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The Emerging Complexity of the Genome

Recently, a friend who thinks about (and has published on) the nature of the eukaryotic genome, said to me, “Paul, no one really knows what the genome is any more.” He went on to explain that the picture most biologists carry around in their heads, of the relationship of genes to organismal form and function — indeed, the very concept of the “gene” itself — had been seriously challenged by discoveries in comparative genomics and molecular biology within the past few years. How all this will shake out eventually, he said, is anyone’s guess. But the theory of evolution, he concluded, cannot escape the coming turbulence.

For an overview of some of the discoveries my friend had in mind, see this article from today’s Boston Globe. [Registration may be required.]

And welcome to the Golden Age of Biology. Without question, it’s now the most exciting science going. Unfolding astonishing vistas of puzzling data, theory nowhere in sight, hard creative thinking required.

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70 Responses to The Emerging Complexity of the Genome

  1. “Science is just starting to probe the wilderness between genes,” said John M. Greally, molecular biologist at New York’s Albert Einstein School of Medicine. “Already we’re surprised and confounded by a lot of what we’re seeing.”

    I’ve said it before, and I’ll keep on saying it: Darwinists are “surprised and confounded” all the time by real-life findings.

    A slew of recent but unrelated studies of everything from human disease to the workings of yeast suggest that mysterious swaths of molecules – long dismissed as “junk DNA” – may be more important to health and evolution than genes themselves.

    This is something long predicted by both panspermia and ID proponents.
    Which are the better, and more scientific, theories; the ones that accurately predict subsequent findings, or the ones that are consantly surprised by them?

  2. Dawkins disciples will argue that the discovery of ever greater complexity is evidence AGAINST ID, since the designer of all of this must necessarily be even more complex than the thing designed.

  3. This is squarely a confirmed prediction of the ID hypothesis. Such clear predicitive value should rightly move ID from spurious hypothesis to respected theory. Ah but the religion of darwinism would never allow that.

  4. I still fail to see how ID predicts no junk DNA. Random mutation definitely happens and if it’s good at *anything* it’s good at producing unorganized, non-functional crappola. It can produce crap out of nothing and it’s even better at making crap out of stuff that wasn’t crap to begin with.

  5. DaveScot, there have definitely been a number of IDers who have loudly predicted that ID would reveal that much (most?) of the “junk DNA” would have value. See the strength of that prediction in Denton’s “Nature’s Destiny”. He says that failure of the prediction will bring down ID.

    I would be surprised if there were no junk DNA. I know that when I compile a program, a significant number of functions get included in my compile just because they were in an object that I used some functionality of. But the 95% junk view is not a very “intelligently designed” view.

    Bottom line, significant IDers have said for a long time “there’s value in that junk”, and the darwinists have said the opposite, that “there cannot be value in that junk because there would be too many mutations per generation to be managed by RM+NS.”

    The IDers said it, it proved to be true, it’s a confirmed prediction.

  6. A question about the human genome project, if you all don’t mind:

    The article referenced speaks of the successful mapping of the entire human genome in 2003. And of course, since that time I’ve heard this claim dozens of times in the media, about how wonderful it is that we’ve managed to map the entire human genome.

    But, and pardon me for being so slow to ask this question, is that an accurate description of the human genome project?

    What do they really mean by “mapping” here? Because if they mean that they’ve figured out what genes– in the 1.5% of the genome that actually codes for proteins–make what proteins, then pardon me if I’m not as impressed as I once was. I’m still impressed, mind you… but less so.

    Or does this “mapping” really just mean figuring out which genes code for proteins and which do not? Or does it mean just taking the human genome and ‘reading’ it so that we can see the entirety of the code, whether we understand what it means or not?

    Understand my question?

    Thanks in advance.

  7. I am one who thinks that “junk DNA” is mostly not junk. I have been saying that for many years.

    There are those who use organisms such as the onion to say that complexity and genome size are unrelated and I concur with the logic of that conclusion in the few cases they specify.

    Then there are those who do experiments taking large segments of introns out of the geneome and find the organism is essentially working fine. Often a novel would still make sense with a chapter removed. These organisms may lose something that is hard to test for in the lab. I have had patients who have had brain surgery and lost fairly large clumps of brain tissue. I am unable to easily detect any deficiency. No one would claim that those parts of their brain were “junk”. Either my testing is poor or there are alternative methods available to achieve a test result.

    Depending on the energy and resource cost of producing a long genome, it may be of no special disadvantage for some organisms to do better with duplicated sectors of genome.

    My take on junk DNA for many years has been that the so called genes code for the protein machines and building materials. That is relatively easy. They contain the hardware shop of the organism. The “junk DNA” contains the plans for constructing and maintaining organisms.

    It is hard enough to imagine bricks evolving, but very rarely we may find a rock shaped like a brick. It is even harder to imagine a factory being made of many bricks that are put in a special order in a form that makes a functioning brick factory without intelligent design.

    I suppose that is an argument from credulity and NDE does not have to be credulous. It has a special exemption from critical analysis.

  8. In answer to a challenge to show a prediction of ID that could be falsified I wrote this this morning:

    Almost all Junk DNA will be found to have purpose. That is a major ID prediction and one that has found substantial validation in the preliminary ENCODE study of 1% of the Human genome.
    The Theistic prediction for ID will predict that the complexity of the remaining 99% of the genome to be decoded will exponentially add to the impressive complexity we are currently finding and will definitely challenge man’s ability to comprehend it. Indeed, the complexity that will be found can be tentatively predicted to far far surpass man’s ability to comprehend it fully, since even a simple protein folding on itself takes a entire years worth of computing time on the world’s most powerful supercomputer.

    And now this quote from the Boston Globe article this afternoon:

    However none dispute that biology is at an extraordinary pivotal point – one in which the pace of discovery seems faster than the ability of even the most brilliant minds in the field to comprehend.

  9. It is the joy of physics to find simplicity behind apparent cosmic complexity.

    It is the joy of biology to discover in the essential complexity of the biosphere, the greatness of the Mind behind it.

  10. Thanks, Paul. Great article.

    Regarding junk DNA, one might of course suspect some junk, even in the ID context (nobody should be surprised that a designed system can eventually run down or break). However, what does the consistent, rolling drumbeat of the evidence suggest? That the general trend is the more we understand (think mammalian eye, for example), the more we see a highly complex, astonishingly coordinated, well-regulated system, rather than junk. This is completely consistent with design and completely anathema to a blind, bumbling, cobbled-together assortment proposed by Darwin and his modern followers.

    It is interesting to see the science-stopping stranglehold of the old paradigm, even in the face of the kind of evidence outlined in the article. Look at Lander’s statement: “Half of it may be doing something very useful. The other part may turn out to be, well, just junk . . .” Why would anyone take that view today? Perhaps because of a lifetime of indoctrination in the central dogma?

    I am willing to stand up and go on record with a different prediction: While there may turn out to be some non-functional DNA, the *vast* majority of DNA (more than 95%) will turn out to have biological function.

    Time will tell which of us is currect.

  11. TRoutMac:

    But, and pardon me for being so slow to ask this question, is that an accurate description of the human genome project?

    I believe that the mapping of the human genome is a complete mapping of every DNA base-pair in one sample human being. Call her Lucy if you will. (I am also sure that they have mapped significant segments of hundreds of other humans.) As far as generating a DNA/Gene correlation, well, I don’t believe that this was the assignment of the human genome project.

  12. Thanks Paul, This article is gold:

    Just four years after scientists finished mapping the human genome – the full sequence of 3 billion DNA “letters” folded within every cell – they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.

    Then they have the audacity to state:

    But few had predicted the complex orchestration of genes and nongenetic DNA suggested by the Encode research. Even more sunning was the Encode finding that most “junk DNA” is transcribed, or copied, into more RNA molecules than can be accounted for by most prevailing theories.

    Hey Guys, How about the all the ID proponents that have been predicting this development all along..

  13. I guess we’re the few and the proud. ;)

    Also, when Craig Venter’s genome sequence was published, geneticists were surprised at the number of differences–4.1 million!–between his and the “reference genome” of the Human Genome Project.

    Background on Wired.

    The Genome Sequence Itself

    The Full Paper

    Abstract:

    Presented here is a genome sequence of an individual human. It was produced from ?32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.

  14. “The picture that’s emerging is so immensely more complicated than anyone imagined, it’s almost depressing,” Rigoutsos said.

    I love it!

  15. idnet.com.idu (#7): “My take on junk DNA for many years has been that the so called genes code for the protein machines and building materials. That is relatively easy. They contain the hardware shop of the organism. The “junk DNA” contains the plans for constructing and maintaining organisms.”

    This has also been my view, based just on the insufficient information carrying capacity of the protein coding portion of the genome. The recent ENCODE research clearly points in this direction.

    However, there seems to be a contradiction here that needs to be resolved, in the science findings from two types of research. Both the ENCODE data and necessary information content considerations mean much or most of the DNA code must be intricately interlinked, with many areas of deep multiple translations. Then random mutations changing the base sequences of most of the genome would be even more astronomically likely to be deleterious. Much of the non-coding DNA, if it is functional, would have to be “conserved” in evolution – that is, prevented from accumulation of random changes.

    However this seems to be contradicted by the other research findings that appear to establish that only approximately 15% of the genome is conserved. The vast majority of the genome is supposed to accumulate sequence changes proportionate to the time elapsed from when the lineages apparently diverged (this picture seems to be roughly true regardless of debates over the rates of sequence divergence).

    There must be some error in the data, or in the assumptions and reasoning from the data. Where is this error? One idea I have is that some of the changes accumulated in “non-conserved” regions are not really random, but actual design changes (mainly developmental regulation modifications).

