understood Domains of Biology: The “glycome”—the full set of sugar molecules in living things and even viruses—has been one of the least understood domains of biology. While the glycome encodes key information that regulates things such as cell trafficking events and cell signaling, this information has been relatively difficult to “decode.” Unlike proteins, which are relatively straightforward translations of genetic information, functional sugars have no clear counterparts or “templates” in the genome. Their building blocks are simple, diet-derived sugar molecules, and their builders are a set of about 250 enzymes known broadly as glycosyltransferases.,,,
    http://phys.org/news/2012-06-t.....ycome.html

    Glycans rival DNA and proteins in terms of complexity;

    Glycans: What Makes Them So Special? – The Complexity Of Glycans – short video
    http://www.youtube.com/watch?v=WXez_OyNBQA

    The Membrane Code: A Carrier of Essential Biological Information That Is Not Specified by DNA and Is Inherited Apart from It – Jonathan Wells – published online May 2013
    Excerpt: ,,In 1985 Ronald Schnaar wrote, “There appears to be a code on the surface of each cell that specifies its function and directs its interactions with other cells, a code in some ways comparable to the genetic code carried on the DNA molecules inside each cell.” The “letters” of the cell surface code to which Schnaar was referring are sugar molecules. A few monosaccharide building blocks can produce the enormous diversity of “words” needed to identify the many different kinds of cells in a complex organism, Schnaar explained, because “each building block can assume several different positions. It is as if an A could serve as four different letters, depending on whether it was standing upright, turned upside down, or laid on either of its sides. In fact, seven simple sugars can be rearranged to form hundreds of thousands of unique words, most of which have no more than five letters. (This alphabet is even more efficient than the genetic code: the four nucleic acids that constitute DNA — guanine, adenine, thymine, and cytosine — can be connected only front to back, like roller coaster cars.) So, not only are sugars in the right place to serve as the alphabet for the cell-surface code, they have the requisite structural flexibility too.” Schnaar concluded, “It may be that as much control over the cell’s fate, and as much of the language of life’s unfolding, reside on the cell’s surface as in its nucleus” [63].,,
    Membrane patterns in ciliates are known to be heritable independently of the information in DNA sequences, and there is evidence that some cytoskeletal and membrane patterns in the cells of multicellular organisms can also be inherited apart from the DNA. Taken together, the data suggest that embryo development is not controlled by DNA alone, and thus that DNA mutations are not sufficient to provide raw materials for evolution.
    http://www.worldscientific.com.....08728_0021

    Yet Glycans, despite their complexity and importance to cell function, are, like DNA and Proteins, now being found to be ‘rather uncooperative’ with neo-Darwinian evolution;

    This Non Scientific Claim Regularly Appears in Evolutionary Peer Reviewed Papers – Cornelius Hunter – April 2012
    Excerpt: Indeed these polysaccharides, or glycans, would become rather uncooperative with evolution. As one recent paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” This dizzying array of glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only. In other words, the evidence is not what evolution expected.
    Here is how another paper described early glycan findings:
    There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages. It appears that closely related species may not necessarily share close similarities in their glycan diversity, and that more derived species may have simpler as well as more complex structures. Intraspecies diversity can also be quite extensive, often without obvious functional relevance.
    http://darwins-god.blogspot.co.....larly.html

  56. 56
    Roy says:

    Jerry, do you actually believe, in all the links you cited, that he has ANY real time experimental evidence showing unguided material processes generating a single gene/protein? If so, I have a bridge for you!

    You asked me to pick one. OK how about the this one?: [abstract omitted]
    All I see is one big romp through imagination, (i.e. just so stories), with no empirical support whatsoever.

    Did you read the full paper, or only the abstract?

  57. 57
    jerry says:

    Did you read the full paper, or only the abstract?

    I read the paper a few times and parts of it additional times. I have the book in which it appeared as well as a pdf of the journal article. It was the lead article in a book that was a tribute to Stephen Gould.

    I have commented on it several times here over the years. It was first recommended by Allen MacNeill over 6 years ago.

  58. 58
    bornagain77 says:

    jerry,

    “I read the paper a few times and parts of it additional times.”

    And the real time experimental evidence of a gene/protein being generated by unguided material processes is where exactly?

    That’s the whole thing jerry. Darwinists are notorious for making up elaborate far fetched just so stories based on little more than their unconstrained imagination, but when push comes to shove, they NEVER deliver on the real time empirical evidence that would give their just so story credibility.

    Moreover, they consistently ignore insurmountable empirical difficulties with their theory.

    Dr. Behe states:

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe – 29:24 mark of following video
    http://www.youtube.com/watch?f.....fM#t=1762s

    and

    Finally, a Detailed, Stepwise Proposal for a Major Evolutionary Change? – Michael Behe – March 10, 2015
    Excerpt: I would say its (Nick Matzke’s 2004 proposal for the evolution of the flagellum) chief problem is that it’s terminally fuzzy, bases most of its speculation on sequence comparisons, and glides over difficulties that would have to be dealt with in nature.,,, That’s one reason I wrote The Edge of Evolution — to say that we no longer have to rely on our imaginations, that we have good evidence to show what Darwinian processes are capable of doing. When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage.
    http://www.evolutionnews.org/2.....94271.html

  59. 59
    Virgil Cain says:

    Mapou:

    I see no reason to change my mind that genes (DNA) are the primary determinants of the wide ranging diversity of life on earth.

    When you find the evidence that supports that view please share it with us. Thank you.

    BTW guys, it was Wells, not Meyer, who talked about information in the egg-cell wall and cytoskeleton. Wells is the developmental biologist, not Meyer.

  60. 60
    Box says:

    Stephen Meyer on electromagnetic fields; “Darwin’s Doubt”, ch.14, ‘Epigenetic Revolution’, ‘Beyond Genes’, ‘Ion Channels and Electromagnetic Fields’.

    Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism. In particular, some experiments have shown that the targeted disturbance of these electric fields disrupts normal development in ways that suggest the fields are controlling morphogenesis.22 Artificially applied electric fields can induce and guide cell migration. There is also evidence that direct current can affect gene expression, meaning internally generated electric fields can provide spatial coordinates that guide embryogenesis.23 Although the ion channels that generate the fields consist of proteins that may be encoded by DNA (just as microtubules consist of subunits encoded by DNA), their pattern in the membrane is not. Thus, in addition to the information in DNA that encodes morphogenetic proteins, the spatial arrangement and distribution of these ion channels influences the development of the animal.

    Here an interesting article by Richard H. W. Funk.

  61. 61
    bornagain77 says:

    Besides being a lead player in morphogenesis during embryological development, biophotons are also heavily involved in the cellular communication of an organism throughout an organism’s entire life.
    http://www.uncommondescent.com.....ent-569470

  62. 62
    jerry says:

    BTW guys, it was Wells, not Meyer, who talked about information in the egg-cell wall and cytoskeleton. Wells is the developmental biologist, not Meyer.

    If you want to split hairs, maybe. We learned about it from Meyer’s book and Meyer gives full credit to his introduction to the topic by Wells in Chapter 14 of his book. He includes a photograph of Wells at this point. See this in Meyer’s book

    ABOVE AND BEYOND: EPIGENETIC INFORMATION

    In 2003, MIT Press published a groundbreaking collection of scientific essays titled Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, edited by two distinguished developmental and evolutionary biologists, Gerd Muller, of the University of Vienna, and Stuart Newman, of New York Medical College. In their volume, Muller and Newman included a number of scientific articles describing recent discoveries in genetics and developmental biology—discoveries suggesting that genes alone do not determine the three-dimensional form and structure of an animal. Instead, many of the scientists in their volume reported that so-called epigenetic information—information stored in cell structures, but not in DNA sequences—plays a crucial role. The Greek prefix epi means “above” or “beyond,” so epigenetics refers to a source of information that lies beyond the genes. As Muller and Newman explain in their introduction, “Detailed information at the level of the gene does not serve to explain form.”s Instead, as Newman explains, “epigenetic” or “contextual information” plays a crucial role in the formation of animal “body assemblies” during embryological development.

    Muller and Newman not only highlighted the importance of epigenetic information to the formation of body plans during development; they also argued that it must have played a similarly important role in the origin and evolution of animal body plans in the first place. They concluded that recent discoveries about the role of epigenetic information in animal development pose a formidable challenge to the standard neo-Darwinian account of the origin of these body plans—perhaps the most formidable of all.

    In the introductory essay to their volume, Miiller and Newman list a number of “open questions” in evolutionary biology, including the question of the origin of Cambrian-era animal body plans and the origin of organismal form generally, the latter being the central topic of their book. They note that though “the neo-Darwinian paradigm still represents the central explanatory framework of evolution,” it has “no theory of the generative.”? In their view, neo-Darwinism “completely avoids [the question of] the origination of phenotypic traits and of organismal form.”s As they and others in their volume maintain, neo-Darwinism lacks an explanation for the origin of organismal form precisely because it cannot explain the origin of epigenetic information.

    I first learned about the problem of epigenetic information and the Spemann and Mangold experiment while driving to a private meeting of Darwin-doubting scientists on the central coast of California in 1993. In the car with me was Jonathan Wells (see Fig. 14.1), who was then finishing a Ph.D. in developmental biology at the University of California at Berkeley. Like some others in his field, Wells had come to reject the (exclusively) “gene-centric” view of animal development and to recognize the importance of nongenetic sources of information.

