Home » 'Junk DNA', Books of interest » New book: Junk DNA junked … in favour of what?

New book: Junk DNA junked … in favour of what?

Jonathan Wells’ book, The Myth of Junk DNA (Discovery, 2011), is now being advertised at Amazon:

According to the modern version of Darwin’s theory, DNA contains a program for embryo development that is passed down from generation to generation; the program is implemented by proteins encoded by the DNA, and accidental DNA mutations introduce changes in those proteins that natural selection then shapes into new species, organs and body plans. When scientists discovered forty years ago that about 98% of our DNA does not encode proteins, the non-protein-coding portion was labeled “junk” and attributed to molecular accidents that have accumulated in the course of evolution.

Recent books by Richard Dawkins, Francis Collins and others have used this “junk DNA” as evidence for Darwinian evolution and evidence against intelligent design (since an intelligent designer would presumably not have filled our genome with so much garbage). But recent genome evidence shows that much of our non-protein-coding DNA performs essential biological functions.

The Myth of Junk DNA is written for a general audience by biologist Jonathan Wells, author of Icons of Evolution. Citing some of the abundant evidence from recent genome projects, the book shows that “junk DNA” is not science, but myth.

Junk DNA was one of those ideas that just had to be true. Genome mapper and NIH head Francis Collins saw it as a slam dunk for his beloved Darwinism in his first book, The Language of God, (“Darwin’s theory predicts … That is exactly what is observed”) but seems to have changed his tune in his second, The Language of Life.

I’ll be interviewing Wells on the book next week, but in the meantime, two questions occur to me: To what extent did Darwinism cause the myth to be retained longer than it otherwise would be? Given that Darwinists must now be in search of another guiding myth, any idea out there which one it will be?

Now, one prediction:

Darwinists who used to point to all the alleged junk in DNA, as Collins did, will resort – seeing anything they don’t like – to saying God wouldn’t have done it that way” implying that, unlike the rest of us, they are on familiar terms with God, and cold take over the desk themselves on his lunch break, with no interruption in service.

I thought Disney covered that one off in The Sorcerer’s Apprentice.

  • Delicious
  • Facebook
  • Reddit
  • StumbleUpon
  • Twitter
  • RSS Feed

122 Responses to New book: Junk DNA junked … in favour of what?

  1. Denyse, you’ve promised in the past to stop using the term “Darwinism” to refer to all of evolution. What happened to that promise?

    In evolutionary biology, “Darwinism” refers to those who focus on adaptation as the almost exclusive mechanism of change. They are also called adapationists.

    Those Darwinists are the ones who OPPOSE the concept of junk DNA. Dawkins is a good example.

    So you’ve got it exactly backwards and you are misleading your readers. Darwinists oppose junk DNA. Pluralists and others who have a broader view of evolutionary biology are the ones who support the concept of junk DNA.

    I’m a pluralist who promotes the importance of random genetic drift and accidental evolution. That’s perfectly consistent with junk DNA. I am not a Darwinist.

    Adaptationism (Darwinism) is NOT consistent with junk DNA. That’s why Darwinists usually reject junk DNA.

  2. 2

    Ahhh Larry, do you need a hug?

    Poor baby.

    You stand at the edge of a crater created by modern biology and whine about the confusion back at headquarters.

    Yes we all know you’ve had an bone with the adaptationist issue for a while – but to piss and moan about labels?

    It’s like you’ve gone to the Darwinist shopping mall and are walking around in one of those t-shirts with the big arrow on it that says “I’m with stupid”.

    Perhaps Denyse would be more sympathetic if you had made an effort to label ID correctly from time to time. For instance, its not helpful when you post threads on your blog entitled:

    Denyse O’Leary Thinks Intelligent Design Creationism Is Winning!

    I mean really Larry-Boy, do you really have grounds to complain?

    I’m one of those people who use the term “Intelligent Design Creationism…Those who believe in Intelligent Design are characterized as IDiots—this is just a short-hand way of referring to them since “Intelligent Design Creationists” is too hard to type.

  3. Excellent point upright! and Moran just to inform you, if you will even listen to an ‘IDiot’ (your words not mine), Junk DNA is used by all neo-Darwinists, no matter what their particular stripes, wherever and whenever it will suit their purpose, especially when they try to establish the case for common ancestry!