  16. One should keep in mind that prokaryotes have precious little DNA that is not coding genes. Nor do they have introns which lead to polylayered encoding and transcription editing. They basically have none of the junk DNA so common in eukaryotes.

    Years ago I asked myself what is a primary difference between prokaryotes and complex eukaryotes. The answer I arrived at was instinctual behaviors. I believe a lot of the junk somehow encodes instinctive behaviors. It informs a bird how to build nests and sing songs characteristic of its species. It informs a human infant how to suckle and cry for attention. These are exceedingly complex coordinated behaviors that don’t yield to being under the control of mechanical protein cascades.

    It might also explain why when experimentors recently cut a 1.5mbp swath of DNA highly conserved between mouse and man there was no adverse effect found in the GM mice. Maybe they cut out some instinctive behaviors like fear of snakes and birds that didn’t subsequently show up in the lab-raised GM mice.

    A subsequent question, if it’s true that instincts are encoded in non-coding DNA, how is that hard learned behaviors eventually find their way into DNA? Any mechanism that goes backward, from protein to DNA, goes against the core principle of molecular biology first put forward (I believe) by Crick and Watson – that information only flows one way from DNA to RNA to protein and never the reverse.

  17. 17

    dacook:

    I’ve said it before, and I’ll keep on saying it: Darwinists are “surprised and confounded” all the time by real-life findings.

    On June 21, 2007 I noted in another thread that a Google search for “more complex than expected” +evolution returns almost 10,000 results. Today, only three months later, the same search returns 11,700 results. It would be interesting to continue tracking this to see what happens.

  18. You all might like to check out the work of John Mattick in Australia.

    “We are working on the alternative hypothesis that the majority of the genomes of complex organisms is devoted to the regulation of development and that most of this information is transacted by noncoding RNAs. Both logic and the available evidence suggest that these RNAs form a highly parallel digital network that integrates complex suites of gene expression and controls the programmed responses required for the autopoeitic development of multicellular organisms. If this is correct, our current conceptions of the genomic information content and programming of complex organisms will have to be radically reassessed, with implications well beyond biology.”

    http://jsm-research.imb.uq.edu.au/jsmgroup/

  19. I would also like to point out that since ENCODE found “an extensive overlapping network” for the human genome, this recently discovered fact clearly indicates that scientists are completely misinterpreting the genetic data from their preconceived evolutionary perspective, since the Evolution hypothesis requires that the genome be a “multiple independent collection of selectable genes”. Thus I predict all similarity based evidence culled from different genomes in support of the evolution hypothesis will have to be reinterpreted, from the proper engineering perspective, since it is now clearly impossible for the evolutionary scenario to overcome the the demonstrated poly-constrained nature of a poly-functional genome (Sanford Gentic Entropy; 2005)!!!

  20. DaveScot, you are surely correct that DNA somehow encodes instinctive behavior. Further, there must be a back propogation system that allows life-patterns to become instincts. Is this the only reason why prokaryotes have virtually no non-coding DNA whereas eukaryotes have tons of the stuff? I suspect that it is only a very small piece of the reason. Eukaryotes, after all, are vastly more complex of creatures in many ways.

  21. Dave and bFast – what are the instinctive behaviours in cereal mildews? For their genomes are large and full of, err, junk.

    Bob

  22. Non coding DNA has always been one of my favourite subjects. So, allow me to add a few considerations to the very interesting discussion above.

    1) Mattick was indeed one of the first researchers to really believe in the importance of non coding DNA, and to carry on serious research about that. One of the main points in Mattick’s reasearch is the consideration that the rate of non coding DNA versus coding DNA is the main single feature which seems to correlate with the complexity of an organism. In that sense, it seems that it is probably our non coding DNA which makes us humans and not, say, rats. That would be consistent with the really disappointing homogeneity of the coding part, which seems to change very little between very different organisms, both as gene number and as gene quality.

    2) The important thing to remember is that we really don’t know where the biological code is, least of all how it works. What I mean is: genes, as we know them, are the final effectors constituting the biological machines. But the real code, the real information, is the sum of all the possible procedures, regulations, networks, which make life possible, and which make possible the astounding differentiation of each cell starting from the same genetic information, and which build and control the multicellular network, that is the from, both macroscopic and microscopic, of the organism. That “code” must certainly amount to a very huhe quntity of information, and I have real difficulties in beieving that it may be stored not only in the few megabytes of the coding genes, but even in the few hundreds of megabytes of the total genome.

    2) In my opinion, non coding DNA has certainly a cery important role, but still we must understand that that role is really elusive if we look at the apparent structure of most of it: repetitive sequences, transposons, and similar. If the fundamental code is written there, it is certainly written in a way that defies all imagination.

    3) Finally, I would like to mention again that it is not necessary that all the information may be found in the genome, or at least in DNA. We have some evidence of the importance of epigenetic factors. I think we should reevaluate the role of cytoplasm. After all, even in cloning experiments, we need two different factors to generate a new living being: the DNA, which in that case is taken from a somatic cell, and the enucleated ovum cell. As the somatic DNA is, in normal conditions, totally incapable to generate a living being, or even to de-differentiate, for instance, to the state of stem cell, it seems that something in the ovum cell has the power to reactivate the full potential of a genomic store which, in its present conditions, is differentiated and practically inert.

    4) However we look at it, the present state of our biological knowledge is totally incompatible with any known theory. That’s the beauty of it. The truth is that we don’t understand, and we are daily facing a lot of apparent contradictions. And the more we know, the more contradictions arise. But, while the darwinian evolution hypothesis becomes every day more unthinkable, not to say totally impossible, the design scenario is totally compatible with the development of new hypotheses, and with the development of both empirical reasearch and theoretical understanding. The Intelligent Design framework, indeed, is not a single, specific hypothesis, but rather a fundamental theoretical assumption which allows rational hypotheses about the biological reality to be made. It is as important, in biology, as the assumption that the physical universe is mathematically structured, in physics. And both assumptions are constantly verified by known facts.

  23. gpuccio

    I favour the phrase “working hypothesis” to “assumption”.

    The working hypothesis of ID is as important to biology, as the working hypothesis that the physical universe is mathematically structured, is to physics. Both hypotheses are constantly being verified by emerging data.

  24. idnet:

    Working hypothesis is perfectly fine for me.

  25. First I would like to point out that Craig Venter’s work in transplanting a genome from one bacteria into another bacteria gives tentative indication that much if not all of the information for “life” is encoded in the genome.