    By that time, I had studied many questions and challenges to standard evolutionary theories arising out of molecular biology. But epigenetics was new to me. On our drive, I asked Wells why developmental biology was so important to evolutionary theory and to assessing neo-Darwinism. I’ll never forget his reply. “Because” he said, “that’s where the whole theory is going to unravel.”

    In the years since, Wells has developed a powerful argument against the adequacy of the neo-Darwinian mechanism as an explanation for the origin of animal body plans. His argument turns on the importance of epigenetic information to animal development.

  63. 63
    jerry says:

    BA,

    I have read everything I wrote on this page. I suggest you point out where you disagree with me. You may disagree with Juergen Brosius, and that is fine, because I do too and I say so more than once. But what did I say that was wrong?

  64. 64
    bornagain77 says:

    jerry, when I asked if you Disagree with me on the state of empirical evidence you are the one who brought up Juergen Brosius as if he had some empirical evidence that would counter my claim that Darwinists have no real time empirical evidence to support their grandiose claims.

    You have suggested I read him twice as a matter of fact. And sent a flurry of links insinuating that the evidence would be in those links.

    You are the one insinuating that he had some actual real time evidence that counters my claim as to the state of empirical evidence.

    Plain and simple, he does not.

    Thus why did you bring him up in the first place?

    The only person who went along with you was roy for crying out loud.

    You told roy you read him. Twice in some places, and you also mentioned that you disagree with him, but commented no further as to the fact that he has no actual real time evidence to support his claims. Which is what you originally insinuated against my claim for the actual state of the empirical evidence.

    I happen to be able to read myself

    http://www.uncommondescent.com.....ent-570052

    http://www.uncommondescent.com.....ent-570056

  65. 65
    Roy says:

    @ jerry:

    I didn’t mean you.

    @bornagain77:

    Did you read the full paper?

  66. 66
    jerry says:

    Did I say anything that was wrong? That was the question I asked?

    You are the one insinuating that he has something that counters my claim as to the state of empirical evidence.

    He certainly claims he does and he is a very respected researcher. Do you deny that he claims to have shown new informnation arising through genetic processes.

    He does not. Thus why did you bring him up in the first place.

    You have no way of knowing this unless you have read all of his research. Do you think that someone would have gotten where he has by making it up?

    It is absurd to think that no new information will be created by these processes over billions of years. It is quite another thing to suggest that it explains the origin of all the information or even most of it.

    But none?

    I suggest you make Juergen Brosius your friend in your position by pointing out this is the best they have. This has been what I have done since first reading about him. I have been consistent about this for over six years since I first read his articles.

  67. 67
    bornagain77 says:

    “You have no way of knowing this unless you have read all of his research. Do you think that someone would have gotten where he has by making it up”

    Yes I do think he is making it all up. Apparently you don’t!

    Fine, you read him, twice in some places, thus cite the actual experimental research that shows a gene/protein being generated in real time by unguided material processes.

    The evidence simply does not exist. You are invited to try to prove Dr. Behe, for one, wrong:

    “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.
    http://behe.uncommondescent.co.....evolution/

  68. 68
    bornagain77 says:

    Does he cite Lenski’s e-coli as a prime example of unguided material processes creating functional information as do other neo-Darwinists?

    Hype from New Scientist Aside, Lenski’s E. coli Research Shows Evolution of Nothing New – Casey Luskin June 25, 2015
    As we reported in April, the pro-Darwin media love to print triumphalist articles, declaring on the thinnest of evidence that the “creationists” are deathly scared of the latest discoveries in science. Now New Scientist takes a turn, claiming that the E. coli research of Richard Lenski “has become a poster child for evolution, causing consternation among creationists trying to explain away its compelling evidence.” Yet read the article carefully, and you’ll see that it confirms Lenski’s research did not show the evolution of anything new.
    New Scientist frames the article this way:
    “The biggest evolutionary shift occurred after about the 31,500 generation, when one line in one of the 12 populations evolved the ability to feed on citrate”
    Except that’s not true. Normal E. coli already have the ability to feed on citrate — they just don’t typically do it under oxic conditions (i.e., where oxygen is present). The interesting thing about Lenski’s research is that his bugs evolved the ability to uptake citrate under oxic conditions. But did anything new evolve? Here’s what the article says:
    “But a mutation in the citrate-eaters allowed them to make an “antiporter” protein, CitT, that allows citrate to cross the membrane and enter the cell. The gene for this protein already existed, but it’s usually switched off when oxygen is present.
    The antiporter is a kind of revolving door. It allows one molecule to be swapped for another. In this case, the citrate is imported into the cell in exchange for one of three smaller, less-valuable molecules: succinate, fumarate or malate.”
    What really happened? A switch that normally represses expression of CitT under oxic conditions was broken, so the citrate-uptake pathway got turned on. This isn’t the evolution of a new molecular feature. It’s the breaking of a molecular feature — a repressor switch. Of course none of this is disclosed in the article.
    But New Scientist isn’t done. It goes on:
    “Those citrate feeders soon became dominant, outcompeting all but one other strain of E. coli, which in turn evolved to exploit the changed environment — which now contained the three exported molecules.
    It did this by making more of a transporter protein called DctA, which imports – at a small energy cost – succinate and other molecules exported by the citrate-eating strain.
    But things did not stop there. The citrate-eaters then also started making more DctA to try to claw back some of the succinate and other molecules they were losing in the process of acquiring citrate.”
    Again, did anything new evolve? No — all we see is overexpression of pre-existing genes.
    So in the end, E. coli are able to eat things that they could already metabolize before the experiments began. A molecular repressor switch has been broken, and another protein has been overexpressed.
    Nothing new to see here: these are all the kinds of changes we already know Darwinian evolution can do — breaking things at the molecular level, or making more of something you already have. This is how New Scientist spins it:
    “Turner’s findings are also yet another example of the mindlessness of evolution. The best solution would be to use a little energy to import citrate directly, the paper says, rather than swapping it for succinate and then spending energy to try to get that succinate back before other bacteria can feed on it.”
    Bacteria are found almost everywhere on the earth — from inside virtually every living organism to the deep sea to deep underground. They seem designed to be able to feed on just about anything they encounter. What Lenski may be seeing is the designed ability of bacteria to adapt to new environments using a diverse suite of metabolic pathways they have been gifted with, including the ability to break things or make more of them when needed.
    The media will tell you that this shows the amazing power of “mindless” Darwinian evolution. A closer look at the facts reveals nothing of the sort.
    http://www.evolutionnews.org/2.....97151.html

    Lenski’s Long-Term Evolution Experiment: 25 Years and Counting – Michael Behe – November 21, 2013
    Excerpt: Twenty-five years later the culture — a cumulative total of trillions of cells — has been going for an astounding 58,000 generations and counting. As the article points out, that’s equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski’s project the best, most detailed source of information on evolutionary processes available anywhere,,,
    ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, –
    http://www.evolutionnews.org/2.....79401.html

  69. 69
    Mung says:

    Hi jerry,

    I’ve read the Brosius chapter in the Vrba book.

    If you were to pick a paper in the list you provided that best addresses the topic raised in the OP could you link to that one paper? I’d like to read it.

    Not being critical or implying it doesn’t exist, just asking. Truly curious. Thanks

  70. 70
    jerry says:

    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.

    A couple things. Notice Behe does not say no positive information was generated. He just says the great majority of mutations, not all. This has been my position from early on.

    My first finding of the term “devolution” on this site was from 2006.

    http://www.uncommondescent.com.....ment-23062

    Here is my first usage of this concept 7 1/2 years ago in

    http://www.uncommondescent.com.....ent-155059

    In it I describe what ID should be about. I have not changed much since then. I have learned a lot but it nearly all reinforced my position back then.

    The full quote from 2007.

    I personally believe that ID should embrace neo Darwinism for two very important reasons

    1. It describes a process that produces a lot of change in living organisms and these changes have highly significant effects on life’s progress. Consequently, it is foolish to rail against it.

    2. I believe it is part of the design of life and as such is totally in sync with ID.

    I have often used the phrase that ID subsumes neo Darwinism and I firmly believe it because without neo Darwinism life would be very limited and stilted on this planet. People who support ID go immediately to what many neo Darwinists claim about the ability of this process to produce all the changes in biological organisms and then trash the whole theory. That is not good science. That is not logical. That is foolishness.

    I believe we should add a term to the concepts we use and that is “devolution” and point out that devolution is also part of the life change process and its main engine is neo Darwinism. While the term devolution usually carries a negative connotation, not all devolution is negative.

    We have had peripheral discussion over the last two years about where does all the variation come from in a population. It is something that neo Darwinism would not predict because the processes of neo Darwinism tend to remove variation from a population. Of course the obligatory response by those who support gradualism is that mutations are the source for this variation but what the Edge of Evolution has shown is that is highly unlikely. I remember great_ape saying that this was a problem for gradualism or naturalistic evolution. The genetic side of neo Darwinism causes population variation to decline.

    And while Sanford’s book argues that this will eventually lead to extinction of a species, new species constantly appear suddenly in life’s history and presumably the new populations appear with lots of variation because they seem to radiate out into many sub-species.

