Design inference Intelligent Design

How long should we believe the prophet Matheson?

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Jonathan Witt
Jonathan Witt

So says Jonathan Witt:

Historical scientists proceed like a detective at a crime scene. They begin by identifying one or more causes “now in operation” that seem capable of producing the mystery under investigation. Then they accumulate additional clues in order to narrow the field of viable explanations. If all goes well, patient study will narrow the options until only one viable cause is left standing. So, for instance, careful study of a large Arizona crater and various natural processes convinced geologists that an ancient meteor left the crater. Other explanations were ruled out while the crater explanation grew stronger and stronger the longer they studied the scene. A meteor, as it turned out, was the only type of cause with the demonstrated ability to cause the mystery in question. This mode of reasoning, common to the historical sciences, has been described by philosophers of science as inference to the best explanation (IBE).

Now think of the sophisticated digital information found in DNA. Even a microscopic, single-celled organism is loaded with this data. How did all this information first arise? A broad and intensive exploration over many decades has uncovered only one type of cause active in the present with the demonstrated ability to generate new information: mind. That is, creative intelligence.

Of course, the design argument described above is controversial, but not every part of it. In a public debate at Biola University in California, an old Discovery Institute colleague of mine, philosopher of science Stephen Meyer, laid out that argument, and biologist and intelligent design skeptic Steve Matheson actually agreed with him — up to a point. “You said that we reason backwards from what we know works, which is that intelligence makes codes,” Matheson said. “I’ll agree with that. … We reason back and say, therefore, this is the one explanation we know that can do this. I buy that. I get it.”

But then Matheson demurred: “Everywhere I look, and every time I look, if I wait long enough, there is a natural and even materialistic explanation to things.” This strong historical trend, he insisted, decisively counsels against swallowing Meyer’s intelligent design explanation. More.

Okay sure. But for how long?

At a less sophisticated level than Witt’s, Matheson’s remark remind one of an all-too-frequent situation in the life around us:

An explanation is regularly trotted out to explain something odd. Sudden, unexplained disappearances, perhaps of cash from the till, or people from the neighbourhood… are explained away as random, unrelated events.

Certain assumptions about what is happening are socially risky, so we don’t make them—or at least don’t make them public (like “religion,” they belong to a fully private sphere).

The disappearances continue. A complex pattern emerges. We try to talk about it, but are warned of the social and career implications.

A movement starts, to make sure that the growing private knowledge is not to be shared, lest it become general knowledge in venues where it could be studied.

Much is at stake. The Big Idea—that the complex, specified pattern is random effects—is the single greatest idea anyone ever had. It can withstand any amount of contrary evidence!

At that point, some of us grow restless…

How much contrary evidence are we expected to ignore? How much must accumulate before we are justified in looking for other accounts of the matter?

A great prophet arises to tell us … essentially, continue to ignore everything!

Because, he says, “Everywhere I look, and every time I look, if I wait long enough, there is a natural and even materialistic explanation to things.”

File:A small cup of coffee.JPG A thought forms: Hey, wait a minute. If that guy were just plain fooling himself, he’d be saying the same things…

As the contrary evidence mounts, we had maybe better do some thinking for ourselves, whatever the social or career costs.

See also: What the fossils told us in their own words (Quit talking at us and listen for once.)

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28 Replies to “How long should we believe the prophet Matheson?

  1. 1
    NickMatzke_UD says:

    Now think of the sophisticated digital information found in DNA. Even a microscopic, single-celled organism is loaded with this data. How did all this information first arise? A broad and intensive exploration over many decades has uncovered only one type of cause active in the present with the demonstrated ability to generate new information: mind. That is, creative intelligence.

    That’s just false. Gene duplication and subsequent modification by mutation and selection can also generate new information. There is abundant, massive, overwhelming, ubiquitous evidence for this explanation. Even Behe and Berlinski accept that it occurs and is a reasonable explanation for at least some new genes. Therefore, there are more causes of new information than just intelligence, and therefore the Meyer/Witt argument, as they themselves have constructed it, falls to pieces.

  2. 2
    Mung says:

    Nick seems to think you can take one book and make a copy of it and turn it into a different book by gradually altering the letters and sequences.

    Didn’t Berlinski already show that idea is utterly absurd?

  3. 3
    bornagain says:

    Dr. Matzke claims:

    “There is abundant, massive, overwhelming, ubiquitous evidence for this explanation.”