    Go here for overview:
    http://www.sciencemag.org/cgi/.....ct/1144622

    A little bit more on the complexity and wonder of the genome:
    To illustrate the complexity and wonder in the DNA of man, let’s look at some of the work of Samuel Braunstein who is a quantum physicist at the Weizman Institute in Israel.
    Samuel Braustein was asked to present a talk to the science-fiction club in Rehover. What better topic, he thought, than quantum teleportation? Because of the limitations, imposed by the laws of physics, of ever teleporting any material object, Braunstein suggested the secret to teleportation would lie not in transporting people, or material objects, but would lie in teleporting the molecular information about whatever was to be teleported. Somehow, this Star Trek type teleporter must generate and transmit a parts list and blueprint of the object being teleported. This information could be used in reconstructing the object at its final destination. Presumably, the raw materials would be available to reconstruct the object at its final destination. Naturally this process raises a lot of questions that the script writers for Star Trek never answered. For example, just how much information would it take to describe how every molecule of a human body is put together?
    In a human body, millimeter accuracy isn’t nearly good enough. A molecule a mere millimeter out of place can mean big trouble in your brain and most other parts of your body. A good teleportation machine must be able to put every atomic molecule back in precisely its proper place. That much information, Braunstein calculated, would require a billion trillion desktop computer hard drives, or a bundle of CD-ROM disks that would take up more space than the moon. It would also take about 100 million centuries to transmit the data for one human body from one spot to another. “It would be easier,” Braunstein noted, “to walk.”
    Yet the DNA of man contains the parts list and blueprint of how all these trillions upon trillions of protein molecules go together in just 3 billion base pairs of DNA code. As well, the DNA code contains the “self assembly instructions” that somehow tells all these countless trillions of proteins molecules how to put themselves together into the wonder of a human body. Yet far from the billion-trillion computer hard drives calculated by Braustein, these 3 billion letters of information in the DNA of man could easily fit onto the single hard drive of the computer I’m writing this article on with plenty of room left to spare! That ratio of a billion trillion hard drives reduced to one hard drive is truly an astonishing amount of data compression that far exceeds the capacity of man to do as such. It is abundantly clear that all that required information for exactly how all the protein molecules of man are put together is somehow ingenuously encrypted in some kind of “super code” in the DNA of man. Amazingly, many evolutionary scientists “used” to say the majority of DNA that didn’t directly encode for proteins (genes) was leftover “junk” DNA from man’s falsely presumed evolutionary past. Now this blatantly simple-minded view of the required complexity that is inherent in the DNA of man has been solidly overturned. In June 2007, an international research consortium, named ENCODE, published a huge body of preliminary evidence that gives a glimpse into the world of the DNA’s complexity. This is a quote from a Science Daily article about the landmark study.
    In a group paper published in the June 14, 2007 issue of Nature and in 28 companion papers published in the June issue of Genome Research, the ENCyclopedia Of DNA Elements (ENCODE) consortium, which is organized by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported results of its exhaustive, four-year effort to build a parts list of all biologically functional elements in 1 percent of the human genome. Carried out by 35 groups from 80 organizations around the world, the research served as a pilot to test the feasibility of a full-scale initiative to produce a comprehensive catalog of all components of the human genome crucial for biological function. The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active. The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact.
    The revelation of a complex interwoven network is a major blow to evolutionists. Now bear in mind, this is only a “feasibility study” of 1% of the Genome. The interwoven complexity is sure to be multiplied exponentially as the effort extends to decipher the remaining 99% of the DNA. This preliminary study, of how DNA is actually encoded, clearly indicates that most, if not the entire 100%, of the DNA is “poly-functional”. Poly-functional simply means the DNA exhibits extreme data compression in its character. “Poly-functional” DNA sequences will exhibit several different meanings on several different levels. For instance, if you were to write a (very large) book similar to the DNA code, you could read many parts of the book normally and it would have one meaning, you could read the same parts of the book backwards and it would have another completely understandable meaning. Yet then again, a third equally coherent meaning would be found by reading every other letter of the same parts. A fourth level of meaning could be found by using a simple encryption program to get yet another meaning. A fifth and sixth level of meaning could be found in the way you folded the parts of the book into specific two and three dimensional shapes. Please bear in mind, this is just the very beginning of the mind bending complexity scientists are finding in the DNA code. Indeed, a study by Trifonov in 1989 has shown that probably all DNA sequences in the genome encrypt for up to 12 different codes of encryption!! No sentence, paragraph, book or computer program man has ever written comes close to that staggering level of poly-functional encryption we find in the DNA code of man. Here is a quote on the poly-functional nature of the DNA from renowned Cornell Geneticist and inventor Dr. John Sanford from his landmark book, “Genetic Entropy”:
    There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
    Dr. John Sanford (PhD in Genetics; inventor of the biolistic “gene gun” process! Holds over 25 patents! If you ate today you probably ate some food that has been touched by his work in manipulating the genetics of food crops!)
    Though the ENCODE consortium is about to undertake the task of deciphering the remaining 99% of the humane genome, I firmly believe that they, and all their super-computers, are soon to be dwarfed by the sheer and awesome complexity at which that much required information is encoded into the three billion letters of the DNA code of man. As a sidelight to this, it takes the most powerful super-computer in the world an entire year just to calculate how a single 100 amino acid protein sequence will fold into a 3-dimensional shape from its 1-dimensional starting point. Needless to say, this impressive endeavor by ENCODE to decipher the entire genome of man will be very, very interesting to watch. Hopefully ENDODE’s research will enable doctors to treat a majority of the over 3500 genetic diseases (mutational disorders) that afflict man without having to fully understand that much apparent complexity in the DNA of man.
    The only source for purely evolutionary change to DNA, that is available to the atheistic evolutionists, is the natural selection of copying errors that occur to DNA. This is commonly known as natural selection of random mutations to DNA. What evolutionists fail to ever mention is that natural selection is actually just some totally random selection of some hypothetical beneficial mutation that has never actually been clearly demonstrated to occur in the laboratory. For all practical purposes, All random mutations to DNA, that have been observed in the laboratory (we are talking millions of observations here), are either clearly detrimental or slightly detrimental, to the organism having the mutation. All mutations that are deemed to be somewhat beneficial to the organism, such as the anti-biotic resistance of bacteria, all turn out to involve loss of function in the genome. In fact, at least 99.9999% of the copying errors that do occur to DNA are proven to be somewhat harmful and/or to the organism having to mutation (Gerrish and Lenski, 1998). Evolution assumes a high level of beneficial flexibility for DNA. But alas for the atheistic evolutionists, the hard evidence of science indicates an astonishingly high level of integrity in the DNA code! A code which Bill Gates, the founder of Microsoft, states is far, far more complex than any computer code ever written by man.
    Sometimes a mutation to the DNA is found to be the result of a “complex feedback” of preexisting information that seems to be somewhat beneficial to the organism at the macroscopic level (such as lactase persistence). Yet, even in these extremely rare examples of “beneficial” mutations, the questioned beneficial mutation never shows a violation of what is termed “Genetic Entropy”. Genetic Entropy is a fundamental principle of science that means functional information in the DNA cannot increase “above the level of parent species” without an outside source of intelligence putting the information in the DNA. To be absolutely clear about this, evolutionists have never proven a violation of genetic entropy in the laboratory (Sanford; Genetic Entropy, 2005), thus they have never even proven a gain in information in the DNA of organisms above the level of parent species, thus they have never conclusively proven evolution as a viable theory at the molecular level in the first place! To make matters worse for the evolutionists, even if a purely beneficial random mutation were to ever occur it would be of absolutely no use to the evolutionary scenario for it would be swallowed in a vast ocean of slightly detrimental mutations. Yet evolutionists act like evolution has been conclusively proven on the molecular level many times %
    DNA is extremely resilient in its ability to overcome copying errors to the DNA, yet, as stated earlier, evolutionary scientists claim that the copying errors in the DNA that do occasionally slip through are what are ultimately responsible for the sheer and awesome complexity we find in the DNA code of man. Contrary to their materialistic beliefs, mutations do not create stunning masterpieces!
    As well, the overwhelming “slightly detrimental” nature of all observed mutations to DNA in the laboratory has been thoroughly established by Dr. J.C. Sanford, in his book “Genetic Entropy”. He shows in his book that there is a indeed a slightly negative effect for the vast majority of mutations. These slightly detrimental mutations are not readily apparent at the macroscopic level of the organism. These slightly negative mutations accumulate over time in all higher species since they are below the power of natural selection to remove them from a genome. These “slightly negative” mutations accumulate in a higher species until “genetic meltdown” occurs in a species. Indeed, if mutation rates for higher species have stayed similar to what they currently are, throughout the history of complex life on earth, then genetic meltdown is the most reasonable cause for the numerous mysterious extinctions in the fossil record. Over 90% of extinctions in the fossil record have occurred by some unknown natural mechanism. The average time for “mysterious extinctions” is rather constant at about 4 million years per species in the fossil record (Van Valen; A new evolutionary law, 1973). Mysterious extinctions which are not part of any known major natural catastrophes in the history of the earth. I would like to point out that since the laws of physics have been clearly proven to have remained stable throughout the history of the universe, then, there is no compelling reason to suspect the naturally occurring mutations to DNA have change significantly from their present rate for any prolonged period of time. Thus the “genetic meltdown theory” is surprisingly strong as the solution to the fairly “constant rate” of mysterious extinctions of higher life-forms in the fossil record.
    I’ll end my paper with a bit of trivia. The capacity of the DNA molecule to store information is so efficient that all the information needed to specify an organism as complex as man weighs less than a few thousand-millionths of a gram. The information needed to specify the design of all species of organisms that have ever existed on earth (a number estimated to be one billion) could easily fit into a teaspoon with plenty of room left to spare for every book that has ever been written on the face of earth. Obviously, I am just barely touching the surface of the complexity that is apparent in the DNA of man. Yet even from this superficial examination, we find truly golden nuggets of astonishing evidence that we are indeed the handiwork of Almighty God.
    Psalm 139:14
    I will praise You, for I am fearfully and wonderfully made;

  26. Bornagain 77

    Long posts like that one should be published as a PDF and a link attached. They are too hard to read.

    May I put an edit of that post on idnet.com.au?

  27. bornagain

    Yet the DNA of man contains the parts list and blueprint of how all these trillions upon trillions of protein molecules go together in just 3 billion base pairs of DNA code.

    That’s not at all true for complex animals. You can’t insert the nucleus from a duck egg into a frog egg and get either a viable duck or a viable frog. What you’ll get is an unviable egg. The structures surrounding the nucleus must be from the same or very similar organism for such a genome transplant to work. Epigenetic factors are critical at least in metazoans.

  28. Sorry for the long post IDNET.au, I didn’t mean to be rude but I don’t know how to attach as a pdf document right now. I will try to learn how to so as to avoid clogging blogs.
    I don’t know what an edit to the post means but you are free to do it,,,but If you don’t mind I would like to know exactly what that is.

    DaveScot,
    Thanks for the correction!
    I did put “gives tentative indication” in the sentence before Venter’s link. I am not intimate with the similarities between the supporting structures of the different bacteria he used so I truthfully cannot say how much similarity is required for such transplants to be viable
    I still think this experiment of Venter’s is a good starting point in finding the edge of how much information is required in support of a genome. And still feel that it gives weight to the fact that most of the “essential” information for “life” is indeed in the genome.

  29. I would love to see the data and/ or evidence that demonstrates that culled genetic accidents can cobble together command and control functions.

    We do have such data and evidence which demonstrates that intelligent agencies do so on a daily basis- that is design and implement command and control functions.

    Command and control is yet another hallmark of Intelligent Design.

  30. bornagain77:

    thank you for the link to Venter’s paper, I was not aware of that information. Unfortunately, I could not access the whole text, because I think it would be extremely interesting. Anyway, I understand that it is rather new information, and probably it should be confirmed in further studies.

    That said, the concept is certainly relevant to our discussion. But, as Davescot has mentioned, bacteria are very different from eukariotes and from multicellular organisms. Although bacteria are certainly very complex, they are by far simpler than eukariotes. Besides, the almost completely lack non coding DNA, which was the subject of our initial discussion. And, like all single celled organisms, they don’t need any program for specialized differentiation and body plan. So, not everything that applies to bacteria can propbably apply to more complex beings.
    Besides, if I understand the paper (from the abstract), the general model is similar to cloning (DNA transplanted in a cytoplasm), the only difference being that here two different “species” are involved (even if the concept of species is probably different in relation to bacteria). The fact that the final characteristics are those of the “DNA donor” should not surprise, because nobody has ever doubted that in cloning the final genetic characteristics are those of the nucleus donor. The point is that, anyway, we need a recipient cytoplasm to be able to exploit the information in the DNA, and the role of epigenetic factors is probably greater than a simple role of protein synthesis.