    And this is where neo Darwinism is essential for survival because given all the new variation, natural selection allows the species to survive in many different environments. In other words it allows sub variants to blossom where if not for neo Darwinism the species might go extinct sooner in the new environment. In other words the built in variation and neo Darwinism allow life to flourish, But we have not built a taxonomy that goes up as gradualist claim but a taxonomy that goes down to finer and finer variations of the original population. And to me this fits ID to a “T.”

    So I suggest we embrace neo Darwinism, argue against gradualism especially the Blind Watchmaker Thesis but point out how neo Darwinism helps make life flourish in many cirucmstances.

    I already above have made the point that neo Darwinism is essential for modern medicine. If one wants to go over again how that discussion started, read Seekandfind’s comment at #40 where he points out that the perception is that those who believe in ID are backward and a hindrance to science and that this hurdle has to be overcome. One way to overcome this is to embrace neo Darwinism and it devolution effects, some of which are good and some of which are bad for life. In evolution some are good and some are bad; in medicine nearly 100% are bad.

  71. 71
    jerry says:

    Not being critical or implying it doesn’t exist, just asking. Truly curious. Thanks

    I am off for a couple hours, but will try to find you an article. He lists several. This sounds promising

    Singer, S. S., D. N. Männel, T. Hehlgans, J. Brosius, and J. Schmitz. 2004. From “junk” to gene: curriculum vitae of a primate receptor isoform gene. Journal of Molecular Biology 341:883–886.

    I will have to see if I can get a copy. My access to journals is sometimes spotty.

    By the way one of the earliest uses of the term “devolution” on this site was by you.

  72. 72
    Mung says:

    jerry: By the way one of the earliest uses of the term “devolution” on this site was by you.

    And? You think I was using it to argue for YEC?

    I was likely using it to refer to evolution to a simpler more streamlined or more efficient state and not in any sense arguing that something or other was degrading, which means I was arguing the opposite of the view adopted by YECs.

  73. 73
    REC says:

    Curious. I asked: “What is the ID position on where the “instructions for the full diversity of life” reside?”

    Answers:
    1) Durston: “We now know that the instructions for the full diversity of life, are digitally encoded in the DNA of all living things”
    2) Virgil Cain: “It isn’t the DNA.”
    3) Jerry: “Meyer indicates there may be a sophisticated information system in the cell wall of the egg ”
    4) Mapou: “The genome holds > 99% of the information an organism carry, IMO. But the environment and epigenetics will contribute information content that is not inherited.”

    Now, whatever I post, I’m sure I’ll be accused of not understanding, or misrepresenting the “ID position.”

  74. 74
    REC says:

    Durston seems to suggest he’s inferring a general trend, but then provides us only specific examples of loss of DNA in parasites (which don’t need a full metabolic repertoire) or loss of non-functional DNA in Drosophila.

    The point he misses is that genetic information is lost when it is not needed. When essential, it is maintained in populations. The articles he cites specifically state the relationship of the environment, selection and information.

    He seems to suggest information was downloaded in early genomes, and retained without selection. Just waiting around, uncorrupted for billions of years. This is obviously internally contradictory.

  75. 75
    jerry says:

    Now, whatever I post, I’m sure I’ll be accused of not understanding, or misrepresenting the “ID position.”

    None of your excerpts are the ID position. So feel free to use what you think makes sense and no one can accuse you or misrepresenting ID. However, Durston is wrong because his he is too narrow in his wording. All the building blocks are encoded there but not all the instructions on how they are used.

  76. 76
    jerry says:

    I was likely using it to refer to evolution to a simpler more streamlined or more efficient state and not in any sense arguing that something or other was degrading

    You tell us what you were arguing for. Even then your love for Salvador came through.

    http://www.uncommondescent.com.....ment-43597

  77. 77
    REC says:

    jerry @ 75:

    “None of these are the ID position.”

    I guess we have another vote, despite what I listed as answer 3 above quotes Jerry’s response to my query on the ID position.

    Answers:
    1) Durston: “We now know that the instructions for the full diversity of life, are digitally encoded in the DNA of all living things”
    2) Virgil Cain: “It isn’t the DNA.”
    3) Jerry: “Meyer indicates there may be a sophisticated information system in the cell wall of the egg ”
    4) Mapou: “The genome holds > 99% of the information an organism carry, IMO. But the environment and epigenetics will contribute information content that is not inherited.”
    5) Jerry: “None of these are the ID position.”

  78. 78
    bornagain77 says:

    Interestingly, the gain of function mutations listed by Behe in his paper all involve ‘compensatory mutations’ that are implemented by the programming in the cell in response to a deletion/loss of a gene/protein.
    i.e. Compensatory mutations are ‘directed’ mutations, as opposed to purely random mutations, which compensate for the deletion and/or loss of a gene and/or protein.
    Yet, even these ‘directed’, i.e. ‘guided’, compensatory mutations have never been shown to surpass wild type bacteria in a fitness test.

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    https://www.youtube.com/watch?v=rYaU4moNEBU

    Thus compensatory mutations are not evidence for a gain of functional information over and above what was already present in the cell and/or life.

    In regards to the ‘fitness test’, the following is of related interest”

    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

    “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.”
    http://www.physicsforums.com/s.....p?t=281961

    In reply to a personal e-mail from myself, Dr. Cano commented on the ‘Fitness Test’ on the ancient bacteria that I had asked him about:
    Dr. Cano stated:

    “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    RJ Cano and MK Borucki – Fitness test which compared ancient amber sealed bacteria to its modern day descendants

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

  79. 79
    REC says:

    “Interestingly, the gain of function mutations listed by Behe in his paper all involve ‘compensatory mutations’ that are implemented by the programming in the cell.”

    Which paper? This one:
    http://www.lehigh.edu/~inbios/....._first.pdf

    “Compensatory” doesn’t appear. How did you, or he, determine they are “implemented by the programming in the cell”?

  80. 80
    Mapou says:

    Virgil Cain:

    Mapou:

    I see no reason to change my mind that genes (DNA) are the primary determinants of the wide ranging diversity of life on earth.

    When you find the evidence that supports that view please share it with us. Thank you.

    I will do no such thing. It’s a scientific fact that our genes dictate what we are. I’m not the one making an obviously absurd contrary claim. You, on the contrary must provide evidence to support your claim that something other than genes is the primary determinant of the wide ranging diversity of life on earth.

  81. 81
    Mapou says:

    Jerry, please stop using quotes without mentioning their sources. It’s confusing and unfriendly.

    And also, stop putting words in the mouths of prominent IDists. I’m still waiting for the evidence where Meyer (or anybody else) claims that the full diversity of life is the result of information not contained in the genes.

  82. 82
    Virgil Cain says:

    Mapou:

    It’s a scientific fact that our genes dictate what we are.

    And yet scientists say otherwise. If it was a scientific fact then it should be found in some science journal and yet it isn’t.

    Genes control traits. Being human is not a trait nor is it a collection of traits.

  83. 83
    bornagain77 says:

    REC, that’s not the paper.

    here it is, with a list of all the mutations:

    EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS, AND “THE FIRST RULE OF ADAPTIVE EVOLUTION”
    http://behe.uncommondescent.co.....evolution/

    I believe the fact that purposeful deletions were implemented prior to gain of function mutations is mentioned in this following excellent interview of Dr. Behe

    Michael Behe: Intelligent Design – interview on radio program – ‘The Mind Renewed’
    https://www.youtube.com/watch?v=H9SmPNQrQHE

  84. 84
    Virgil Cain says:

    Mapou:

    I’m still waiting for the evidence where Meyer (or anybody else) claims that the full diversity of life is the result of information not contained in the genes.

    Already provided and I didn’t even quote Wells yet.

  85. 85
    REC says:

    ba77 @83

    “REC, that’s not the paper.”

    I suspect it is, but that you don’t know what your copy/pasting mess actually contains or references.

    It could be this one:
    http://www.lehigh.edu/~inbios/....._paper.pdf

    …but it seems to challenge your own conclusion about it:
    “these were determined to be generally beneficial
    and not strictly compensatory for T3 RNAP.”

    Anyway, since you’re referencing it, can you get me the link to the paper where Behe concludes gain of function mutations are only compensatory, and that they are “implemented by the programming in the cell”?

  86. 86
    Mapou says:

    This thread has degenerated into crap. Durston’s original arguments are lost. I’m out of here.

  87. 87
    Roy says:

    Does he cite Lenski’s e-coli as a prime example of unguided material processes creating functional information as do other neo-Darwinists?

    If you’d bother to read the article you picked rather than simply pasting the abstract, you might not need to ask.

    But that’s the ID position. GThe designerod did it, but we won’t say how because that’d give the game away, and science must be wrong, so there’s no need to look.

  88. 88
    bornagain77 says:

    REC: contrary to what you believe as a neo-Darwinist, mutations are now found to be not truly random, i.e. ‘unguided’, as was postulated within Darwinism’s core theoretical framework, but are found to be ‘directed’

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations – Kevin Kelly – 2014
    Excerpt: What is commonly called “random mutation” does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it.
    On the contrary, there’s much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism’s predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern.
    http://edge.org/response-detail/25264

    James A. Shapiro PhD. Genetics:
    “What I ask others interested in evolution to give up is the notion of random accidental mutation.”
    http://www.huffingtonpost.com/.....11144.html

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    Evolution Is Not Random (At Least, Not Totally) – Tanya Lewis, – 02 October 2014
    Excerpt: Evolution is often said to be “blind,” because there’s no outside force guiding natural selection. But changes in genetic material that occur at the molecular level are not entirely random, a new study suggests. These mutations are guided by both the physical properties of the genetic code and the need to preserve the critical function of proteins, the researchers said.,,,
    “So in the end, most mutation is not random, at least for the DNA sequences we analyzed here,”
    http://m.livescience.com/48103.....2_32724136

    New Research Elucidates Directed Mutation Mechanisms – Cornelius Hunter – January 7, 2013
    Excerpt: mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations.,,,
    These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time.,,,
    http://darwins-god.blogspot.co.....ected.html

    etc.. etc..