    And not so surprisingly, since it is characteristic of Matzke, that claim is all bluff and bluster:

    Hopeless Matzke – David Berlinski & Tyler Hampton August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

    A short history of Matzke’s literature bluffing
    http://www.uncommondescent.com.....ent-589458

  4. 4
    johnnyb says:

    Nick – you continue to mix up design and material continuity, presuming one negates the other.

  5. 5
    scordova says:

    Believe Matheson as an honest Christian Darwinist Professor at a Christian college right up until he’s caught cheating on his wife with an undergrad and then humiliated by the administration and dragged around the city news wires by Fox News:

    http://www.uncommondescent.com.....my-bishop/

    FOX 17 received a letter from the college Monday that was sent out to the student body late last week.

    According to the letter, allegations of a relationship came to light this past may, when a student revealed to the Provost’s office that Professor Steve Matheson had a sexual relationship with her.

    Calvin College initiated an internal review and investigation, and put a special task force together to handle such situations.

    The task force will aim to educate students on how to prevent and properly address allegations of sexual harassment.

    In the letter, the college says “We are deeply grieved by this news. We want to believe that such behavior doesn’t occur in a Christian community such as ours, but it can. On behalf of the college, we are very sorry that this took place here.”

    He portrayed himself as a Christian professor at a Christian college, defending Darwin’s “science”.

    Steve Matheson, Liar for Darwin. He posted a lot at Larry Moran’s blog. Larry and friends loved him.

  6. 6
    bornagain says:

    Of related note:

    Evolutionists: Give Us Your Best Shot – Dec. 2, 2015
    Excerpt: About 70% of our genes trace their ancestry back to the acorn worm,,,
    It’s an early deuterostome (a fancy word meaning two holes—mouth and anus).,,,
    Nature’s last comment revealing lack of evolution over 500 million years:
    “The conservation of so many features across deuterostome genomes, which is brought into sharp focus with Simakov and colleagues’ addition of hemichordate genome sequences, reinforces the fact that radical morphological changes are not necessarily related to radical changes in genomes. This fact will shape the search for which of the variable features of deuterostome genomes are responsible for the great diversity we see across the group.”
    http://crev.info/2015/12/evolution-best-shot/

    Perhaps they should read “Darwin’s Doubt”?

    “These different sources of epigenetic information in embryonic cells pose an enormous challenge to the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops—for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand.”
    Stephen Meyer – Darwin’s Doubt (p. 281)

    Darwin’s Doubt narrated by Paul Giem – The Origin of Body Plans – video
    http://www.youtube.com/watch?l.....page#t=290

    Body Plans Are Not Mapped-Out by the DNA – Jonathan Wells – video
    http://www.youtube.com/watch?v=meR8Hk5q_EM

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

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

  7. 7
    mahuna says:

    Peace & joy. We are on a voyage of discovery, and our goal is Truth. And every time we discover a new Truth, we write it down very carefully and clearly so we don’t lose it.

    I can accept that the Materialists are arguing about Certainty of a Theory such as Intelligent Design. And what none of the ID proponents are claiming is air-tight, 100% Certainty.

    In studies of human activities under the label History, Historians are constantly presented with conflicting details about undisputed historical events (e.g., the death of JFK). But the WHY and HOW get fuzzy, and so individual Historians choose to find certain facts and claims convincing while other, equally competent Historians denounce those same facts and claims as lies or misinterpretations.

    I find ID to be a more convincing explanation for life on Earth than Evolution. But where should we peg Certainty? 90%? 10%? 66.67%??

    I’m guessing that Evolution has fallen from 75% Certainty in 1900 CE to probably less than 10% today because of the MANY things (Stasis, sudden appearance of whales and bats, etc., etc.) we now know that conflict with all previous understanding of what The Theory of Evolution predicts.

    But there remains the chance that some new Discovery will rescue Evolution from the Dustbin of History. And so we should be having a polite but spirited conversation about how much is Certain and how much of what we know is still Interpretation.

  8. 8
    Steve says:

    Nick Matzke,

    Get a grip. Gene duplication, mutation, and selection cannot be explained by non-teleological step wise change.

    You (pl) always, always require the co-option of designed objects to kick start any NTSWC argument.

    How does KF say it? You can do better….Sir!

    That’s just false. Gene duplication and subsequent modification by mutation and selection can also generate new information. There is abundant, massive, overwhelming, ubiquitous evidence for this explanation. Even Behe and Berlinski accept that it occurs and is a reasonable explanation for at least some new genes. Therefore, there are more causes of new information than just intelligence, and therefore the Meyer/Witt argument, as they themselves have constructed it, falls to pieces.