    Regarding the huge amount of information necessary in principle to build up a complex organism, like a human, I perfectly agree with you: it is certainly huge beyond our conception. That’s why I can’t believe that it is all in DNA, or at least not in DNA merely as a base sequence. Although I share with you the faith in the supreme intelligence of a Creator, I think that, in the science of information as we presently understand it, there are limits to how much information can be compressed, especially in a digital form, like a base sequence. With all my goodwill, I don’t believe that such a great amount of information could be compressed in less than 1 gigabyte, even with multiple encriptions and codes. I prefer to think that, if that information is all in the DNA molecule (which I am not sure of), it is probably stored in other ways, and not only in the base sequence. DNA is a very complex molecule from the biophysic point of view, and one possibility could be that much information could be stored in biophysic properties of the molecule, independently, at least in part, from the base sequence. Information could be stored at a quntum level, just to make an example. Although these are extreme suppositions, we must also consider that the problem we are facing is really extreme (unless, like the darwinists, one chooses to shut one’s eyes and to believe that 18000 genes can do the trick).

  31. I’m just so happy that research is emerging to warrant re-evaluation of Darwinian Theory. Opponents of Darwinism are basically regarded as lunatics! Hopefully this will all begin to change now.

  32. gpuccio:

    I understand fully your reservation at that much data compression in the genome,So i will reiterate this “educated” look at the complexity we are actually looking at in the genome.

    Here is a quote on the poly-functional nature of the DNA from renowned Cornell Geneticist and inventor Dr. John Sanford from his landmark book, “Genetic Entropy”:

    There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
    Dr. John Sanford (PhD in Genetics; inventor of the biolistic “gene gun” process! Holds over 25 patents! If you ate today you probably ate some food that has been touched by his work in manipulating the genetics of food crops!)

  33. idnet.com.au (#18):

    ““We are working on the alternative hypothesis that the majority of the genomes of complex organisms is devoted to the regulation of development and that most of this information is transacted by noncoding RNAs. Both logic and the available evidence suggest that these RNAs form a highly parallel digital network that integrates complex suites of gene expression and controls the programmed responses required for the autopoeitic development of multicellular organisms. If this is correct, our current conceptions of the genomic information content and programming of complex organisms will have to be radically reassessed, with implications well beyond biology.”” (Mattick)

    This seems in the right direction to me. Intricate interconnected parallel control of multiple gene expressions must be one of the major, if not the most important techniques by which the incredibly complex biological designs of higher organisms are built. Assuming instinctual behaviors are ultimately the function of specific neuronal structures in the brain, these instincts would just be one of many physical designs built up during embryonic development.

    But the apparently non-conserved nature of most of the “junk” DNA is still a major problem with this picture. It’s interesting that Mattick carefully ignores the issue.

    If the junk DNA actually somehow specifies organismal structure in great detail, we would expect much of the developmental design description data to be conserved between classes and genera in mammals, for instance. The design data for the liver, heart, kidney, etc. would be expected to be mostly the same between mouse and man. Even the brain design data would be much the same in having the same basic overall structure and microstructure. This part of the information would need to be conserved between lineages. How can it be in non-conserved “junk” DNA?

    I wonder if there can be a form of data encoding on DNA sequences that works like digital data encryption, where much of the information can be the same between two different messages, but the two message data strings are very different from each other because of the use of two different decryption “keys”. Continuing the digital data transmission/storage analogy, then data compression schemes would be a possibility, perhaps dealing with some of the problems of apparently insufficient base pairs in the genome for the total data. Another conceptual model would be successive holograms of similar but different objects (like an Edsel, a Pinto and a Fairlane). The data detailing the interference fringes of the different holograms would be completely different between images, but the 3-dimensional object information encoded by this data would have great generic similarities.

  34. How can it be in non-conserved “junk” DNA?

    Indeed. Junk DNA doesn’t just contain a single class of sequences – there are certainly sequences that regulate gene expression, but there are also sequences that are transposons, dead transposons, pseudo-genes, centromeres, telomeres, retrovisuses and probably all sorts of other weird things.

    Some is functional, and we’ve been aware of this for a long time. Some is also probably genuine rubbish that has just accumulated. And no doubt there is the digital sequence of one of Slartibartfast’s colleagues (although not in humans, obviously).

    Bob

  35. For some, the apparent inexplicability of such aspects of our existence is a pointer towards God. For others, the fact that we can understand, and that simple laws of nature give rise to great complexity, points towards God. The problem with treating these things as ‘proof’ is that, as Van Till points out, this is a ‘heads I win, tails you lose’ situation.

    http://exploringourmatrix.blog.....ge-of.html

  36. ReligionProf:

    I have read your linked article. I don’t want to seem rude, but frankly I must say that you seem to understand nothing of the matter when you speak about monkeys, probabilities, etc. It would be too long to open again this discussion from scratch (plese, just read something from Dembski or Behe, trying to understand what they say), so I will only comment briefly your post here.

    You say:

    “For some, the apparent inexplicability of such aspects of our existence is a pointer towards God. For others, the fact that we can understand, and that simple laws of nature give rise to great complexity, points towards God. The problem with treating these things as ‘proof’ is that, as Van Till points out, this is a ‘heads I win, tails you lose’ situation.”

    But what do you mean? Both the sense of wonder for the complexity of things and the fundamental fact that the universe seems to be mathematically understandable can be valid arguments, for different reasons, in the context of a philosophical discussion about the possible existence of God. Indeed, you are not giving here, not addressing in any way, any kind of philosophical argument in a real context.

    But both the points you mention have nothing, absolutely nothing to do with science and with ID.

    Although I am a little bit tired, like many others here, of repeating the same things, ID is a scientific theory about the interpretation of available data, including a tight demonstration of the complete inadeguacy of the currently accepted theory (darwinian evolution).

    ID has no need to rely on “the apparent inexplicability of such aspects of our existence”. ID relies on the obvious inexplicability of biological beings in a darwinian scenario, and on its possible explanation in a ID scenario.

    ID has no need to rely on “the fact that we can understand, and that simple laws of nature give rise to great complexity”. That point is simply one fundamental “working hypothesis” of the whole scientific framework, and as such it naturally applies to ID. ID relies, strongly, on the demonstration, given many times and in many different ways, that no known law, either simple or complex, can explain the kind of complexity observed in living beings, while the working hypothesis of a designer certainly can.

    So, there is no “heads I win, tails you lose’ situation” here, just simple and very, very valid scientific arguments, which can be understood or not, but are absolutely true.

  37. ReligionProf,

    At your blog you wrote,

    Michael Behe is one of the few people in the intelligent design movement with qualifications in a relevant field.

    You also wrote,

    [T]here is no room for actually testing and assessing the validity of [ID's] “hypothesis” in its 20-year strategic plan. This isn’t science.

    So despite the fact that philosophers of science have largely given up on trying to distinguish science from non-science or pseudo-science you, an assistant professor of religion, feel qualified to determine what is, and what is not, science.

    Dear me. Your qualifications aren’t in a relevant field. Maybe you should be more circumspect with your assertions.

    You also wrote,

    Anyone who has read the “Wedge Strategy” document will know one thing for certain about intelligent design: it has its mind made up from the outset.

    Really? Anyone? Or just you and those who, like you, perceive what they want to perceive and believe what they want to believe?

    To the best of my knowledge few science faculties teach logic to their undergraduate students as a matter of course and this is one reason why so many “scientific” research papers aren’t worth the paper they’re printed on or the bandwidth they consume. Now you have given me just one more reason to believe that the same shortcoming affects theology faculties too.

    So which are you? A whited sepulchre full of dead men’s bones, one of a brood of vipers, or just a foolish person who has only a vague understanding of what he’s talking about?

    You want to be a teacher? Think about millstones, necks and the depths of the sea and then get your act in order if you can – if, that is, you’ve been chosen since before the foundation of the world. Otherwise just enjoy the rewards you have now because they’re all you’re going to have.

    If you’d called yourself JoeBlogs or JohnDoe, I wouldn’t feel so angry towards you. But you call yourself ReligionProf! Proud of what you’ve accomplished in this dying world, are you? Oooh! I have an assistant professorship! What a clever person am I!

    Go away, young man. Stop talking rot and grow up. After you’ve grown up come back and tell us what you’ve learned. I wish you well on the journey.

  38. Janice, I hope I am at least clever enough to know that attempting to carry on a conversation in the tone you have adopted will not be very profitable.

    As for what science is, I am simply repeating the views of mainstream scientists. Proponents of Intelligent Design are pretty open about wanting to redefine science, and so perhaps instead of engaging in insulting rhetoric, you should actually read some of the writings of the proponents of ID and see if you have in fact understood what they are saying. The Wedge document says nowhere that it will TEST the HYPOTHESIS of design in the hundreds of peer-reviewed articles it aims to see published. The message is clear – this is not about testing a hypothesis scientifically, but promoting an ideology. Personally, I opt for the view of the mainstream of scientists who are persuaded that neither religious nor materialistic worldviews are required results of using the scientific method to investigate the natural world.

    I wish I could wish you well on the journey, Janice, but it sounds like you are not on a journey. You sound very much like me in my teenage years – certain you are right, with no room for anyone, even God, to get through to you and teach you something. I hope he manages to in spite of your attitude, as he did with me.

  39. ID redefine science? What’s the definition you’re working with? Are you equating “Science” with a particular philosophy? Many ID proponents do take issue with people imposing a preferred philosophy upon science, but not all ID proponents seem to consider this subject a matter to fight over.

  40. ReligionProf,

    There are hundreds, possibly thousand of research projects every year that are ID oriented. They just do not state ID expected results in their introduction, results, discussions or conclusions. If an ID proponent could examine the research proposal prior to execution of the study, ID predictions could be included and evaluated by the findings.

    In present day science this would never happen as the study would probably be de-funded or made to exclude any ID relevant predictions and conclusions.

    You mention that Behe is a legitimate ID scientist and he has recently pointed out how current and recent research has supported ID conclusions while the research itself would never admit it had anything to do with supporting ID.