    Perhaps, since this undercuts a primary tenet of Darwinism, you can explain to me exactly why this does not falsify neo-Darwinism?

  89. 89
    bornagain77 says:

    So Roy, perhaps you can point out the exact experimental evidence that I missed instead of just pronouncing that the pseudo-science of Darwinism is science and ID is not?

    of note: You do realize that Darwinism undercuts scientific rationality in the first place don’t you?

    i.e. Plantinga’s Evolutionary Argument Against Naturalism!

  90. 90
    Mung says:

    jerry: You tell us what you were arguing for. Even then your love for Salvador came through.

    I already told you what was arguing for. And yes, hate the sin, love the sinner.

    My record on YEC is well-documented here and elsewhere. And you might look into what I think of the “genetic entropy” argument. But really, you should just drop the whole line. It will not benefit you in the least and it seems rather pointless. But it is your time to do with as you wish.

  91. 91
    Mung says:

    REC, you’re misrepresenting ID or don’t understand the ID position, or something.

  92. 92
    butifnot says:

    Jerry your statement on Neo-Darwinism just seems like an unnecessarily long self evident truth: Things change.

  93. 93
    butifnot says:

    Mapau, I firmly believe we do not even know what we don’t know yet. So I don’t think pronouncements either way are warranted. DNA is looking more like a list of ingredients and not the recipe. There is, must be a level of control which we have not found yet.

  94. 94
    jerry says:

    Jerry your statement on Neo-Darwinism just seems like an unnecessarily long self evident truth: Things change.

    Then it wasn’t on this site. Today maybe you are right. I hope so.

  95. 95
    Box says:

    butifnot: DNA is looking more like a list of ingredients and not the recipe. There is, must be a level of control which we have not found yet.

    I agree that there must be even more levels of control which are not discovered yet. However we already found levels of control above and beyond DNA; see e.g. #42 and #60.

  96. 96
    jerry says:

    Mung,

    Not being critical or implying it doesn’t exist, just asking. Truly curious. Thanks

    Here are two

    Singer, S. S., D. N. Männel, T. Hehlgans, J. Brosius, and J. Schmitz. 2004. From “junk” to gene: curriculum vitae of a primate receptor isoform gene. Journal of Molecular Biology 341:883–886.

    Exonization of Alu retroposons awakens public opinion, particularly when causing genetic diseases. However, often neglected, alternative “Alu-exons” also carry the potential to greatly enhance genetic diversity by increasing the transcriptome of primates chiefly via alternative splicing. Here, we report a 5? exon generated from one of the two alternative transcripts in human tumor necrosis factor receptor gene type 2 (p75TNFR) that contains an ancient Alu-SINE, which provides an alternative N-terminal protein-coding domain. We follow the primate evolution over the past 63 million years to reconstruct the key events that gave rise to a novel receptor isoform. The Alu integration and start codon formation occurred between 58 and 40 million years ago (MYA) in the common ancestor of anthropoid primates. Yet a functional gene product could not be generated until a novel splice site and an open reading frame were introduced between 40 and 25 MYA on the catarrhine lineage (Old World monkeys including apes).

    I found the pdf here:

    http://www.researchgate.net/pu.....oform_gene

    If you or anyone have an opinion on this, I would be curious.

    And

    Biochimie. 2011 Nov;93(11):1928-34. doi: 10.1016/j.biochi.2011.07.014. Epub 2011 Jul 26.
    Exonization of transposed elements: A challenge and opportunity for evolution.
    Schmitz J1, Brosius J.

    Abstract
    Protein-coding genes are composed of exons and introns flanked by untranslated regions. Before the mRNA of a gene can be translated into protein, the splicing machinery removes all the intronic regions and joins the protein-coding exons together. Exonization is a process, whereby genes acquire new exons from non-protein-coding, primarily intronic, DNA sequences. Genomic insertions or point mutations within DNA sequences often generate alternative splice sites, causing the splicing system to include new sequences as exons or to elongate existing exons. Because the alternative splice sites are not as efficient as the originals the new variants usually constitute a minor fraction of mature mRNAs. While the prevailing original splice variant maintains functionality, the additional sequence, free from selection pressure, evolves a new function or eventually vanishes. If the new splice variant is advantageous, selection might operate to optimize the new splice sites and consequently increase the proportion of the alternative splice variant. In some instances, the original splice variant is completely replaced by constitutive splicing of the new form. Because of the fortuitous presence of internal splice site-like structures within their sequences, portions of transposed elements frequently serve as modules of exonization. Their recruitment requires a long and versatile optimization process involving multiple changes over a time span of millions, even hundreds of millions, of years. Comparisons of corresponding genes and mRNAs in phylogenetically related species enables one to chronologically reconstruct such changes, from ancient ancestors to living species, in a stepwise manner.

    We will review this process using three different exemplary cases: (1) the evolution of a constitutively spliced mammalian-wide repeat (MIR), (2) the evolution of an alternative exon 1 from an alternative 5′-extended primary transcript containing an Alu element, and (3) a rare case of the stepwise exoniztion of an Alu element-derived sequence mediated by A-to-I RNA editing.

    I was able to get this through a college library and could not find a pdf on the internet.

    Most of the rhetoric in this article implies these things are a done deal. They may not be which is why some high level talent above my pay grade has to decipher what is probably correct and what is speculative.

  97. 97
    Roy says:

    So Roy, perhaps you can point out the exact experimental evidence that I missed…

    Why should I waste time providing another reference that you can dismiss unread?*

    …instead of just pronouncing that the pseudo-science of Darwinism is science and ID is not?

    That may be the shortest example of double standards that I’ve ever seen.

    On which topic it is discrediting that you of all people would be complaining about being offered a “myriad of links”

    of note: You do realize that Darwinism undercuts scientific rationality in the first place don’t you?

    1) It doesn’t, and 2) that’s a blatant attempt to change the subject.

    *Also, UD’s recent policy means there’s no point attempting anything unsuperficial here anyway

  98. 98
    bornagain77 says:

    Roy, so you don’t provide any evidence for your position because you say it will be ignored? how convenient.

    Actually, despite your denials to the contrary, neo-Darwinism, since it assumes naturalism as true and denies free will as being real, does undercut rationality.

    Sam Harris’s Free Will: The Medial Pre-Frontal Cortex Did It – Martin Cothran – November 9, 2012
    Excerpt: There is something ironic about the position of thinkers like Harris on issues like this: they claim that their position is the result of the irresistible necessity of logic (in fact, they pride themselves on their logic). Their belief is the consequent, in a ground/consequent relation between their evidence and their conclusion. But their very stated position is that any mental state — including their position on this issue — is the effect of a physical, not logical cause.
    By their own logic, it isn’t logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order.
    http://www.evolutionnews.org/2.....66221.html

    (1) rationality implies a thinker in control of thoughts.
    (2) under materialism a thinker is an effect caused by processes in the brain.
    (3) in order for materialism to ground rationality a thinker (an effect) must control processes in the brain (a cause). (1)&(2)
    (4) no effect can control its cause.
    Therefore materialism cannot ground rationality.
    per Box UD

    Darwin’s Robots: When Evolutionary Materialists Admit that Their Own Worldview Fails – Nancy Pearcey – April 23, 2015
    Excerpt: Even materialists often admit that, in practice, it is impossible for humans to live any other way. One philosopher jokes that if people deny free will, then when ordering at a restaurant they should say, “Just bring me whatever the laws of nature have determined I will get.”
    An especially clear example is Galen Strawson, a philosopher who states with great bravado, “The impossibility of free will … can be proved with complete certainty.” Yet in an interview, Strawson admits that, in practice, no one accepts his deterministic view. “To be honest, I can’t really accept it myself,” he says. “I can’t really live with this fact from day to day. Can you, really?”,,,
    In What Science Offers the Humanities, Edward Slingerland, identifies himself as an unabashed materialist and reductionist. Slingerland argues that Darwinian materialism leads logically to the conclusion that humans are robots — that our sense of having a will or self or consciousness is an illusion. Yet, he admits, it is an illusion we find impossible to shake. No one “can help acting like and at some level really feeling that he or she is free.” We are “constitutionally incapable of experiencing ourselves and other conspecifics [humans] as robots.”
    One section in his book is even titled “We Are Robots Designed Not to Believe That We Are Robots.”,,,
    When I teach these concepts in the classroom, an example my students find especially poignant is Flesh and Machines by Rodney Brooks, professor emeritus at MIT. Brooks writes that a human being is nothing but a machine — a “big bag of skin full of biomolecules” interacting by the laws of physics and chemistry. In ordinary life, of course, it is difficult to actually see people that way. But, he says, “When I look at my children, I can, when I force myself, … see that they are machines.”
    Is that how he treats them, though? Of course not: “That is not how I treat them…. I interact with them on an entirely different level. They have my unconditional love, the furthest one might be able to get from rational analysis.” Certainly if what counts as “rational” is a materialist worldview in which humans are machines, then loving your children is irrational. It has no basis
    within Brooks’s worldview. It sticks out of his box.
    How does he reconcile such a heart-wrenching cognitive dissonance? He doesn’t. Brooks ends by saying, “I maintain two sets of inconsistent beliefs.” He has given up on any attempt to reconcile his theory with his experience. He has abandoned all hope for a unified, logically consistent worldview.
    http://www.evolutionnews.org/2.....95451.html

    Existential Argument against Atheism – November 1, 2013 by Jason Petersen
    1. If a worldview is true then you should be able to live consistently with that worldview.
    2. Atheists are unable to live consistently with their worldview.
    3. If you can’t live consistently with an atheist worldview then the worldview does not reflect reality.
    4. If a worldview does not reflect reality then that worldview is a delusion.
    5. If atheism is a delusion then atheism cannot be true.
    Conclusion: Atheism is false.
    http://answersforhope.com/exis.....t-atheism/

  99. 99
    bornagain77 says:

    roy, a more direct example of how naturalism undercuts rationality is in the following example.