  9. 9
    Andre says:

    Nick Matzke believes that mud not only made itself but it also magically became alive and if you disagree with him he’ll bully you into submission.

  10. 10
    bornagain says:

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

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

    Michael Behe – Observed Limits of Evolution – video – Lecture delivered in April 2015 at Colorado School of Mines
    25:56 minute quote – “This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not.”
    27:50 minute mark: no known, or unknown, evolutionary process helped.
    https://www.youtube.com/watch?v=9svV8wNUqvA

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

  11. 11
    bornagain says:

    Whereas no one has ever witnessed unguided material processes creating new functional complexity, on the other hand, intelligence just did this:

    Engineers build biologically powered chip – December 7, 2015
    Excerpt: Columbia Engineering researchers have, for the first time, harnessed the molecular machinery of living systems to power an integrated circuit from adenosine triphosphate (ATP), the energy currency of life.
    http://phys.org/news/2015-12-b.....-chip.html

  12. 12
    tjguy says:

    “I’ll agree with that. … We reason back and say, therefore, this is the one explanation we know that can do this. I buy that. I get it.”

    VERY Encouraging!

    It seems then that he, if he is honest, must allow this explanation on the table as a possible explanation. He may have faith based on past experience, that some day we will come up with a “plausible explanation”, but IDers already have a plausible explanation for it.

    So, is Matheson willing to allow the ID hypothesis to be entertained as a possible explanation, especially in light of the fact that there is no naturalistic explanation?

    ID seems to me to the the IBE here(best inferred explanation).

    Again, at least Matheson should surely be willing to admit that of all the possible explanations on the table now, the ID explanation makes the most sense!

  13. 13
    Virgil Cain says:

    Matzke:

    Gene duplication and subsequent modification by mutation and selection can also generate new information.

    And yet you cannot say such a thing is a blind watchmaker process. It’s as if you are willfully ignorant over what is being debated.

    Tell us Nick Matzke, why do you think your ignorance is an argument?

  14. 14
    REW says:

    Are you guys saying that Behe, Berlinski and Matzke are wrong when they say that gene duplication and divergence generates new information in the genome?
    One copy of Tolstoy’s War and Peace has the same information content as 2 copies, on the other hand it seems pretty obvious to me that merely duplicating a gene changes the overall information content of the genome- to say nothing of subsequent divergence.

  15. 15
    Virgil Cain says:

    REW:

    Are you guys saying that Behe, Berlinski and Matzke are wrong when they say that gene duplication and divergence generates new information in the genome?

    If gene duplications are designed, ie a design mechanism, then they do not add information to the system as that information was already there.

  16. 16
    REW says:

    VirgilCain,

    If gene duplications are designed, ie a design mechanism, .

    The mechanisms that lead to gene duplication are well understood. This process happens all the time in all of our cells.

    then they do not add information to the system as that information was already there.

    So you’re saying that merely duplicating a gene doesn’t add new information as in my War and Peace example above? If that were true then duplicating a gene should have no effect on the cell…do you agree?

  17. 17
    bornagain says:

    “it seems pretty obvious to me that merely duplicating a gene changes the overall information content of the genome- to say nothing of subsequent divergence.

    Which is all fine and well since there is really nothing further that can be said of ‘subsequent divergence’ since ‘subsequent divergence’ is basically just minor variations on the same theme.

    Hopeless Matzke – David Berlinski & Tyler Hampton August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

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

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

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

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

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

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

  18. 18
    bornagain says:

    The regulatory utilization of genetic redundancy through responsive backup circuits – 2006
    Excerpt: Duplicate genes and paralogous gene families long have been perceived as genomic sources of genetics robustness (1–5). The assumption is that a functional overlap of these genes acts to compensate against mutations. Yet, this very fact also renders redundancy evolutionarily instable (5, 6), and functional overlaps, typically, are rapidly lost because of divergence (7).
    Nevertheless, numerous examples of paralogs retaining their functional overlap for extended evolutionary periods (for examples, see refs. 6 and 8–12) suggest that, at least for a fraction of gene pairs, redundancies are conserved throughout evolution despite their predicted instability.,,, In fact, although retention of redundancy is much less frequent than its loss, its widespread existence is nontrivial and cannot (6) be dismissed as leftovers of recent duplication events.,,,
    the paradigm that has emerged is that genes that are functionally redundant are not often independently controlled but rather they are regulated by a system that both monitors and responds to their intactness.
    http://www.pnas.org/content/103/31/11653.full