  41. If the definition of science doesn’t allow for the possibility of the actions of intelligent agency in the universe then the definition needs to change. Intelligent agency is a proven quantity. It’s proven that intelligent agency can do all sorts of things from building spacecraft to manipulating the DNA sequences in living things.

    There is no rational basis for thinking that human agency is the sole instance of intelligent agency at work in the universe. If materialist philosphy refuses to admit any other intelligence then it’s a philosophy in denial of the plain evidence before it.

    Statistical mechanics tells us what to expect from undirected laws of physics operating on matter/energy. Statistical mechanics is rational and reliable about explaining and predicting what we observe. However, when we observe something that appears to defy the predictions of statistical mechanics then we’re either missing something in our calculation or an intelligent agency has intervened to cause organization that shouldn’t otherwise exist.

    A space shuttle can, in principle, assemble from the undirected interaction of matter and energy. However, statistical mechanics informs us that the probability of a space shuttle assembling without guidance is so improbable in a finite universe the size and age of ours that we can confidently predict we’ll never observe one. Yet there’s a whole fleet of them.

    The actions of intelligent agency explain how things almost impossible become quite possible. Statistical mechanics is a reliable positive indicator of intelligent agency. It doesn’t work in the negative – it can’t rule out the actions of intelligent agency but rather it makes it unneccessary.

    This is the real basis (or should be) of rational materialist science. It attempts to explain what we observe without resort to the actions of intelligent agency. It’s quite reasonable to resist any inference of intelligent agency by all rational and evidentiary means because, after all, it remains a fact that there is just one observed instance of intelligent agency and its actions are bounded in time and space. If evidence of intelligent agency acting outside the scope of human agency is presented I have no problem with taking extraordinary pains to find an explanation that doesn’t involve agency. I’ll resist such an explanation as long as reason allows but no longer. I won’t take the unreasonable position that there is no possibility of non-human intelligent agency.

    However, there must come a point when it becomes reasonable to make an intelligent design inference. At some point all other explanations for observed organization become inadequate. I think we’ve reached that point in trying to explain the organization of organic life without resort to intelligent agency. The final nail in the unintelligent coffin for me was the observation of random mutation & natural selection working over billions of trillions of generations in p.falciparum and generating nothing in the way of non-trivial organization. This was a fair trial for RM+NS and it failed to produce what neo-darwinian theory predicted it would produce. It obeyed the predictions of statistical mechanics as ID proponents held. Unless there’s some other unknown unintelligent mechanism that IS adequate the only reasonable explanation still on the table is intelligent design. It’s time to admit it as the best explanation. That’s not to say it’s the only possible explanation but it deserves top billing at this point in time. Anything less than top billing is understandable given the inertia of the RM+NS theory but active suppression of the intelligent design explanation is driven by irrational desire and/or hidden agendas rather than honest and open scientific inquiry and education.

  42. I have no problem with the possibility of an ‘intelligent design’ inference in principle. My principle concern is when this is used as a justification for asserting knowledge (i.e. that something was produced through intelligent agency) where admitting ignorance (i.e. we don’t at present know how something came about) would seem more appropriate. The idea that the eye could evolve was once thought ludicrous. Now it can be shown to be plausible.

    How do we know at what point we are dealing with something inexplicable in naturalistic terms, as opposed to merely as yet unexplained? I do not find the appearance of irreducible complexity a persuasive basis, because it has proved an inaccurate guide in the past (see the eye, again) and does not appear to me to be as readily quantifiable as Dembski’s work maintains. To make a comparison, at what point does one give up investigating a criminal case and say that it not only has not been solved but CANNOT be solved in principle?

    My own view is that once one is dealing with intervention by a personal agent (whether human or supernatural), one is not doing science in the traditional sense. To use an example, if a scientist is running an experiment, and a rival sneaks into his lab late at night and tampers with the apparatus, this would invalidate the experiment’s aims, which is to study what happens in the absence of such interventions.

    Of course, this also leads nicely to the question of how we detect intervention by a personal agent. One possibility would be to compare this individual’s results with others conducted independently. The fact that his results were so different would probably lead him, quite logically, to suspect personal interventions.

    If we find other planets at a comparable distance from their suns and with similar starting points, and they all fail to produce life through natural processes, that might be more suggestive of something other than natural processes having caused life on earth. But at present, we can only say ‘One out of one people surveyed said…’, which is not an adequate basis for assessing the probability or otherwise of life emerging through natural processes.

    I am not sure why I am more comfortable than some other Christians seem to be with natural explanations for things. Perhaps it is because it seems that if one finds natural explanations threatening, then the fact that our individual form is shaped by DNA instructions rather than inexplicably by God’s hand, that whirlwinds and lightning can be explained in meteorological terms – in short, all of science should be threatening to a religious viewpoint that seeks to hold on to a prescientific view of the world. For me, science has shown its ability to explain the world adequately, and I concur with most Christians that speaking about God is another way of looking at the same events, and not a competing explanation.

  43. ReligionProf:

    Janice was probably a bit ruder than me, and in a spirit of friendly communication I regret that, although I can certainly agree with most things she says. As you have answered her and not me, maybe her strategy was better than mine.

    Anyway, back to your new post. Some comments:

    1) I don’t see why you go on referring to the wedge document to judge the ID scientific movement. I have no interest in the wedge document, which was in no way a scientific act. Similarly, I have no interest in darwinist foolish political ramblings. I am only interested in scientific discussion, and so should you, at least as far as we are discussing ideas, and not politics. Politics, even scientific politics, has its role, and I would not run away from a bit of fight for the things I believe, but science and the search for truth are another thing.

    2) About hypothesis testing. Here is one of the most confounding and misled arguments in the darwinist field. First of all, it is obvious that most research is made today from a darwinist point of view, because all resources are owned by the darwinist lobby. Second, darwinism and ID are really alternative hypotheses about the origin and evolution of life, and therefore, as I have said many times, any research in the field is a research about both darwinism and ID. Facts are owned by nobody. As far as a researcher honestly gathers pertinent facts, for me he is testing ID as much as he is testing darwinism. The interpretation of the facts, obviously, is another matter, and there anyone can see how the darwinist interpretation of new facts is always forced, partial, often completely inconsistent. The mapping of the human genome, the low number of genes, the 98,5% of non coding DNA, the similiratities between genomes of very distant species, are only a few of a huge amount of facts which have no explanation in the traditional, darwinian scenario. What is happening is in reality what Thomas Kuhn calls a scientific revolution: the darwinist paradigm, totally inadequate to explain reality as we know it today, is being defended against all reason, after having been falsified many times. With time (not too much, I hope), it will crash under the weight of its own lies.

    3) About redefining science. I think you, and not Janice, should read the ID sources (not the wedge document) trying to understand what they say. Neither Dembski nor Behe, who are certainly the most important ID thinkers, have ever tried to redefine science. The ID arguments are completely within the boundaries of science. The opposite is true. Darwinists, in a desperate attempt not to discuss ID on a peer level, have often adopted philosophical, non scientific arguments (see the “who designed the designer” and similar crap), and have totally redefined science in the sense of materialistic, reductionist philosophy, which has nothing really scientific in it (if we consider science as a search for an objective truth), and is rather a squalid antireligious religion, rationally poor and cognitively depressing.

    4) About conformism (your conformism): you say: “I am simply repeating the views of mainstream scientists”. That’s true. You are simply repeating things which are wrong, although believed by many people, without even understanding what they mean. At least, you should try to express some personal argument, although wrong.

    5) Oops! I am wrong. You have definitely expressed some personal arguments, in the article you linked in your first post. At least, I hope it is only your personal argument, because at least you are, it seems, a religion prof, and you may be excused for understanding nothing of mathematics and probability. But you are not excused when you try to judge, on such a shallow basis, people like Dembski or Behe, who, believe me, “do” understand what they say. Your treatment of the monkey problem is, at best, ridiculous. You should ask yourself what information is, what an informational search is, the meaning of statistics and probabilities. How can you think that there is any difference if one randomly types on a keyboard or, say, randomly moves blocks of something with letters on them, or if the alphabet is made of four or twenty letters? Just make correct calculations of the probabilities, and believe me, there is no difference if you are using a binary code, or a decimal code, or any letter code. Numbers are numbers, and mathematics is, thanks God, a universal language.

    6) You say: “Personally, I opt for the view of the mainstream of scientists who are persuaded that neither religious nor materialistic worldviews are required results of using the scientific method to investigate the natural world.”
    What do you mean? What are you saying? I, and like me any serious ID believer, am totally convinced that “neither religious nor materialistic worldviews are required results of using the scientific method to investigate the natural world”. Why are you saying that this is “the view of the mainstream of scientists”? This is only the correct view of any scientist. This is the correct view of ID. This should be the correct view of darwinian scientists, if they were not too ocuupied in trying to defend themselves from ID by recurring to materialistic ideology. For the last time, I repeat: ID has nothing to do with religion or phylosophy. It is science. You can agree or not agree with its arguments, but you have to do that on a scientific level. Darwinists don’t do that. I have not found a serious scientific objection to ID in years, in the darwinian field. Only arrogant intolerance, and a strict adherence to concepts of science so deformed as to not allow discussion of ID. Religion, religion religion of the worst kind. Pure intolerance and fear. And conformism, everywhere, the depressing conviction that “I must be right because a lot of important people think like me”.

    7) Anyway, if I am wrong, and if you “do” have personal and credible arguments against ID, please let me know. I am here to answer, and I love a good discussion.