    Anybody in their right mind would readily admit that the human brain was created by God:

    The Half-Truths of Materialist Evolution – DONALD DeMARCO – 02/06/2015
    Excerpt: but I would like to direct attention to the unsupportable notion that the human brain, to focus on a single phenomenon, could possibly have evolved by sheer chance. One of the great stumbling blocks for Darwin and other chance evolutionists is explaining how a multitude of factors simultaneously coalesce to form a unified, functioning system. The human brain could not have evolved as a result of the addition of one factor at a time. Its unity and phantasmagorical complexity defies any explanation that relies on pure chance. It would be an underestimation of the first magnitude to say that today’s neurophysiologists know more about the structure and workings of the brain than did Darwin and his associates.
    Scientists in the field of brain research now inform us that a single human brain contains more molecular-scale switches than all the computers, routers and Internet connections on the entire planet! According to Stephen Smith, a professor of molecular and cellular physiology at the Stanford University School of Medicine, the brain’s complexity is staggering, beyond anything his team of researchers had ever imagined, almost to the point of being beyond belief. In the cerebral cortex alone, each neuron has between 1,000 to 10,000 synapses that result, roughly, in a total of 125 trillion synapses, which is about how many stars fill 1,500 Milky Way galaxies!
    A single synapse may contain 1,000 molecular-scale switches. A synapse, simply stated, is the place where a nerve impulse passes from one nerve cell to another.
    Phantasmagorical as this level of unified complexity is, it places us merely at the doorway of the brain’s even deeper mind-boggling organization. Glial cells in the brain assist in neuron speed. These cells outnumber neurons 10 times over, with 860 billion cells. All of this activity is monitored by microglia cells that not only clean up damaged cells but also prune dendrites, forming part of the learning process. The cortex alone contains 100,000 miles of myelin-covered, insulated nerve fibers.
    The process of mapping the brain would indeed be time-consuming. It would entail identifying every synaptic neuron. If it took a mere second to identify each neuron, it would require four billion years to complete the project.
    http://www.ncregister.com/dail.....evolution/

    “Complexity Brake” Defies Evolution – August 8, 2012
    Excerpt: Consider a neuronal synapse — the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse — about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years…, even though it is assumed that the underlying technology speeds up by an order of magnitude each year.
    http://www.evolutionnews.org/2.....62961.html

    Roy, IMHO, for you to insist that the human brain is the product of mindless undirected material processes is not only irrational but is sheer insanity.

  100. 100
    bornagain77 says:

    jerry in your first example, that is NOT real time empirical evidence but is a just so story that was made up out of comparing sequences:

    Many more examples of Darwinists doing the same type thing, with other sequence comparisons, are found here and are refuted:

    Hopeless Matzke – David Berlinski & Tyler Hampton (Refutation of all popular examples purporting to show the origination of new information by Darwinian processes) – August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

    The second paper you cited jerry looks to be in the same vein as the first paper.

    Moreover, if they did demonstrate the feasibility of their scenario in the lab, (which I doubt they did), they almost certainly accomplished the transformation by purposely changing what they wanted to change and certainly did not sit around and wait for it to just accidentally happen!

    I suggest you look more closely at Behe, Axe, and Gauger’s work so as to give you a bit more proper context as to how far off the base these Darwinian explanations are so that you won’t be so easily led astray in the future by these ‘just so’ stories of Darwinists:

    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

    Of note: although Dr. Behe had been mercilessly vilified by neo-Darwinists for daring to suggest that there could possibly be an ‘Edge’ to evolution (i.e. possibly be a limit to what Darwinian processes could be expected to accomplish), Dr. Behe’s was vindicated and his 10^20 number was recently verified in the lab.

    The Vindication of Michael Behe – podcast/video – 2014
    https://www.youtube.com/watch?v=itkxFbyzyro

    An Open Letter to Kenneth Miller and PZ Myers – Michael Behe July 21, 2014
    Dear Professors Miller and Myers,
    Talk is cheap. Let’s see your numbers.
    In your recent post on and earlier reviews of my book The Edge of Evolution you toss out a lot of words, but no calculations. You downplay FRS Nicholas White’s straightforward estimate that — considering the number of cells per malaria patient (a trillion), times the number of ill people over the years (billions), divided by the number of independent events (fewer than ten) — the development of chloroquine-resistance in malaria is an event of probability about 1 in 10^20 malaria-cell replications. Okay, if you don’t like that, what’s your estimate? Let’s see your numbers.,,,
    ,,, If you folks think that direct, parsimonious, rather obvious route to 1 in 10^20 isn’t reasonable, go ahead, calculate a different one, then tell us how much it matters, quantitatively. Posit whatever favorable or neutral mutations you want. Just make sure they’re consistent with the evidence in the literature (especially the rarity of resistance, the total number of cells available, and the demonstration by Summers et al. that a minimum of two specific mutations in PfCRT is needed for chloroquine transport). Tell us about the effects of other genes, or population structures, if you think they matter much, or let us know if you disagree for some reason with a reported literature result.
    Or, Ken, tell us how that ARMD phenotype you like to mention affects the math. Just make sure it all works out to around 1 in 10^20, or let us know why not.
    Everyone is looking forward to seeing your calculations. Please keep the rhetoric to a minimum.
    With all best wishes (especially to Professor Myers for a speedy recovery),
    Mike Behe
    http://www.evolutionnews.org/2.....88041.html

    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

    “Shared Evolutionary History or Shared Design?” – Ann Gauger – January 1, 2015
    Excerpt: The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    http://www.evolutionnews.org/2.....92291.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/

  101. 101
    Roy says:

    Roy, so you don’t provide any evidence for your position because you say it will be ignored? how convenient

    My position here is that you rejected an article without reading it.

    My evidence is that
    1) You only pasted the freely available abstract, and nothing from the less-accessible the main text
    2) Despite replying multiple times you have carefully avoided answering the direct question “Did you read the full paper?

    I did post earlier about Durston’s essay being an unwarranted extrapolation, but you don’t seem interested in that.

    Everything else you have asked about is a diversion – a dishonest attempt to get me to defend claims I have not made.

  102. 102
    bornagain77 says:

    Roy, your excuses are pitiful.

    I never claimed to have read the paper in this thread, and certainly never gave the impression that I had read it. In fact, I have been pressing jerry for ANY substantiating real time evidence from that paper or any other paper he cited. No real time evidence came from that paper. In fact, jerry did not even try to cite from it. Moreover, the papers that jerry finally did end up citing to support his position were merely sequence comparisons, not real time demonstrations, just as I had originally assumed the papers would be!

    Disingenuous sequence comparisons that assume the desired conclusion of Darwinists into the premises of their hypothetical reconstruction of a sequence, with never an actual demonstration of the feasibility of the mutational pathway by undirected material processes!

    It is an absolutely dishonest way to try to establish the feasibility of a transformation that I hold, from a empirical basis (i.e. Behe, Axe, Gauger), to be impossible.

    For you to even ask the question of if I had read the paper was completely pointless, since it was clear I had not. The only reason you would even ask such a stupid question is because you were trying to play rhetorical tricks instead of trying to find the actual truth of the matter.

    Moreover, I rejected the article based on what I do know to be true already about reality.
    Number one, the inherent capabilities of undirected material processes are to degrade functional complexity, (in fact I listed many, many, empirical evidences supporting this position, which is far more than I can say for Darwinists doing for their position)
    http://www.uncommondescent.com.....ent-570044

    and, number two, I based my rejection on the fact that out of all the claims I’ve seen from Darwinists in the past, All the grand claims always have turned out to be based on unconstrained imagination, not on any substantiating empirical evidence that would support the grand claim.

    If anyone has ever been guilty of the ‘unwarranted extrapolation’, as you accuse Durston of being guilty of, it would be Darwinists themselves.

    It is pure intellectual hypocrisy on your part to accuse Durston of something, i.e. ‘unwarranted extrapolation’, that Darwinists are absolutely dependent on to try to make their case.