    The regulatory utilization of genetic redundancy through responsive backup circuits – 2006
    Excerpt: many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. … We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation.
    http://www.pnas.org/content/103/31/11653.full

    Can Random Mutations Create New Complex Features? A Response to TalkOrigins – Casey Luskin June 22, 2012
    Excerpt: the (talkorigins) page suggests searching for “gene duplication” on PubMed to find “more than 3000 references” on the topic. These papers, we’re meant to assume, show how evolutionary mechanisms can create new information. But a survey of major review articles on gene duplication I published here on ENV in 2010 revealed that the studies never established that mutations could have produced the complex features in question. After taking a close look at this literature, I found:
    The NCSE’s (and Judge Jones’s) citation bluffs have not explained how neo-Darwinian mechanisms produce new functional biological information. Instead, the mechanisms invoked in these papers are vague and hypothetical at best:

    *exons may have been “recruited” or “donated” from other genes (and in some cases from an “unknown source”);
    *there were vague appeals to “extensive refashioning of the genome”;
    *mutations were said to cause “fortuitous juxtaposition of suitable sequences” in a gene-promoting region that therefore “did not really ‘evolve'”;
    *researchers assumed “radical change in the structure” due to “rapid, adaptive evolution” and claimed that “positive selection has played an important role in the evolution” of the gene, even though the function of the gene was unknown;
    *genes were purportedly “cobbled together from DNA of no related function (or no function at all)”;
    *the “creation” of new exons “from a unique noncoding genomic sequence that fortuitously evolved” was assumed, not demonstrated;
    *we were given alternatives that promoter regions arose from a “random genomic sequence that happens to be similar to a promoter sequence,” or that the gene arose because it was inserted by pure chance right next to a functional promoter.
    *explanations went little further than invoking “the chimeric fusion of two genes” based solely on sequence similarity;
    *when no source material is recognizable, we’re told that “genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors” because they are simply “hypermutable”;
    *we even saw “a striking case of convergent evolution” of “near-identical” proteins.

    To reiterate, in no case were the odds of these unlikely events taking place actually calculated. Incredibly, natural selection was repeatedly invoked in instances where the investigators did not know the function of the gene being studied and thus could not possibly have identified any functional advantages gained through the mutations being invoked. In the case where multiple mutational steps were involved, no tests were done of the functional viability of the alleged intermediate stages. These papers offer vague stories but not viable, plausibly demonstrated explanations for the origin of new genetic information.
    I haven’t gone through all “3000 references” cited by TalkOrigins. Neither, in all likelihood, has the author of the TalkOrigins page. But my strong suspicion is that if you went through many of those pages, you’d reach the same conclusion.
    This 3000-unnamed-paper citation bluff — and much other material on this TalkOrigins page, are not to be taken seriously.
    http://www.evolutionnews.org/2.....61221.html

    Gene Duplication and the Origin of Novel Biological Information: A Case Study of the Globins JonathanM – Oct. 2012
    Excerpt: In summary, we have seen that the scope for evolution of novel genes and proteins by virtue of gene duplication and subsequent divergence or recruitment is very limited, even in facilitating relatively trivial functional innovations. Given the extremely diverse array of protein conformations found in living systems, the likelihood of the relatedness of genes — even within gene families — may be treated with suspicion and healthy skepticism. It is somewhat ironic that biologists are all too willing to accept a statistical argument against two or more proteins with similar sequences arising independently by chance, but are completely unwilling to consider statistical arguments against them arising by chance at all.
    http://www.evolutionnews.org/2.....64971.html

  19. 19
    Virgil Cain says:

    REW:

    The mechanisms that lead to gene duplication are well understood. This process happens all the time in all of our cells.

    Nice non-sequitur. The way computer programs operate are well understood. Does that mean computer programs are unguided processes? The way that cars function is well understood, too.

    So you’re saying that merely duplicating a gene doesn’t add new information as in my War and Peace example above? If that were true then duplicating a gene should have no effect on the cell…do you agree?

    You seem unable to grasp what I posted. Look, REW, say Dawkin’s “weasel” allowed for duplications. No new information would be added as it would all be part of the program.

  20. 20
    bornagain says:

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

  21. 21
    REW says:

    The way computer programs operate are well understood. Does that mean computer programs are unguided processes?

    Of course not. Part of what we mean when we say we ‘understand something well’ is knowing the basic mechanism through which it operates. So we know computers are made by people and we know that duplications arise through TE transposition and errors in meiotic recombination (among other things). If we sequenced the whole genome of cells from various parts of your body we’d find duplications and deletions in every one of them.