  44. Perhaps some background information would be appropriate. I’m a Christian (a Baptist, to be more specific, although I’ve spent time in other church contexts as well) and I used to be a young-earth creationist. It was the presentation of the evidence by mainstream biologists and other relevant scientists that persuaded me that the books I had been reading by young-earth creationists had been misconstruing the evidence. Although I am ready to acknowledge differences between the YEC and ID positions, there is at least one similarity that I think comes across in what you wrote. Both have to maintain that there is a conspiracy by “Darwinists” to prevent those who are doing good honest science from having their results published in peer reviewed journals. I do not find that argument persuasive. On the one hand, I am not a scientist, and that can be held against me. On the other hand, the proponents of intelligent design are certainly not unwilling to appeal to the general public to take a stand on these matters, and so I think it would be hypocritical to do what Janice did and reject my views simply because they are those of a non-specialist, and yet expect there to be intelligent, well-informed discussion and adoption of the ID viewpoint among non-scientists.

    My viewpoint, at the end of the day, is this. In the past, an appeal was made to things in the observable world that appeared to be designed, as proof of a designer. Appeals were made to the inexplicable as pointers to God as explanation. These sorts of arguments led, as scientific knowledge advanced, and God was not needed as a ‘hypothesis’ (to make an allusion to Laplace) in scientific explanations, to the perception that science was disproving God. I am persuaded that most Christians today are willing to accept scientific explanations of phenomena that were in the past attributed to God and otherwise inexplicable. I thus do not see why the current frontiers of our knowledge should continue to be proclaimed as the gaps into which God may be reinserted as an explanation. My own view is that God is not a competing explanation but a complementary one, just as the movements of my hands as I type this can be adequately described in terms of electrical impulses and muscle contractions, with an explanation in terms of my will and my desire to communicate being a different level of explanation, rather than an alternative one.

  45. Religious prof, I am going to suggest you do two things to increase the qualiry of your dialogue. I know I am being presumptious and even a bit didactic, but here goes:

    1) Read “The Design Inference,” by William Dembski from cover to cover. It is only fair that you come to this conversation with a working understanding of the concepts involved. Surely, you can afford such an investment in time and effort.

    The reason I recommend this book in particular is because it not only deals with ID science, it also provides important information about the intersection between science and philosophy/theology, subject matter I believe you would find interesting. If you are sincere, you will charter this territory.

    2) Be wary of those who do not understand or will misrepresent the issues involved. I have visited the link you refer to several times, and I assure you that it is not a reliable source of edification on the subject of ID. It’s OK to get both sides, but do get both sides.

  46. ReligionProf:

    As you have expressed a few more specific argomentations, I feel obliged to answer them.

    1) YEC, ID and science. I have never been a YEC, and though I respect them (after all, Salvador Cordova is one of them) I don’t think there is anything scientific in what they believe. The problem is that, in science, you cannot make the assumption that your personal, philosophical or religious, view of reality must necesserily be proven, or that it has to guide all your scientific reasoning. That’s exactly the difference with ID. I believe in God, and I have never needed ID for that. I need ID to respect myself as a scientist and as a rational person. I have bever understood how the darwinian evolution theory could work, and ID has made me understand fully that it cannot, and I mean cannot, work. The work of Dembski has given me the formalism and rational analysis to support what was for me intuitionally evident. The work of Behe has provided other fundamental insights, of a different kind. Both approaches, the mathemathical and the biological, are complemetary and strongly support one another.

    2) From the standpoint of the philosophy of science, ID is much more natural and scientific than darwinian evolution. There is a huge mistake in most discussion about that, about the word “naturalism”. Naturalism, be it philosophical or methodological, is never a scientific approach, it is always ideological. Any “naturalism”, indeed, presumes to know exactly what nature is. That is a big mistake, both philosophically and scientifically. “Nature” may be many different things, but it is not a scientific concept. In reality, naturalists consider as “nature” everythinh consistent with their view of reality. Let me make an example. At present, a physicist would probably consider “nature” anything he can explain with what is known to him, that is the 3-4 fundamental forces and the current models for big bang etc. Anything unexplainable that way would be rejected or considered just something which will be explained in the future, but always according to what is known now.
    Only a minority of scientists usually accept the prospect that their understanding of reality could be easily and completely changed, that a scientific revolution could happen any moment.

    That’s a very important point. ID is not about proving God. It is about proving that our present understanding of a reality that we observe daily, that is biological beings, is indeed beyod all present mechanical explanations. That means that not only God could well be a fundamental part of nature, but also that all our understanding of nature could be revolutioned.

    I have said many times on this blog that, in my opinion, ID is a door open towards many fundamental problems in our present scientific understanding of reality. ID brings strongly into discussion the “problems” (you may call them Mysteries, if you prefer) of consciousness, of life, of intelligence, of the relationship between spirit and matter, of the mystery of matter itself, of the nature of freedom and creativity, of the meaning of meaning. All these themes are indeed elated, and all of them are related to the problem of life. It is not by chance that Denyse O’ Leary, one of the main supporters of ID, has a parallel blog against the so called “naturalistic” explanation of consciousness in neurosciences: the theory of strong Artificial Intelligence, indeed, is the perfect companion of darwinian evolution in the squalid defeat of rationality in the last 50 years of human thought.
    As a person interested to the complex interreletions between science, philosophy and religion, you should perhaps understand that what is at stake here is much more than a simple “role” of one kind or another for a Creator. Here we are discussing a whole conception of reality. So called atheistic materialists, like Dawkins and co., are supporting a vision of reality which has the merit of being consistent, and none other. For the rest, it is irrational, simplistic, disappointing, completely detached from any perception of reality, and if people could understand it really, they would run away orrified.
    Such an ideology denies (and I mean denies) the existence of consiousness, of free will, of purpose, of meaning, and tolerates the concept of life only if defined in terms of its support to the darwinian theory. It is inhuman, it is ugly, it is boring. There is nothing in it. But, at least, it is consistent. More or less.

    But theistic evolutionists, people like Ken Miller and, perhaps, you, those are really a mystery to me. What do they mean? What is their view of life? Do you realli think that your hands typing can be explained in two different ways, one purely mechanical and purposeless, rigidly defined by physical laws, and the other spiritual, pertaining to intentions and consciousness and perceptions and meaning? Do you really believe that?
    Do you really believe (like Dawkins) that the display of intelligence, beauty, function, meaning, creativity, originality, love for diversity, and so on, which we daily observe in the living world is the result of blind, mechanical forces, and yet (unlike Dawkins), that those mechanical forces were designed by an intelligent God so that all those things could be obtained by themselves? Do you believe that consciousness is abyproduct of the physial activity of the brain, and yet that we have something called soul in some unknown part of all that?
    Naturalism is not science. It is a poor caricature of science. It is the arrogant assumption, always so frquent among conformist people of all times, that we understand all, at least in principle, and that we only need to “develop” and apply what we already know. It reduces science to a dull application of known rules, to a boring lab activity.
    The great advancements of science in the first half of the twentieth century were not due to costly experimentation, although experiments certainly have their role. Einstein, Plank, Bohr, Schroedinger, Dirac and others have developed a view of reality which was not only new, but totally unpredictable. Today, with the unknown entities of dark matter and dark energy to rule the field of our view of the universe, physics is facing a new, fundamental challenge. Shall we find our Einsteins and Bohrs?

    And biology? Biology is at present the worst of sciences, in the sense that it has the sad primate of witnessing perhaps the biggest advancements in the collection of astounding data, practically daily, and of defending at the same time the oldest, the most stupid, and the most irrational of scientific ideologies: darwinian evolution and strict materialism-determinism.

    No, ID is not about proving God. God has no need of being proved that way, there are other and better ways for that. Id is about us, human beings searching a scientific comprehension that, although it may be essentialy limited, deserves better treatment and more sincere pursuit.

  47. Someone accuses someone else of “engaging in insulting rhetoric” and then goes on to say about that someone else,

    You sound very much like me in my teenage years – certain you are right, with no room for anyone, even God, to get through to you and teach you something.

    Looks like the pot calling the kettle black to me.

    You know what, ReligionProf? I sincerely do wish you well. Too bad that you, a religious scholar and a professed Christian of the Baptist persuasion, can’t do the same for me.

    But leaving all that aside, you wrote:

    My principle concern is when [the intelligent design inference] is used as a justification for asserting knowledge (i.e. that something was produced through intelligent agency) where admitting ignorance (i.e. we don’t at present know how something came about) would seem more appropriate. The idea that the eye could evolve was once thought ludicrous. Now it can be shown to be plausible.

    You know all that stuff you read in the papers about how scientists have shown, say, that drinking coffee causes pancreatic cancer? These researchers come to their conclusions probabilistically. That is, they look for statistically significant results. P

  48. cont. (technical difficulties)

    P is less than 0.1 gets no one interested. It means there’s a 10% chance that the result is due to chance. P is less than 0.05 is getting sort of interesting but P is less than 0.001 is very interesting indeed. Such a result is always considered highly significant.

    If you’d read and understood anything much of Dr Dembski’s work on detecting intelligent design you would realise that he is talking about probabilities that are so very, very, very, very much smaller than 1 in 1,000 that there is, indeed, justification for asserting knowledge. Appealing to ignorance in those circumstances is not appropriate in the slightest. To do so would be next door to either crazy or stupid.

    As for the idea being shown to be plausible that the eye could evolve, do let us all know who has accomplished this amazing feat. Better still, please give us a link to a page in which this person has argued his or her case. I do hope there’s more to the argument than the same old talk of light sensitive cells and dermal cupping.

  49. My principle concern is when this is used as a justification for asserting knowledge (i.e. that something was produced through intelligent agency) where admitting ignorance (i.e. we don’t at present know how something came about) would seem more appropriate.

    If we don’t know then there is no reason to push the blind watchmaker and reject ID.

    The idea that the eye could evolve was once thought ludicrous. Now it can be shown to be plausible.

    Only the gullible believe that.