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe – 29:24 mark of following video
    http://www.youtube.com/watch?f.....fM#t=1762s

    Finally, a Detailed, Stepwise Proposal for a Major Evolutionary Change? – Michael Behe – March 10, 2015
    Excerpt: I would say its (Nick Matzke’s 2004 proposal for the evolution of the flagellum) chief problem is that it’s terminally fuzzy, bases most of its speculation on sequence comparisons, and glides over difficulties that would have to be dealt with in nature.,,, That’s one reason I wrote The Edge of Evolution — to say that we no longer have to rely on our imaginations, that we have good evidence to show what Darwinian processes are capable of doing. When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage.
    http://www.evolutionnews.org/2.....94271.html

  103. 103
    Box says:

    Every once in a while an evolutionist enters the debate claiming that there is evidence for his position—while we all know that there is none.
    It’s like taking candy from a baby.

  104. 104
    Roy says:

    I never claimed to have read the paper in this thread, and certainly never gave the impression that I had read it.

    Are you capable of actually addressing what people say, or have you spent so long ducking, dodging and weaving that erecting scarecrows is first nature?

    I didn’t say you gave the impression of having read that paper. I said you were giving the impression that you hadn’t. Which you have now confirmed. You have also confirmed that you rejected the paper unread.

    So when I suggested that you had rejected that paper without bothering to read it I was 100% correct. Any claims you have made about the contents of that paper (or indeed any other paper) can be immediately rejected on the grounds that you literally do not know what you are talking about.

    Perhaps in ID circles it is acceptable to comment on the contents of something one has not read, but in most endeavours it leads to complete loss of credibility and instant derision.

  105. 105
    bornagain77 says:

    Roy, did it escape your notice that I was completely vindicated in my assessment of exactly what type of evidence that jerry must referring to? (i.e. referring to unsubstantiated sequence comparisons), Or does your fundamentalist atheism inflict such blindness on you that not even that development, which is there for all to read, is able to be fairly evaluated by you?

    As well, I noticed that you conveniently, and completely, ignored these two posts which decimate your atheistic naturalism as being a, ‘ahem’, rational scientific worldview:

    http://www.uncommondescent.com.....ent-570207

    http://www.uncommondescent.com.....ent-570208

    Perhaps you should worry about the beam in your own eye before you worry about a splinter in mine?

    Matthew 7:3-5
    And why beholdest thou the mote that is in thy brother’s eye, but considerest not the beam that is in thine own eye?
    Or how wilt thou say to thy brother, Let me pull out the mote out of thine eye; and, behold, a beam is in thine own eye?
    Thou hypocrite, first cast out the beam out of thine own eye; and then shalt thou see clearly to cast out the mote out of thy brother’s eye.

  106. 106
    jerry says:

    Every once in a while an evolutionist enters the debate claiming that there is evidence for his position—while we all know that there is none.

    I would not get too cocky. I spent a lot of this thread about a research program that thinks that naturalized evolution is a slam dunk and has a research trail that supposedly supports that position.

    After Mung asked me about some articles, I found about 30 journal articles on how new coding regions arose in the past in various species. I have no way of assessing this research but someone who is knowledgeable in genetics/micro biology should review the research.

    I was at Research Gate and many of the works of Juergen Brosius and his colleague Juergen Schmitz are available for download.

    The article that started me looking, however, was not available there for download. In it Brosius is incredibly cocky and condescending to anyone who does not believe in naturalized evolution. He trashes Simon Conway Morris for suggesting there may be a God.

    We have not addressed anything like them on this site nor does the average commenter here have the ability to do so. Maybe we could get gpuccio but he may not have the background to do so. Probablay Axe, Behe and Gauger could give it a go to say what is actually there.

    My guess it is interesting but not enough to explain much. But they act as if it explains everything and is the basis for punctuated equilibrium.

    Here is what Brosius said about Simon Conway Morris

    Although it is highly beneficial to occasionally challenge entrenched concepts, I wonder whether this a poorly disguised attempt to let religion participate in evolutionary thought: if you can’t fight evolution?join it? Instead of catering to the ultra-naive creationists, Conway Morris (2003) appeared to target a more intelligent segment of our non-rationalist population, perhaps those who should know better but cannot liberate themselves from infantile imprinting and religious indoctrination, those who seem to possess a full deck of cards but are unable or unwilling to use them all?at least in certain games.

  107. 107
    bornagain77 says:

    jerry, you have yet to provide any real time empirical evidence for your position.

    The two papers you said ‘look promising’ are a farce as far as empirical science is concerned.

    They are sequence comparisons that assume the conclusion of Darwinian evolution into the reconstruction of a supposed mutational pathway with no real time empirical demonstration that the supposed transmutation is possible in reality.

    Whereas I cited Behe, Axe, and Gauger’s actual empirical work that shows even exceedingly trivial transmutations are impossible for unguided material processes (over time frames that exceed hundreds of millions of years and even the age of the universe itself!).

    You have, apparently, minus any actual empirical evidence, opted to believe neo-Darwinists must have some empirical evidence somewhere.

    As I said earlier, the empirical evidence simply does not exist!

    You apparently disagree with me (and mung, Behe, Axe and Gauger), but it is a disagreement based on a unfounded belief you have since you have, thus far, cited no actual experimental work showing that the unguided material processes of Darwinian evolution are capable of what you apparently believe they must be capable of.

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

  108. 108
    Silver Asiatic says:

    jerry

    Most of the difference are in control mechanisms that affect expression of proteins in the brain. See Wilcox

    RNA control mechanisms. As Wilcox states in the cited article:

    Most of these unique RNA transcripts – and there are thousands, if not millions of them – are uniquely active in developing human neural tissue – uniquely active compared to their activity in chimpanzees, much less other primates or mammals. It is the new epigenetic world.

    So, not correct to state that the full diversity of life can be traced to DNA encoding.

    And the follow-up question should be on the origin of those millions of unique RNA transcripts.

  109. 109
    jerry says:

    So, not correct to state that the full diversity of life can be traced to DNA encoding.

    I would say that this is obvious. My guess is that Durston’s comment is about the available proteins for each species and he would not deny any form of epigenetics. What expresses the proteins is separate from the DNA itself and what constructs the body plans is also separate. The latter is almost unknown at present.

    And the follow-up question should be on the origin of those millions of unique RNA transcripts.

    Yes, but my guess is that the number is overstated. But I am not one to judge at this moment. Maybe it is millions.

  110. 110
    jerry says:

    You apparently disagree with me (and mung, Behe, Axe and Gauger),

    Are you sure you want to include Mung? Let him speak for himself. I am not sure that Behe, Axe and Gauger should be included also since they have not commented specifically on the research. When they do, I will look at it as quickly as I learn about it. What they say will be of great interest.

    Please do not unleash another set of quotes. Let’s wait till someone deals with the specific research of Brosius and his colleagues. They are showing that new coding regions arise in various species over time. Most of it a long time ago. This was dealing with the premise of the OP which I believe is false. From what I read of Axe, he would not disagree either. I believe his work is on the origin of novelties, or completely new independent coding regions. Most of Brosius’ work, as best as I can see, is on the modification of coding regions with inputs from non-coding regions.

    And I have said several times if not hundreds, that it may not be close enough to be meaningful. And that the process that generates the new coding regions is great design. And I maintain that this research process is what will falsify Darwinian evolution.

    Disagree, fine. I have no problem with that. I believe my assessment is the most logical there is out there and nothing you have presented shows me otherwise.

  111. 111
    bornagain77 says:

    “They are showing that new coding regions arise in various species over time.”

    They are ‘showing’ nothing of the sort. They PRESUPPOSE it must have happened by unguided material processes and try to reconstruct a narrative that fits their presupposition.

    i.e. They have ZERO actual empirical evidence!

    “From what I read of Axe, he would not disagree either. I believe his work is on the origin of novelties, or completely new independent coding regions.”

    Axe (and Gauger’s) most recent work, which I referenced and you apparently did not bother to read, deals with exceedingly trivial transmutation of a existing protein into a similar protein of a similar, but different, function. Unguided material processes were found to be grossly inadequate for the trivial transmutation by a factor of trillions of years!

    “And that the process that generates the new coding regions is great design.”

    So you cite no actual empirical evidence that transmutations are possible for unguided material processes, but that if they did happen by unguided material processes, which you apparently hold that it did, it would be great design?

    Do I really have to point out the incoherence of your position?

  112. 112
    bornagain77 says:

    Jerry on another thread you claimed that

    “Darwinism can be falsified” by “an examination of genomes and a determination of what is different between two different populations and if there is similarity between non coding areas with coding areas”

    It might interest you to know that your falsification threshold has been met and exceeded:
    http://www.uncommondescent.com.....ent-569958

  113. 113
    Silver Asiatic says:

    What expresses the proteins is separate from the DNA itself and what constructs the body plans is also separate. The latter is almost unknown at present.

    I think the answer to what distinguishes humans from non-human ancestors is unknown also. Things like levels of self-consciousness and the human mind which commands and controls it’s own mind, recognition of truth, goodness, moral awareness and growth, purpose and identity are irreducible to physical components alone. They cannot be explained even by RNA differences. The gap between human and chimp just in terms of rationality alone is infinite.

    Obviously, the 1% difference in DNA explains almost nothing in that regard.

  114. 114
    Mung says:

    SA: The gap between human and chimp just in terms of rationality alone is infinite.

    Else chimps would be known as the rational animal or we would be known as chimps.