    You seem unable to grasp what I posted. Look, REW, say Dawkin’s “weasel” allowed for duplications. No new information would be added as it would all be part of the program.

    I think I understand it, I just wanted to be clear. I don’t think theres any way to measure the information content of a cell but we can say with certainty that gene duplications change the information content of the cell. One copy is not the same as two copies.

  22. 22
    Virgil Cain says:

    REW:

    So we know computers are made by people and we know that duplications arise through TE transposition and errors in meiotic recombination (among other things).

    How did you determine they were errors?

    And one copy is the same as two copies if only one copy gets expressed. Two copies are worse than one copy if the both get expressed when only one is needed and the other one causes fatal cross-reactions by binding to other proteins and preventing them from binding with their proper partner.

    Just duplicating a gene does nothing unless that duplicated gene also has all of the other stuff required for it to be expressed, including being in the correct position in the DNA coil.

  23. 23
    Virgil Cain says:

    In Lenski’s LTEE the only gene that was capable of transporting citrate was duplicated and put under the control of a promoter that was on in the presence of O2, giving it an advantage in the environment it was in. That doesn’t seem like an error.

  24. 24
    Mapou says:

    Andre:

    Nick Matzke believes that mud not only made itself but it also magically became alive and if you disagree with him he’ll bully you into submission.

    Matzke is a superstitious fool. Soon, he’ll be just an old fool. His opinion on anything is worth diddly squat.

  25. 25
    REW says:

    Two copies are worse than one copy if the both get expressed when only one is needed and the other one causes fatal cross-reactions by binding to other proteins and preventing them from binding with their proper partner

    Two copies can also be better than one.

    How did you determine they were errors?

    I didn’t determine it; I’m not a scientist. During meiosis homologous chromosomes are lined up based on sequence and pieces are exchanged. If these is repetitive DNA present the chromosomes may misalign and result in one chromosome with a duplication and another with a deletion.

    In Lenski’s LTEE the only gene that was capable of transporting citrate was duplicated and put under the control of a promoter that was on in the presence of O2, giving it an advantage in the environment it was in. That doesn’t seem like an error.

    I don’t think anyone would call it an error, but they’d call it a random event (not due to meiotic recombination).
    Are you saying that you think the intelligent designer created the citrate mutation?

  26. 26
    Virgil Cain says:

    I am saying that organisms were intelligently designed to be able to adapt as much as possible. And that gene duplication is part of that ability.

  27. 27
    bornagain says:

    A Key Evidence for Evolution Involving Mobile Genetic Elements Continues to Crumble – Cornelius Hunter – July 13, 2014
    Excerpt: The biological roles of these place-jumping, repetitive elements are mysterious.
    They are largely viewed (by Darwinists) as “genomic parasites,” but in this study, researchers found the mobile DNA can provide genetic novelties recruited as certain population-unique, functional enrichments that are nonrandom and purposeful.
    “The first shocker was the sheer volume of genetic variation due to the dynamics of mobile elements, including coding and regulatory genomic regions, and the second was amount of population-specific insertions of transposable DNA elements,” Michalak said. “Roughly 50 percent of the insertions were population unique.”
    http://darwins-god.blogspot.co.....lving.html

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

    “It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works’
    James Shapiro – Evolution: A View From The 21st Century – (Page 82)

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

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

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

    Failed Darwinian Prediction – Mutations are not adaptive – Cornelius Hunter – 2015
    Excerpt: In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual.,,,
    But that assumption is now known to be false.,,,
    (References on site)
    https://sites.google.com/site/darwinspredictions/mutations-are-not-adaptive

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

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

  28. 28
    RexTugwell says:

    Regarding Behe and gene duplication:

    Darwinists like to think that genome duplication is one of the magic bullets of random mutation—it suddenly granted vast new possibilities to the genome. Yet genome duplication—a spare copy of each and every gene to play with—and a hundred million years of time seem not to have given baker’s yeast any advantage it wouldn’t otherwise have had. 15 This leads to a very important point. Randomly duplicating a single gene, or even the entire genome, does not yield new complex machinery; it only gives a copy of what was already present. Although duplicated genes can be used to trace common ancestry, neither individual gene duplications nor whole genome duplications by themselves explain novel, complex forms of life.

    Behe, Michael J. (2007-06-05). The Edge of Evolution: The Search for the Limits of Darwinism (p. 74). Free Press. Kindle Edition.

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