    Francis Collins, Darwin of the Gaps, and the Fallacy Of Junk DNA – video
    http://www.evolutionnews.org/2.....40361.html

  4. Adaptationism (Darwinism) is NOT consistent with junk DNA. That’s why Darwinists usually reject junk DNA.
    ….
    Those Darwinists are the ones who OPPOSE the concept of junk DNA. Dawkins is a good example.

    That’s revisionist history. Darwinists lined up on both sides of the issue, only lately pretending the majority rejected the notion of junk DNA.

    Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true “purpose” of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.
    ….
    “creationists…might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”

    Richard Dawkins
    Selfish Gene

    You don’t seem to well adapted for internet debate. That claim that Dawkins opposed the concept of junk is a howler.

    I am not a Darwinist.

    Larry Moran

    The goldmine quote of the day!

  5. Larry Moran –

    Since you are so keen to see us stop (in your opinion) ‘mis-using’ the term “Darwinism”, would you care to stop using the terms “creationist” and “IDiot” to refer to ID proponents?

    J

  6. Larry Moran,

    I’m sorry, but I have to weigh in on this one also. My biggest gripe with the opponents of ID is their habit of trashing the intelligence of the proponents of ID. You may disagree with them, but to call them IDiots and thus imply that they are stupid only makes YOU look stupid.

    Michael Behe, Jonathan Wells, Stephen Meyer, William Dembski, Douglas Axe, Phillip Johnson, Michael Denton, and J.C. Sanford, to name a few, are far from stupid, and they have the credentials to prove it. All have Ph.D.’s from major universities. Most have published papers in peer reviewed journals. One clerked for a Supreme Court Justice. Most have taught at the University level, many in top institutions, etc., etc. To imply that these men are stupid does you no credit.

    And by the way, your inability to distinguish between proponents of ID and creationists, when that distinction has been made crystal clear by ID proponents any number of times doesn’t attest to any notable intelligence on your part, either.

    It is my opinion that the reason you and others fighting tooth and nail against ID resort to this tactic is that you are genuinely afraid that in an unbiased competition you will be unable to prevail in the court of public opinion. I can sympathize. I don’t think you will be able to, either. Even so, resorting to the shabby tactic of belittling the intelligence of your opponents is not going to help you in the long run, and only serves to destroy your credibility.

  7. Bruce David, excellent point. A minor correction, though: Phillip Johnson does not have a Ph.D. He has a law degree.

  8. QuiteID,

    Thank you, I stand corrected.

  9. So, how much of the 98% of our DNA that does not code for proteins has been found to perform essential biological functions? Any educated (and by that I mean: evidence-based) guesses in Wells’ book how many % might actually perform essential biological functions and what types of functions those are?

  10. Jonathan M asks,

    Since you are so keen to see us stop (in your opinion) ‘mis-using’ the term “Darwinism”, would you care to stop using the terms “creationist” and “IDiot” to refer to ID proponents?

    If Intelligent Design Creationists would stop referring to everyone as Darwinists then it wouldn’t be right to call them IDiots.

    Some years ago I made a deal with Bill Dembski. If he would stop using the incorrect term “Darwinist” and stop misrepresenting evolution then I would stop referring to him as an Intelligent Design Creationist and an IDiot.

    It was too much for him to give up. His part of the bargain only lasted a few months.

    As for junk DNA, a great many evolutionary biologists are skeptical about the existence of junk DNA. I think they’re wrong but that’s not the point. The point is that it is completely incorrect to imply that all “Darwinists” believed in the “myth” of junk DNA.

    What I don’t understand is whether Denyse and her friends are deliberately misrepresenting evolutionary biology or whether they are just uniformed.

  11. scordova says,

    That’s revisionist history. Darwinists lined up on both sides of the issue, only lately pretending the majority rejected the notion of junk DNA.

    So, we agree that evolutionary biologists lined up on both sides of the issue, right? Therefore, it would be completely wrong to say or imply that junk DNA was a myth that all Darwinists fell for, right?

    I hope you will correct all of your fellow travelers who make the mistake of assuming that all evolutionary biologists believed in junk DNA. Indeed, I expect that the new book will be full of statements from evolutionary biologists that dispute the notion of junk DNA. This is a genuine scientific controversy and it has been for 40 years.