  115. 115
    bornagain77 says:

    OT:

    Earth’s Biosphere Is Awash in Information – June 29, 2015
    Excerpt: In this remarkable paper, Landenmark, Forgan, and Cockell of the United Kingdom Centre for Astrobiology at the University of Edinburgh attempt “An Estimate of the Total DNA of the Biosphere.” The results are staggering:
    “Modern whole-organism genome analysis, in combination with biomass estimates, allows us to estimate a lower bound on the total information content in the biosphere: 5.3 × 10^31 (±3.6 × 10^31) megabases (Mb) of DNA. Given conservative estimates regarding DNA transcription rates, this information content suggests biosphere processing speeds exceeding yottaNOPS values (10^24 Nucleotide Operations Per Second).,,,”
    ,,,let’s ponder the scale of this information content and processing speed. A yottaNOPS is a lotta ops! Each prefix multiplies the prior one by a thousand: kilo, mega, giga, tera, peta, exa, zetta, yotta. A “yottabase” doesn’t even come close to the raw information content of DNA they estimate: 10^31 megabases. That’s the same as 10^37 bases, but a yottabase is only 10^24 bases (a trillion trillion bases). This means that the information content of the biosphere is 50 x 10^13 yottabases (500 trillion yottabases). They estimate that living computers perform a yottaNOPS, or 10^24 nucleotide operations per second, on this information.
    You can pick yourself off the floor now.
    “Storing the total amount of information encoded in DNA in the biosphere, 5.3 × 10^31 megabases (Mb), would require approximately 10^21 supercomputers with the average storage capacity of the world’s four most powerful supercomputers.”
    How much land surface would be required for 10^21 supercomputers (a “zetta-computer”)? The Titan supercomputer takes up 404 m2 of space. If we assume just 100 m2 for each supercomputer, we would still need 10^23 square meters to hold them all. Universe Today estimates the total surface of Earth (including the oceans) at 510 million km2, which equates to 5.1 x 10^14 m2. That’s 9 orders of magnitude short of the zetta-computer footprint, meaning we would need a billion Earths to have enough space for all the computers needed to match the equivalent computing power life performs on DNA!
    http://www.evolutionnews.org/2.....97221.html

    That finding, gentlemen, has John 1:1-4 written all over it!

  116. 116
    jerry says:

    Do I really have to point out the incoherence of your position?

    There is nothing incoherent in anything I have said. You constantly bring up irrelevant examples (enzyme origins which are interesting but not comparable to the example I point to), blithely say something is not true when it is (comparing coding and non-coding regions is not empirical evidence when it is a standard practice in genetic research) and misrepresent what I say.

    Nothing I have said or have pointed to is a threat to or contradicts anything Axe, Gauger or Behe has said.

    It might interest you to know that your falsification threshold has been met and exceeded:

    The discussion by Hunter is interesting (which is all about the comparison of coding with non coding regions or the lack of similar regions in other species) but it is only a small bit of what has to be done. So while of value it doesn’t come close to all that is necessary. But it is an example of what will eventually be evidence for how new species must have arisen. When this is eventually done, Darwinian evolution will be dead. But it is several years off.

    I have been making my claim for quite awhile and have been on record on this site for about 9 years that the origin of new alleles is at the heart of the evolution debate. I have since expanded that to include the origin of control regions. And I have been asking for years about what causes the organism to unfold in such a way during gestation to provide the final form. It is now clear that no one knows the answers to any of these questions.

    All very coherent questions based on an analysis of the data.

    So just leave it and you can ignore my comments.

  117. 117
    bornagain77 says:

    “So just leave it and you can ignore my comments.”

    No thank you. Not as long as you try to defend the indefensible!:

    “There is nothing incoherent in anything I have said.”

    You position, contrary to how enamored you are with your own position, is incoherent.

    You claimed that they have proven their point by merely comparing sequences and claim this comparing of sequences is real time ’empirical evidence’.

    Excuse me, that is ‘not even wrong’:

    per wiki

    Empirical evidence is a source of knowledge acquired by means of observation or experimentation.[1]
    https://en.wikipedia.org/wiki/Empirical_evidence

    i.e. ‘Real time’ Empirical evidence, which is what I consistently asked you for, is going into the lab and performing experiments to prove your point.

    They have done no such thing. Not even close!

    They, in their ‘standard practice in genetic research’ have merely assumed Darwinian evolution as true at the outset and tried to reconstruct a narrative by comparing sequences to fit their desired conclusion. It is an absolutely horrid way to practice science and is certainly not ‘real time’ empirical science in any meaningful sense of the term!

    This same disingenuous practice of science of assuming your conclusion into your starting assumptions, which you apparently agree 100% with as valid empirical science, was the same disingenuous method by which Darwinists tried to dismiss the real time empirical research of ENCODE which had found widespread functionality across the entire genome.

    DNA mostly ‘junk?’ Only 8.2 percent of human DNA is ‘functional’, study finds – July 24, 2014
    Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution — a clear indication that this DNA matters, it has some important function that needs to be retained.
    http://www.sciencedaily.com/re.....141608.htm

    i.e. So according to these Darwinian critics of the ENCODE study, which found widespread functionality for ‘junk’ DNA by direct experimental research, functionality does not determine if a sequence is actually functional, only ‘conservation of sequence’ determines what is functional?
    So basically, only if Darwinian evolution is assumed as true at the outset will these Darwinists be willing to accept accept that a given sequence of ‘junk’ DNA may be functional!,,

    That is called ‘assuming your conclusion into your premise’ and is absolutely horrible science!

    So jerry, Do you agree with the 8% figure derived by comparing sequences or do you agree with the 80% figure derived by actual experimental work?

    The only one who has cited any actual real time empirical evidence in our exchange thus far, jerry, to support their position, has been me when I cited Behe, Axe and Gauger, (whose work on enzymes you apparently blew off as irrelevant. of note: It is not irrelevant in that it directly addresses functional conversion instead of being merely hypothetical as your, ‘ahem’, empirical evidence is)

    As well, apparently you did not read the entire link I provided on the falsification threshold of neo-Darwinism:

    http://www.uncommondescent.com.....ent-569958

    This is of particular interest to you:

    “Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes.”
    Raymond Bohlin (per Richard Sternberg) – 9:29 minute mark of video
    https://vimeo.com/106012299

    On Human Origins: Is Our Genome Full of Junk DNA? Pt 2. – Richard Sternberg PhD. Evolutionary Biology
    Excerpt: “Here’s the interesting thing, when you look at the protein coding sequences that you have in your cell what you find is that they are nearly identical to the protein coding sequences of a dog, of a carp, of a fruit fly, of a nematode. They are virtually the same and they are interchangeable. You can knock out a gene that encodes a protein for an inner ear bone in say a mouse. This has been done. And then you can take a protein that is similar to it but from a fruit fly. And fruit flies aren’t vertebrates and they certainly are not mammals., so they don’t have inner ear bones. And you can plug that gene in and guess what happens? The offspring of the mouse will have a perfectly normal inner ear bone. So you can swap out all these files. I mentioning this to you because when you hear about we are 99% similar (to chimps) it is almost all referring to those protein coding regions. When you start looking, and you start comparing different mammals. Dolphins, aardvarks, elephants, manatees, humans, chimpanzees,, it doesn’t really matter. What you find is that the protein coding sequences are very well conserved, and there is also a lot of the DNA that is not protein coding that is also highly conserved. But when you look at the chromosomes and those banding patterns, those bar codes, (mentioned at the beginning of the talk), its akin to going into the grocery store. You see a bunch of black and white lines right? You’ve seen one bar code you’ve seen them all. But those bar codes are not the same.,, Here’s an example, aardvark and human chromosomes. They look very similar at the DNA level when you take small snippets of them. (Yet) When you look at how they are arranged in a linear pattern along the chromosome they turn out to be very distinct (from one another). So when you get to the folder and the super-folder and the higher order level, that’s when you find these striking differences. And here is another example. They are now sequencing the nuclear DNA of the Atlantic bottle-nose dolphin. And when they started initially sequencing the DNA, the first thing they realized is that basically the Dolphin genome is almost wholly identical to the human genome. That is, there are a few chromosome rearrangements here and there, you line the sequences up and they fit very well. Yet no one would argue, based on a statement like that, that bottle-nose dolphins are closely related to us. Our sister species if you will. No one would presume to do that. So you would have to layer in some other presumption. But here is the point. You will see these statements throughout the literature of how common things are.,,, (Parts lists are very similar, but how the parts are used is where you will find tremendous differences)
    http://www.discovery.org/multi.....-dna-pt-2/

    also of note:

    An Interview with Stephen C. Meyer
    TT: Is the idea of an original human couple (Adam and Eve) in conflict with science? Does DNA tell us anything about the existence of Adam and Eve?
    SM: Readers have probably heard that the 98 percent similarity of human DNA to chimp DNA establishes that humans and chimps had a common ancestor. Recent studies show that number dropping significantly. More important, it turns out that previous measures of human and chimp genetic similarity were based upon an analysis of only 2 to 3 percent of the genome, the small portion that codes for proteins. This limited comparison was justified based upon the assumption that the rest of the genome was non-functional “junk.” Since the publication of the results of something called the “Encode Project,” however, it has become clear that the noncoding regions of the genome perform many important functions and that, overall, the non-coding regions of the genome function much like an operating system in a computer by regulating the timing and expression of the information stored in the “data files” or coding regions of the genome. Significantly, it has become increasingly clear that the non-coding regions, the crucial operating systems in effect, of the chimp and human genomes are species specific. That is, they are strikingly different in the two species. Yet, if alleged genetic similarity suggests common ancestry, then, by the same logic, this new evidence of significant genetic disparity suggests independent separate origins. For this reason, I see nothing from a genetic point of view that challenges the idea that humans originated independently from primates,
    http://www.ligonier.org/learn/.....-conflict/

  118. 118
    bornagain77 says:

    as to jerry at 116:

    “Nothing I have said or have pointed to is a threat to or contradicts anything Axe, Gauger or Behe has said.”