    How do we know at what point we are dealing with something inexplicable in naturalistic terms, as opposed to merely as yet unexplained?

    We make the best inference given the data, evidence and observations. And yes, as with all inferences, future knowledge can either confirm or refute it.

    I do not find the appearance of irreducible complexity a persuasive basis, because it has proved an inaccurate guide in the past (see the eye, again) and does not appear to me to be as readily quantifiable as Dembski’s work maintains.

    But you are mistaken about the eye/ vision system.

    My own view is that once one is dealing with intervention by a personal agent (whether human or supernatural), one is not doing science in the traditional sense.

    Umm archaeology is all about intervention. Is archeaology not science in the traditional sense?

    What is the option- that is in the absence of ID or special creation? It is nothing more than the science-stopping sheer dumb luck.

    Is that how your “God” does things?

  50. I don’t want to get into the name-calling implicit in suggesting that most evolutionary biologists and other educated people are ‘gullible’ – suggesting that there is an evil, worldwide conspiracy that I once thought was plausible, but now no longer do.

    I’ve responded to Janice’s allusion to ‘millstones’ on my blog – I think it is an important point, but I do not feel that it is appropriate to pursue that conversation further here. If she is so inclined she is welcome to go to http://exploringourmatrix.blog.....locks.html and say anything she wants to about my views and about me personally.

  51. I don’t want to get into the name-calling implicit in suggesting that most evolutionary biologists and other educated people are ‘gullible’ – suggesting that there is an evil, worldwide conspiracy that I once thought was plausible, but now no longer do.

    Name calling aside- there isn’t any data, evidence or observations that demonstrate the eye/ vision system could evolve. Nevermind evolve via culled genetic accidents.

    Therefore anyone who says there is would be either ignorant or a liar.

  52. So am I correct in thinking that you believe most biologists to be ignorant, or liars, or both?

  53. ReligionProf

    So am I correct in thinking that you believe most biologists to be ignorant, or liars, or both?

    I believe they are clinging to the modern synthesis due to an unreasonable faith that time and chance works miracles. I’d just as soon not call people ignorant or liars just because I think their faith doesn’t have a solid grounding in reality. I don’t believe in miracles. I believe in the laws of physics and statistical probabilities.

  54. gpuccio #46

    Bravo!

  55. So am I correct in thinking that you believe most biologists to be ignorant, or liars, or both?

    What biologists have stated that there is is data, evidence and/ or observations that demonstrate that the eye/ vision system has evolved?

    And what is that data, evidence and/ or observation?

    I have heard the claim (that the eye/ vision system has evolved) but that is about it. IOW no one has ever substantiated that claim.

    Most biologists are specialists who rely on other specialists for the data in which they are not a first-hand researcher. So ignorance is a definite possibility.

    Most of the theory of evolution and UCD is based on ignorance. That is just a fact.

  56. ReligionProf,

    There have been several biologist who have posted here and not one has ever been able to provide any evidence of support for Darwin’s ideas other than the trivial. We ask all the time they come but they never can answer.

    So are they liars or ignorant? Or something else. On your site you indicate there is a continuous stream of research supporting evolution. Maybe you should try to to present some of the conclusions of this research here and see if we are ignorant or liars or something else. My guess is that you will start to learn something and have your eyes opened.

    You are a professor at Butler, bring anyone from their biology department to assist you. It will be a positive exercise for everyone. My guess is that they will all have better things to do than to try and debate ID.

  57. When I read the Proceedings of the National Academy of Sciences, for example, I do not get the impression from the many papers related to evolution that those working in that aspect of biology are either ignorant themselves or are promoting ignorance. I think one can only have this impression if one exclusively reads books promoting either intelligent design or young earth creationism. Reading books by major biologists (for instance I’d highly recommend Sean Carroll’s recent books on evolutionary developmental biology, or evo-devo for short) one doesn’t get the impression that they are ignorant, but quite the opposite.

    DaveScot: Presumably you are one of the few people on this forum who attributes intelligent design to aliens or time travellers? If you attribute it to a deity, wouldn’t that involve believing a miracle occurred?

  58. ReligionProf:

    probably it’s not worthwhile continuing to comment about what you write, considering also the general tone of what you go on writing on your blog.

    Anyway, just not to leave important things unsaid:

    1) You say:

    “So am I correct in thinking that you believe most biologists to be ignorant, or liars, or both?”

    Again, it seems that your main argument is conformism. Why are you so sure that the majority of biologist should be right? Are you aware of what the majority of scientists believed at the times of Galileo, just to make an example? Or do you think that science, today, has become absolute knowledge, that it cannot be wrong? Have you ever been interested in the philosophy of science? Have you ever heard of people like Kuhn, Polanyi, Feyerabend?

    Maybe most biologists are not ignorant or liars. I think, anyway, that most biologists have never seriously addressed the problem of the real validity of the general theories they have been trained to accept, like darwinian evolution. In the history of science, the modeling of general theories is usually addressed by a few, not by the general category. In that sense, most biologists are not ignorant (of their personal field of work) or liars, they are just passive and conformist in relation to the general theories underlying their work. That’s not such a strange thing to conceive, it happens in all fields of knowledge.
    The few biologists who are actively working at the modeling and at the defense of the general theory of evolution, the Dawkins and Millers and so on, are probably:

    a) ignorant of the true arguments of their counterpart, that is ID

    b) ideologically motivated, and unfairly partial to the established view, and therefore:

    c) in many cases, liars.

    I hope that’s clear enough for you.

    2) You say:

    “I do not find the appearance of irreducible complexity a persuasive basis, because it has proved an inaccurate guide in the past (see the eye, again)”

    Just to be clear, the eye “is” irreducibly complex, many times irreducibly complex, and no one has ever shown how it could evolve by darwinian pathways. You go on saying that it has been done, but that’s a (maybe unconscious) lie. In his work about irreducible complexity, Behe has always made it clear that any attempt to prove that an irreducibly complex structure can really evolve by darwinian procedures must:

    a) give a credible step by step pathway which can explain how the structure was gradually built, at the biochemical level (not at the cartoon level of gross morphological homologies)

    b) explain how each step could be selected, against the huge improbabilities of pure random search.

    If you know of anyone who has only attempted to do something of that kind for the eye, please let us know. They have attempted to do that for the flagellum, recurring to forced homologies and to fairy tales of cooption. You see, those are lies, gross, political, conscious lies, for which there is no excuse.

    The problem is:

    a) Darwin had expressed some doubts about the possibility of explaining such a complex organ as the eye by step by step methods, and so it was necessary that somebody created a gross fairy tale about light sensitive spots evolving into eyes, just to ease the general conscience.

    b) Behe has shown that there are many, many irreducibly complex structures in biology, and has cited the bacterial flagellum as a good example (just one of the many). So, it was necessary that somebody tried to create a fairy tale explanation of how the flagellum could arise.

    So, in a sense, ID can be criticized: it seems to daily inspire, and is therefore indirectly responsible of, the worst darwinian lies.

  59. ReligionProf

    Presumably you are one of the few people on this forum who attributes intelligent design to aliens or time travellers? If you attribute it to a deity, wouldn’t that involve believing a miracle occurred?

    All I can do is take the evidence available and use it to bound a set of possibilities. As far as I can determine the creation of organic life takes sophisticated but wholly material expertise in biochemistry. This capability is not unlike present human expertise in biochemistry – just more of it. That establishes a lower capability bound so yes, an alien civilization on the order of human civilization is a distinct possibility.

    The upper bound is of course some entity which can create an entire universe and exists outside it. Science has no means and no clue where to start in characterizing anything that exists outside the observable universe so that seems to be a dead end – there’s an impenetrable brick wall beyond which we can’t see.

    It seems to me the entire universe was designed by something but it’s not amenable to scientific investigation so I don’t bother much with cosmological ID. The alternative to a designed universe is the so-called infinite multi-verse but that leads to so many absurdities like Boltzmann Brains that it just doesn’t pass the giggle test.

    Time travel is not possible under our current understanding of the laws of nature so I don’t include that as a possibility. The speed of light is another law of nature which places a bound on any possible designers – it or they must be physically located such that they can or could have had causal connection with the earth.

    I focus on biological ID because that IS amenable to further scientific investigation. I have high hopes that comparative genomics will provide enough data to make some reasonable inferences as to if, when, and where intelligent agency was involved in the evolution of organic life. My hunch is that we’ll find life already had the complexity to produce the diversity we see today as far back in time as we can go. This is congruent with the hypothesis called “Directed Panspermia” which was perhaps most famously described by Francis Crick and Leslie Orgel in the 1970′s.

    From Francis Crick Remembered

    Crick and Orgel wrote in their book ‘Life Itself,’ “an honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.”

    In the intervening 30 years our available knowledge has increased and all it does is make the origin of life appear even more miraculous. Life is vastly more complex than Crick and Orgel knew about it back then. A reasonable definition of “miracle” is anything which is so improbable under our understanding of statistical mechanics that we shouldn’t ever observe it in a finite universe. That said, intelligent agency routinely does things that are, while not violoating any laws of physics, virtually impossible via time and chance and the laws of nature acting alone. A space shuttle or a computer or a Shakespearian play coming into existence without intelligence agency is practically impossible in a finite universe yet when intelligence gets involved such things become commonplace and wholly unmiraculous.

  60. ReligionProf,

    I have read Sean Carroll’s two books on evo devo and Darwin’s ideas and I will repeat. There is nothing in them that supports Darwin’s ideas that isn’t trivial. Where is the meat? He provides none and he is a major spokesperson for evolution so what can we expect from your average biologist?