    I believe that the majority of “Darwinists” did reject the notion of junk DNA but perhaps that’s because I’m using a different definition of “Darwinist”?

    P.S. Your Dawkins quotation from The Selfish Gene doesn’t seem right to me since it conflicts with statements he made later. Can you please supply a page number?

  12. Bruce David says,

    Michael Behe, Jonathan Wells, Stephen Meyer, William Dembski, Douglas Axe, Phillip Johnson, Michael Denton, and J.C. Sanford, to name a few, are far from stupid, and they have the credentials to prove it. All have Ph.D.’s from major universities. Most have published papers in peer reviewed journals. One clerked for a Supreme Court Justice. Most have taught at the University level, many in top institutions, etc., etc. To imply that these men are stupid does you no credit.

    I’m curious about something. There are quite a few scientists with the same credentials who fully accept evolution as the best explanation. They reject your criticisms of evolution.

    Some of them—I am one—have spend a lifetime studying evolution. You must honestly believe that we have failed to see the obvious flaws in evolution in spite of the fact we have credentials and many years of experience studying evolution.

    To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn’t make us look stupid?

  13. Some (very round) numbers to keep in mind when discussing this subject:

    # of protein-coding genes in the human genome – 30,000

    Average size of a protein – 1000 amino acids

    Average protein-coding capacity of a typical gene – 3000 nucleotides

    1. Total number of protein-coding nucleotides – 10^8 nucleotides

    Total number of introns – 200,000

    Average intron length – 6000 bp

    Total intronic content – 1.2*10^9 bp

    “functional” intronic sequences (these include splicing signals and intronic enhancer and suppressor elements) – 600 bp per intron (a very generous overestimate, since most introns probably have a fraction of this extent of functional sequence)

    2. total “functional” intronic sequence content – 1.2*10^8 bp

    promoter elements per gene – 100 (this is probably a huge overestimate, but I have decided to round up to the nearest order of magnitude)

    size of a typical promoter element – 100 bp (another huge overestimate, made to give every benefit of the doubt to supporters of Wells et al.; in particular, it assumes that every human gene includes promoter elements derived from repetitive DNA, that could conceivably be as large as 100 bp)

    3. total content of functional DNA in promoters – 3*10^8 bp

    upper range of estimates of non-coding RNAs (outside of stable RNAs) – 10,000

    size of non-coding RNAs (another huge overestimate) – 10,000 nts

    4. total content of non-coding RNAs – 10^8 bp

    total of “functional” DNA – sum of #’s 1-4 = 6.2 *10^8 bp

    fraction of the human genome that is functional (assume a haploid genome of 3*10^9 bp) – 20%

    So, even when we grant Wells et al. their each and every wish when it comes to functionality of non-protein-coding DNA, we can only account for 20% of the human genome. (Readers should note that this is a wild over-estimate, but it serves as a baseline for discussion.)

    So, for readers here who have looked through Well’s book – what specific and tangible data do Wells point to (or describe – maybe he has been doing some actual experiments) that support the standard ID assertion that there is no such thing as junk DNA? Not vague reference to experiments not done, not hopeful or wishful thinking, but solid experimental results that allow us to state that the remaining 80% of the human genome has some specifiable (and specific) function.

  14. Some more numbers:

    total size of the RNA polymerase II “transcriptome” – 1.3*10^9 bp (from the preceding comment, assuming that these are released from moderation in the order in which I posted them)

    total size of the “stable” transcriptome (that which is not thrown away) – 10^8 bp

    percentage of all polII-transcribed RNA that is thrown away – 92%

    Again, readers who have looked through Wells’ book might tell us just how much of this 92% Wells proves to have function. (This is a tough one, since the RNA actually is not present in the cell, expect transiently). Please be as specific and quantitative as possible.

  15. 15

    … I would stop referring to him as an Intelligent Design Creationist and an IDiot.

    The hypocrite takes a bow.

    - – - – - – -

    “Sincerity makes the very least person to be of more value than the most talented hypocrite.” – C Spurgeon

  16. I’m curious about something. There are quite a few scientists with the same credentials who fully accept evolution as the best explanation. They reject your criticisms of evolution.

    Some of them—I am one—have spend a lifetime studying evolution. You must honestly believe that we have failed to see the obvious flaws in evolution in spite of the fact we have credentials and many years of experience studying evolution.

    To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn’t make us look stupid?