    Yet, jerry at 66 stated

    “It is absurd to think that no new information will be created by these processes over billions of years.”
    http://www.uncommondescent.com.....ent-570135

    of note:

    “Shared Evolutionary History or Shared Design?” – Ann Gauger – January 1, 2015
    Excerpt: The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    http://www.evolutionnews.org/2.....92291.html

    Stephen Meyer Critiques Richard Dawkins’s “Mount Improbable” Illustration
    https://www.youtube.com/watch?v=7rgainpMXa8

  119. 119
    Box says:

    Jerry,

    Jerry: And I have been asking for years about what causes the organism to unfold in such a way during gestation to provide the final form.

    Part of the answer is: Embryonic Electric Fields; see #42, #60
    – – –

    Box: Every once in a while an evolutionist enters the debate claiming that there is evidence for his position—while we all know that there is none.

    Jerry: I would not get too cocky. I spent a lot of this thread about a research program that thinks that naturalized evolution is a slam dunk and has a research trail that supposedly supports that position.

    I’m not worried at all. I’m sure that on closer inspection there is absolutely nothing there.

    Jerry: In it Brosius is incredibly cocky and condescending to anyone who does not believe in naturalized evolution. He trashes Simon Conway Morris for suggesting there may be a God.

    Motivated by envy, no doubt. Unlike evolution, there is actually strong evidence for the existence of God.
    Guys like Brosius—who you yourself call a ‘low life’ back in 2009—excel at wishful thinking, being “cocky” and “condescending”.

  120. 120
    jerry says:

    Box,

    I answered you on the other thread.

  121. 121
    Mung says:

    OT: Earth’s Biosphere Is Awash in Information – June 29, 2015

    I think it’s all that junk DNA that is causing global warming!

  122. 122
    KD says:

    I have been relaxing at a cabin in the northern Canadian wilderness where there was no cellphone or internet, so was unaware of this discussion until I got back into civilization today. I have skimmed all the comments and have a few short points to make by way of response.

    1. ‘functional information’ as used in my post is mathematically defined in the paper I linked to in my post. (for all the links, see goo.gl/2ji22e )

    2. A major point of discussion seems to centre around my statement that ‘… the instructions for the full diversity of life, are digitally encoded in the DNA of all living things …’. One must not forget that maternal effects such as the egg-cell wall may be encoded in the DNA of the mother. Thus we still are forced back to the DNA.

    3. When I speak of the functional information required to build an organism, I am not just speaking of the coding regions as some have assumed. It is becoming more obvious that some non-coding regions can be important as well. Again, we are back to the DNA.

    4. A point that seems to be missed in the ‘comments’ discussion is the distinction between the information required to build a system and information being fed into that system which the system processes and which affects the output. For example, the instructions required to build a fully functioning notebook computer should not be confused with the information that the fully functioning computer processes. Same goes for biological life. It may be the case that when an organism is being built that the exact outcome is influenced by non-maternal environmental input, but the instructions on how to modify the output given a range of inputs must already be encoded in the maternal DNA or the DNA of the progeny (i.e., the capability for variation is already encoded in the genomes of life, but which type or variety is ‘chosen’ may depend upon external inputs).

    5. If one insists that at least some of the information that specifies a given life form is external to all DNA (including maternal), then the onus is on the believer to flesh this out without embracing vitalism. Some have been hammering this home, I see. Right on!

    6. Even if we granted for the sake of argument that some of the functional information is encoded somewhere else, the fact still remains that the general trend in information duplication and storage in this universe, without exception, is error accumulation and deterioration whether we are speaking of DVD’s, flash drives, paper, magnetic tape, stone carvings or DNA. It takes a lot of work by intelligent data technicians to preserve data or at least slow down the information loss. Neo-darwinism makes the quite fantastic prediction, contra everything else we see in science, that this is not the case for biology, but all the experimental evidence we have seen thus far says otherwise (one commenter seems to have missed this point, as well as the paper discussing the deterioration of the human genome).

    7. Natural selection will eliminate non-functional DNA, tending to leave the more genetically fit organisms alone, but our observations reveal that the remaining DNA still nudges steady deterioration. A lot of errors can occur before an area becomes non-functional and, by then, it may be too late to restore the lost information, especially since the rate of destruction exceeds the rate of repair for damaged genes, as my own work reveals (to be discussed in a future blog post).

    8. Yes, there are repair mechanisms but it is obvious that in spite of those impressively designed little nano-machines, information degradation is still marching on. In this world, there is no such thing as a perpetually perfect replicating machine. Everything in the universe slowly runs down. Life is no exception.

    9. Note in my article that I never said that novel information or functions cannot be obtained. It is just simply that the rate of degradation will exceed the rate of improvements on average over time. This is true in every area of information, and biology is no exception. The LTEE is an example of this. One cobbled together function so far, but during this experiment, I have heard that it has also lost about 8 percent of its DNA (I was told this by a biology professor, but do not have a reference, so I stand to be corrected).

    10. I plan to do a special blog post on the Lenski experiment, showing that if we use published methods for determining the change in functional information, the gain in information was trivial, well within the realm of no statistical significance.

    11. I plan to do a blog post on natural selection and what we can learn about it from the field of genetic algorithms. For those who cannot wait, natural selection works wonders for hill-climbing problems such as fine-tuning the fitness of existing organisms (microevolution), but it is utterly useless for needle-in-the-haystack problems such as searching sequence space for protein families with stable repeatable folds. All the sophisticated GA’s produced today are examples of intelligent design in action.

    Bottom Line: nature is destroying biological life, not creating it.

    I am on semi-vacation over the next month or so, so I will not likely be able to respond to new ideas in a timely fashion. Nevertheless, the post being discussed here is only one in a series that I will be writing. Even if I cannot respond, I see the above ‘comments’ discussion as a healthy exchange of ideas.

  123. 123
    bornagain77 says:

    as to:

    “5. If one insists that at least some of the information that specifies a given life form is external to all DNA (including maternal), then the onus is on the believer to flesh this out without embracing vitalism. Some have been hammering this home, I see. Right on!”

    The insurmountable problem of ‘form/shape’ for reductive materialistic explanations has now been demonstrated by a few different methods.
    http://www.uncommondescent.com.....ent-570759

    i.e., there simply is no materialistic explanation for ‘non-local’ quantum entanglement/information in DNA and proteins! A beyond space and time cause must be appealed to in order to explain the non-local effect!

  124. 124
    Mung says:

    Dr. Durston, I trust that being without access to the internet is exactly what you needed!

    Thank you for clearing a few things up. I was accused of taking you too literally but you have confirmed that it is in fact your position that it all comes back to the DNA.

    Frankly I don’t know why this even needs to be a premise of young earth creationism. But given that at the least it is a premise of your argument, then you just do not have the luxury of shifting the burden of proof on to those who do not accept the truth of the premise.

    That said, all sorts of activities take place with incomplete information, and there’s no reason to think that this is not true at the cellular and developmental levels of organisms. Think about it, what would it take to specify, exactly, every single detail of a living organism in it’s DNA?

    Bottom Line: nature is destroying biological life, not creating it.

    Biological life is not separate from nature. You may as well argue that biological life is destroying biological life. Organisms are not passive systems who have no say in their survival or the survival of their species.

  125. 125
    Silver Asiatic says:

    KD

    If one insists that at least some of the information that specifies a given life form is external to all DNA (including maternal), then the onus is on the believer to flesh this out without embracing vitalism.

    Interesting comment. From my reading of it, ‘vitalism’ is the view that living organisms include some immaterial aspect that distinguish them from non-living. Modern science opposes that view with the idea that there is no such distinction between living and non-living things. In other words, living things are entirely reducible to matter. There is no ‘vital’ (immaterial) element.

    The question regarding the statement: “the instructions for the full diversity of life, are digitally encoded in the DNA” seems to be focused on ‘encoding’, and thus all the information (instructions) for life are reducible to encoded information in DNA.

    But as discussed, the similar DNA sequences produce vastly different results (chimp vs human) because of RNA controls. It might be true that the logic switches and control functions are not ‘encoded’, but they are instructions which produce the diversity of life. DNA alone cannot explain this.

    Additionally, as BA77 has mentioned often, DNA sequences do not sufficiently explain information on protein folding (for example) which is the result of quantum entanglement — a non-sequential, non-linear process.

    Again, this seems to be quite a large space for non-DNA information and again, we might also say non-coded information. (Informational instructions do not necessarily need to be encoded anywhere).

    That’s where the comment regarding vitalism comes in. Is it possible that there is, indeed, an immaterial aspect to life that distinguishes it from non-life? That may, indeed, be ‘vitalism’, or perhaps something like ‘dualism’. Or at least, could biological information simply exist that is non-coded but still providing information for functions?

    An example in computers might be something like volitile RAM – where data is not stored on a hard-drive but only exists electronically through high-speed transfers. Once the power is turned off, the information disappears.

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