    The terms liars, ignorant have come up. Let me apply it to Sean Carroll. What is the title of the Introduction to Sean Carroll’s book, “The Making of the Fittest?” This section of his book is titled “Beyond Any Reasonable Doubt” and it is about DNA testing. Is is about showing how species evolved over time. No it is about how DNA testing of criminals have shown that certain criminals were guilty or not guilty of certain crimes. Now I ask you why does that lead off his book on evolution and with the chapter title he gives it. Is that lying or ignorant? Why did he choose to do it?

    By the way I personally think YEC science is nonsense and have no time for it so that stereotype will not work with a lot of us here. Yes, there are a lot of YEC’s involved in ID but there are many who are not and will constantly be a check of YEC claims. So don’t assume that playing the YEC card is your way out of a rigorous understandig of evolutionary processes.

  61. I don’t think it is a card to play in the way you suggest. I simply provided some autobiographical background to my own perspective. But I would point out that the same perception you have of YEC, other scientists have of you and ID. This is one reason why the self-congratulatory use of “obvious” on this forum seems to me dishonest – I for one would not be comfortable claiming that some idiosyncratic result of my research in my own field should be obvious to everyone and that its failure to gain acceptance is because everyone else is stubborn, hard-hearted, dishonest, or misinformed. If I want to change a paradigm in my field, the way to do it is to do research, present papers at conferences, and publish articles and books, and attempt to persuade my colleagues and work together to explore the issue further. The discussion here leaves me feeling that even Biblical studies, which is placed firmly in the humanities, can be more scientific than ID in this regard.

  62. When I read the Proceedings of the National Academy of Sciences, for example, I do not get the impression from the many papers related to evolution that those working in that aspect of biology are either ignorant themselves or are promoting ignorance.

    Do any of those papers deal with the evolution of the eye/ vision system?

    Or are they basically dealing with small scale changes, like the beak of the finch, antibiotic resistance, and othger variations that arise in a population?

    Reading books by major biologists (for instance I’d highly recommend Sean Carroll’s recent books on evolutionary developmental biology, or evo-devo for short) one doesn’t get the impression that they are ignorant, but quite the opposite.

    I have read his latest two books. They are filled with wishful thinking and speculation based on an (untestable) assumption.

    Back to the eye/ vision system- I would say the data, evidence and/ or observation that the eye/ vision system evolved is the same now as it was back in Darwin’s day- That is we observe organisms with differing levels of a vision system- from the light sensitive spot on some single-celled organisms to the human eye/ vision system- and say there is the evidence which shows they evolved- meaning the differing levels of systems are evidence for their evolution.

    Complete trash. But the gullible buy it so it is recycled…

  63. ReligionProf,

    Did you know that all current eyes were present in the Cambrian Explosion, 520 million years ago and none present just a few short million years before.

    Also no new eyes have evolved since then. So eyes come out of nowhere and then go no further. Not a particularly Darwinian idea.

    The series of drawings by Nilsson and Pelger that is often used to justify a gradual evolving of the eye is based on a computer model and in no way mimics anything seen in the real world. Anyone with a good command of Adobe Illustrator could develop similar drawings and then claim it all could happen by small incremental changes. These are called “just so” stories and were a staple of Darwin himself to show how evolution could occur. The only problem with these stories is there never has been any empirical evidence that any occurred.

    So why the sudden appearance of different types of eyes so long ago and no new variations since. Who are the liars and the ignorant? We ask you to show us that ID supporters are either.

  64. Jerry:

    No it is about how DNA testing of criminals have shown that certain criminals were guilty or not guilty of certain crimes.

    Equivocation*- If we can track people via DNA then if chimps and humans have similar DNA we can track both populations back to a common ancestor.

    Another bit of bait for the gullible…

    (*the theory of evolution relies heavily on equivocation, ie because we see slight variations the major transitions are also explained)

  65. Speaking of the eye:

    http://www.nature.com/nature/j.....06105.html

    Discusses it in the context of digital sampling and the Nyquist limit, analog-to-digital conversion, millisecond precision, combinatorial code representation of 4-D signals, motion pictures, image processing, neuronal and genetic codes, etc.

  66. ReligionProf,

    Interesting that what you picked up in my comment was the mention of YEC and you passed over my criticisms of Sean Carroll. That by itself is revealing when we are talking about support for Darwinian evolutionary theory. You wander off to a peripheral point.

    Please provide us with some concrete examples based on science that ID is wrong on as opposed to saying practicing scientists disagree with ID. What specifically do they disagree with? You already admitted that ID and YEC are different so criticism has to be based on what ID alone espouses and have no relation to YEC.

    You offered Sean Carroll and we are willing to discuss any claim he has made. Go to his two books and bring up his claims and we can have a discussion. Have any biologist of your choosing help you with the task. We welcome it. Why don’t you?

    You can then be the judge whether we are more honest and knowledgeable or your experts are. Don’t resort to arguments from authority. Would you have accepted arguments from authority about religion in the early 1500′s.

    The arguments about publishing is nonsense. Follow what has just happened at Baylor to see if you think publishing is all that easy or if it isn’t being actively inhibited. Do you believe ID has obstacles for publication that have nothing to do with the scientific merit? Or are we all just paranoid here?

  67. Thank you, Patrick, for the very interesting link about the eye. I am sure that a lot of darwinist papers can precisely explain how such complex integrations and functions have evolved…

    ReligionProf (again):

    “If I want to change a paradigm in my field, the way to do it is to do research, present papers at conferences, and publish articles and books, and attempt to persuade my colleagues and work together to explore the issue further”

    I have already commented (but you have not answered) about research and publications. Again, you seem to not understand that the issue, here, is not to do specific research in favour of ID (which could anyway be done, if and when the necessary resources will be made available by the prevailing lobby), but rather to correct the false interpretation of the existing data by the general scientific culture. A lot of data already show that ID is right and darwinism is wrong. The problem is not, as you suggest on your blog, that we IDist are imagining a conspiracy. The problem is that we have been trying, as you say, to “attempt to persuade my colleagues and work together to explore the issue further”, and the reaction by the official academy has grown ever more intolerant and dogmatic as the ID arguments became more precise and scientific. That’s a truth that you (or anybody else) have not to accept as “obvious”, but which can be debated in the least details (and has been debated many times, here and elsewhere). But the results? Have you ever read Pharyngula? Have you ever read (and tried to understand) the gross objections to Behe’s and Dembski’s patient arguments, by most biologists? Have you ever read (and tried to understand) what you have been reading in your blog? This is not a conspiracy, it is only a feast of intolerance, superficiality and arrogance. And a desperate defense of what cannot be defended.
    So, before writing again on your blog of typewriters, of probabilities, of DNA bases and similar, or before hiding behind the obstentation of supposed demonstrations of the evolution of the eye which have never been given, I ask you: can you meet a serious discussion about probabilities, random searches, and the meaning of information in biological structures? Can you address in a credible way Dembski’s extremely detailed arguments? Have you read Dembski’s and Marks’ papers (yes, exactly those censored on the Baylor site) demonstrating that evolutionary algorithms used in darwinian simulations are a fraud? Isn’t that research? Isn’t that discussion? And what has been the answer from the other side?

    Let’s not speak of conspiracy. A conspiracy requires intelligence, organization, secrecy. Here we can only see a public display of brute force, of obstination in ignorance, and of self-evident arrogance.

  68. ReligionProf:

    The discussion here leaves me feeling that even Biblical studies, which is placed firmly in the humanities, can be more scientific than ID in this regard.

    As a Biblical studies student I can say without reservation that the fantastic probabilities needed to believe in evolution are no where near the likelihoods used in Biblical studies. For example, the estimate of the date for the writing of the gospel of John is less than 1/200. On the other hand, the likelihood of a living cell forming from pre-biotic molecules is as near to zero as can be calculated. If ID should be placed in the humanities, then evolution must be placed in the department of fictional writing.

  69. Peter – I thought John had written his book before January 200AD. :-)

    Bob

  70. Religion Prof

    “I am persuaded that most Christians today are willing to accept scientific explanations of phenomena that were in the past attributed to God and otherwise inexplicable.”

    I think it would be true of all Christians that they would attribute both all scientific and all miraculous phenomena directly or indirectly to God. For in Him all things hold together.

    There is a common line taken by TEs that Christian ID proponents argue the world is divided into things that God made, and things that made themselves. I do not think that is how we see it. I think we say that extra information, outside fundamental created laws, is necessary for the generation of some observable phenomena. We would also say that this information has not been demonstrated yet to be intrinsic to the cosmic matrix. If it is found in the cosmic matrix, it will simply confirm one model of ID, the fully enabled model.

    It does seem evident that many on the other side (TE) seem to believe that God must by definition be invisible to scientific observation.

    Should we be defining what God must and mustn’t be? Should we not rather build up a picture by observation and interpretation of data?

    I think that the fingerprints of God are easily visible in the maths and physics / chemistry of the cosmos. There is not much room for doubt there. Either there are infinite universes or ours is designed.

    As for biology, there is either a way for unguided physical forces to generate life or there is not. So far there is no scientific theory for the origin of life. There is an open $US1million prize to be claimed if you have one. Dawkins believes and has stated repeatedly that life came from luck. ID argues that the evidence points to a designing intelligence.

    Assuming an origin for life (luck or ID) with DNA/RNA proteins in working order, we may then believe in the Dawkins extension of luck myth, to help us make sense of life or believe in a more grand, extension of ID myth.

    We then explore and interact with reality, and experience either the transformation of myth into a working hypothesis, or we find another myth and start again.

    Dawkins has cemented his myth. He is no longer asking questions. He only builds on what he knows to be true.

    Christians should always ask questions because we believe there is a real God behind the mist, who says He wants to be known.

    Thanks for your many thought provoking comments. The fact that you are still here means that you are respectful of a search for truth and that you are saying things that need to be said. This blog is generally not open to those who themselves are not open.

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