    Geez, Larry. By that standard anytime anyone disagrees with anyone about a topic involving their own profession, someone’s being called stupid.

    And if disagreement suffices for an accusation of stupidity, then being shown to be wrong would have to be a demonstration of one’s stupidity, eh?

    So with that in mind…

    As for junk DNA, a great many evolutionary biologists are skeptical about the existence of junk DNA. I think they’re wrong but that’s not the point.

    So, Larry, putting aside your estimations about what percentage of whom believed what… How do you prefer we frame this? Is it that you think the majority of evolutionary biologists are stupid? Or that a great many evolutionary biologists think you’re stupid?

    (Of course, the alternative is that no, simply disagreeing with a professional about a subject in his field doesn’t add up to a charge of stupidity. But if you believe it does, well…)

  17. Dr. Moran asked:

    P.S. Your Dawkins quotation from The Selfish Gene doesn’t seem right to me since it conflicts with statements he made later. Can you please supply a page number?

    Dr. Moran,

    The quotation can be found on page 45. A full text can be found online at:

    http://www.arvindguptatoys.com.....owkins.pdf

    The page numbers of the PDF browser don’t necessarily align with the page numbers of the orignal books. On my PDF browser page 45 of Dawkins book is page 68 of my browser. The original page numbers can be seen in the PDF, and that should help you find the quote. It is the end of chapter three.

    Regarding the tandem repeats the quote was from Skeptic, “How Evolution Increases Information in the Genome”. It was not from his selfish gene book.

    Available here:
    How Evolution Increases Information in the Genome

    creationist might spend some earnest time speculating on why the Creator would bother to litter genome with untranslated pseudogenes and junk tandem repeats.

    Back to the question:

    P.S. Your Dawkins quotation from The Selfish Gene doesn’t seem right to me since it conflicts with statements he made later.

    I suppose he’ll have to admit he changed his mind or pretend he never said what is now in the historical record of his own writings.

    Regarding Tandem Repeats:

    The fact that tandem repeats occur frequently throughout the genomes of many different species and are often highly conserved between species suggests that they serve important functions (Tompa, 2003; Buschiazzo and Gemmel, 2006). Evidence that tandem repeats can affect brain function and behavior has recently been reviewed (Fondon et al., 2008). However, tandem repeats can also affect other biological processes in a wide range of organisms, from yeast to humans, and may play important roles in evolution
    Genome Tandem Repeat Polymorphisms

    Looks like Richard will have some backpedaling to do. :-)

  18. Dawkins in 1999:

    creationist might spend some earnest time speculating on why the Creator would bother to litter genome with untranslated pseudogenes

    Err, Richard, in 2010 we have some answers as to what the Creator had in mind as hinited in Wiki:

    some pseudogenes play a role in regulating protein-coding transcripts.[25][26] In June 2010, Nature published an article showing the mRNA levels of tumour suppressor PTEN and oncogenic KRAS is affected by their pseudogenes PTENP1 and KRAS1P. This discovery demonstrated an miRNA decoy function for pseudogenes and identified their transcripts as biologically active units in tumor biology; thus attributing a novel biological role to expressed pseudogenes, as they can regulate coding gene expression,

  19. Dr. Moran,

    What term would you prefer that we use to refer to those who believe in non-teleological evolution?

    Collin

  20. Molch at 9: “So, how much of the 98% of our DNA that does not code for proteins has been found to perform essential biological functions? Any educated (and by that I mean: evidence-based) guesses in Wells’ book how many % might actually perform essential biological functions and what types of functions those are?”

    Molch, it’s very difficult to form an educated guess about a large unknown, but I will ask Wells for an opinion when I interview him. Thanks for the suggestion.

    I can offer one suggestion of my own, which is: Look at the history of the 200 “vestigial” organs of the human body, almost all of which turned out to have a function, albeit a redundant one.

    Note: Confusion is created by two different meanings of the word “redundant”:

    1. The administrative meaning – For example, two different bureaucracies requiring functionally identical permits for the same project. Not only is it unnecessary, it is a huge source of avoidable error, conflict, and waste.

    2. The systems meaning: A system works better if a number of components can participate in the same job as one of their functions. For example, all hospital medical staff know the Heimlich manoeuvre, to save choking victims. Here, redundancy pays. The benefit is that any medical personnel who spot the case can act. I suppose the human body often works this way, and seldom the first way.

    So if asked to predict the fate of junk DNA, I would be inclined to say that it will prove useful far more likely than not, simply because that is the way the body works in general, but some study may be required to discover the exact function of specific codes.

  21. scordova says,

    The quotation can be found on page 45. A full text can be found online at:

    http://www.arvindguptatoys.com…..owkins.pdf

    The page numbers of the PDF browser don’t necessarily align with the page numbers of the orignal books. On my PDF browser page 45 of Dawkins book is page 68 of my browser. The original page numbers can be seen in the PDF, and that should help you find the quote. It is the end of chapter three.

    Regarding the tandem repeats the quote was from Skeptic, “How Evolution Increases Information in the Genome”. It was not from his selfish gene book.

    Thanks. I didn’t have a problem with the first quotation because Dawkins is ascribing a function to this “apparently surplus DNA.” He thinks that much of the extra DNA is selfish DNA.

    In fact, he repeats this claim in the article you quote below.

    There are many nonfunctional pseudogenes (see below) and lots of repetitive nonsense, useful for forensic detectives but not translated into protein in the living cells. The crested newt has a bigger “hard disc” than we have, but since the great bulk of both our hard discs is unused, we needn’t feel insulted. Related species of newt have much smaller genomes. Why the Creator should have played fast and loose with the genome sizes of newts in such a capricious way is a problem that creationists might like to ponder. From an evolutionary point of view the explanation is simple (see The Selfish Gene pp 44?–?45 and p 275 in the Second Edition).

    I did have a problem with the second part of your quotation since it was quite inconsistent with anything Dawkins would have said in 1976.

    You cleared that up by admitting that you made a mistake. The second quotation is from an article written 23 years later at a time when Dawkins has come to accept the existence of non-functional pseudogenes and degenerate transposons.

    I’m sorry you screwed up the original attribution but I appreciate the fact you admitted your mistake.

  22. Larry Moran, would you care to hazard a guess on what percentage of DNA is functional?

    Asking Darrel Falk to Pick a Number, Any Number
    Excerpt: So I have a question for him: Exactly what fraction of the transcribed 88.5% of our DNA are you willing to say “plays no role” or can be harmful? All I am asking for is a prediction, such as “90% of these DNA letters is superfluous” (“or 79.5% of the RNAs are nonsensical”). Since he also said “almost certainly” in the above statement, he must have a figure in mind. So I say pick a number, any number…But to be a good sport, I’ll show my prediction: All of the expressed 88.5% of our DNA has diverse roles in our development.
    http://www.evolutionnews.org/2......html#more

    So what do you say the number is Larry Moran? A ball park figure will be fine.

    The reason I ask Larry is that the numbers just aren’t working for neo-Darwinism. First even neglecting the fact that population genetics shows that it would take far too long to fix even a single coordinated beneficial mutation in the hominid lineage,,,

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co.....ns-part-5/

    ,,, is that scientists have uncovered entire genes that are completely unique to Humans,,,

    Human Gene Count Tumbles Again – 2008
    Excerpt: Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. ,,, After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes.
    http://www.sciencedaily.com/re.....161406.htm

    ,,,And Larry, contrary to the preceding study of them dismissing the 1,177 ORFan genes as ‘junk’, simply because they are unique, ORFan genes are actually found to be functional.

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

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

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

    ,,,But Larry the overwhelming problems is that finding JUST ONE completely unique gene is to be considered so rare as to defy comprehension,,,

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

    ,,,On top of that ‘problem’ Larry, +80% of proteins are found to be different between man and chimps:

    Chimps are not like humans – May 2004
    Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that “83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect,” Sakaki said.
    http://cmbi.bjmu.edu.cn/news/0405/119.htm

    Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:
    http://www.ncbi.nlm.nih.gov/pubmed/15716009

    ,,,To put this mildly Larry, this huge +80% difference between chimps and humans is more than a slight problem for evolutionary materialists, for even neo-Darwinists themselves admit that finding unique functional proteins is exceeding rare,,,

    How Proteins Evolved – Cornelius Hunter – December 2010
    Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a
    potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
    http://darwins-god.blogspot.co.....olved.html

  23. ,,,as well Larry, not only are novel proteins rare but existing proteins are themselves found to be severely be intolerant to any variation,,,

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

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

    Proteins with cruise control provide new perspective:
    “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.”
    http://www.princeton.edu/main/...../60/95O56/

    As well Larry Moran, finding severe polyfunctionality in the genome and protein interactions, strongly indicates there are no ‘Junk proteins’ for evolution to even experiment with in the first place;

    Astonishing DNA complexity demolishes neo-Darwinism – Alex Williams
    Excerpt: Not only has the ENCODE project elevated UTRs out of the ‘junk’ category, but it now appears that they are far more active than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes.
    http://creation.com/images/pdf.....11-117.pdf

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

    Poly-Functional Complexity equals Poly-Constrained Complexity
    http://docs.google.com/Doc?doc.....Zmd2emZncQ

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

    ,,,, So basically Larry, do you see the problem here???? you got far too much variation to account for, with precious little resources for evolution to experiment with. So again Larry, how much of the DNA do you say is functional?

  24. nullasalus asks about junk DNA,

    So, Larry, putting aside your estimations about what percentage of whom believed what… How do you prefer we frame this? Is it that you think the majority of evolutionary biologists are stupid? Or that a great many evolutionary biologists think you’re stupid?

    Here are the facts.

    Something like 99.9% of evolutionary biologists agree that genomes contain junk DNA. Pseudogenes are the best example. A somewhat smaller percentage (99%) understand that degenerative virus genomes and transposons are another form of junk pseudogenes.

    Thus, the existence of junk DNA is not in dispute. It’s a fact. The scientific debate is over how much of the genome is junk.

    It’s also a fact that 99.9% of the experts know that noncoding DNA has lots of functions. Most of these functions have been known for 40-50 years. You’re on safe grounds as long as you don’t state or imply that the consensus view was that all noncoding DNA is junk. That would be a lie.

    The proper framework for the discussion is to point out that the experts in the field are debating whether there’s a lot of junk DNA in our genome or just a small amount. Some of the issues have been decided but there’s still lots of room for differing opinions.

    It would be very misleading to imply that the case against junk DNA has been proven to the satisfaction of informed evolutionary biologists and molecular biologists. That’s simply untrue.

    All of the data is in dispute and neither side is even close to surrender.

    I’m looking forward to Wells’ new book. It will provide plenty to blog about ’cause I just know he’s going to distort the evidence and frame the discussion in terms of a diatribe against evolution.

    With respect to the genuine scientific controversy, neither side is stupid at the present time. The only stupid people are those who deny that there’s a genuine scientific controversy.

  25. Collin asks,

    What term would you prefer that we use to refer to those who believe in non-teleological evolution?

    I’ve never thought of it that way. I suppose “atheists,” “agnostics,” and “Deists” would just about cover all the possibilities.

    Why do you ask?

  26. bornagain77 asks,

    Larry Moran, would you care to hazard a guess on what percentage of DNA is functional?

    It depends on the genome. In the case of humans, I’m certain that more than half of our genome is junk [Genomes & Junk DNA].

    As for the rest, in my opinion only about 10% has a function. That means that 90% is junk.

    To put this mildly Larry, this huge +80% difference between chimps and humans is more than a slight problem for evolutionary materialists, …

    I guess we must be really stupid if we don’t see a problem, right?

    Have you considered the possibility that your facts, and your understanding of evolution, might be wrong and that’s why you see imaginary problems?

  27. Larry Moran,

    Here are the facts.

    I didn’t ask about junk DNA. You suggested that to view someone as wrong on a topic within their field, despite their having the right credentials and “spending their whole lives” studying said field, amounted to an accusation of stupidity.

    Again, here’s what you said:

    I’m curious about something. There are quite a few scientists with the same credentials who fully accept evolution as the best explanation. They reject your criticisms of evolution.

    Some of them—I am one—have spend a lifetime studying evolution. You must honestly believe that we have failed to see the obvious flaws in evolution in spite of the fact we have credentials and many years of experience studying evolution.

    To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn’t make us look stupid?

    I pointed out that if disagreeing with someone about a topic of evolution despite having “credentials and many years of experience studying evolution” amounted to a charge of stupidity, then you must think a fair share – maybe the lion’s share – of evolutionary biologists are stupid, and that they in turn must think you’re stupid.

    You insist now that ‘neither side is stupid’. Alright, then apparently mere disagreement isn’t a charge of stupidity after all. Or maybe you just aren’t following your own reasoning.

    It would be very misleading to imply that the case against junk DNA has been proven to the satisfaction of informed evolutionary biologists and molecular biologists. That’s simply untrue.

    All of the data is in dispute and neither side is even close to surrender.

    So… what? There’s two sides to this conflict, both sides think they’re right and the other side is wrong, but all of the data is in dispute and no one is satisfied with the case one way or the other?

    Are you really telling me that if I ask any given person on either side of this dispute, that their response will be “This is what I think is the case. But all of the data is in dispute”? Not, “This is what I think is the case: The data says this, and the other guys are wrong.”? Or respond to ‘But Larry Moran disagrees’ with “Larry is mistaken and isn’t interpreting the data properly”?

    I’m pretty sure that sometimes scientists disagree, and that one interpretation one side says is in dispute, another side says “Talk of dispute is a load. This is the right interpretation, the other guys are wrong.”

    Of course, that’d just lead me to ask again: If someone thinks your interpretation of the evolutionary data is wrong, Larry, are they calling you stupid? Are you calling them stupid if you say their interpretation is wrong?

  28. bornagain77 asks,

    So basically Larry, do you see the problem here????

    Nope. I’m well aware of all the papers you quoted and I don’t see how any of them calls into question the idea that most of our genome is junk.

    They’ve all been discussed and debated among the experts. It will be fun to see how Jonathan Wells handles all the objections to those papers. I sure he’s going to give the counter-arguments the full attention they deserve. Right? (Not holding my breath.)

    you got far too much variation to account for, with precious little resources for evolution to experiment with.

    I don’t have any idea what you’re talking about. Do you?

    So again Larry, how much of the DNA do you say is functional?

    I say that about 10% of our genome contains essential DNA that could not be removed without affecting the survivability of individuals. It’s a much higher percentage in fruit flies and yeast and in bacteria it’s about 90%.

  29. I’ve never thought of it that way. I suppose “atheists,” “agnostics,” and “Deists” would just about cover all the possibilities.

    Why do you ask?

    I don’t know about Collin, but I’d ask because Jerry Coyne suggests otherwise. To him, to accept evolution as teleological means you reject evolutionary biology as scientists understand it.

    Are you saying the evolutionary biology, insofar as it is a science, is silent on the question of guidance or teleology? Because if so, it looks like your view is in dispute.

  30. nullasalus asks,

    Of course, that’d just lead me to ask again: If someone thinks your interpretation of the evolutionary data is wrong, Larry, are they calling you stupid?

    In many cases there is genuine scientific controversy about some evolutionary interpretation. Since the science can’t settle the issue right now, both sides have valid positions and neither side is stupid. (Although one side or the other might propose some stupid arguments to support their case.)

    In cases where there is no genuine scientific controversy, the anti-science proponents are usually either stupid or ignorant. Sometimes both.

    People who claim that the Earth is only 6000 years old (Young Earth Creationists) are good examples. Another example would be people who claim that the existence of junk DNA has been scientifically disproven. We’ve just seen a third example in one of the earlier comments: namely, people who claim that the sequences of the human and chimp genomes pose a problem for evolution.

  31. Larry, I’ve been batting around another problem that perhaps you can help me with. You see Larry the problem starts like this, Quantum Entanglement falsifies local realism (reductive materialism),,,

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

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

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

    ,, Moreover Larry, Quantum Entanglement/Information, is found to be instantaneous and universal in its actions;

    Wheeler’s Classic Delayed Choice Experiment
    Excerpt: So it seems that time has nothing to do with effects of quantum mechanics. And, indeed, the original thought experiment was not based on any analysis of how particles evolve and behave over time – it was based on the mathematics.
    http://www.bottomlayer.com/bot.....choice.htm

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

    ,,, And yet Larry, this ‘spooky’ Quantum Entanglement/Information effect, which falsified the ‘local realism’ of particles, and blatantly defies constraints of time of space, is now found in molecular biology,,,

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

    Further evidence that quantum entanglement/information is found throughout entire protein structures:
    http://www.uncommondescent.com.....ent-373214

    ,,, Thus my problem is as such Larry, the effect of quantum entanglement/information needs to be explained by a cause that is itself not constrained by time and space yet neo-Darwinism purports to explain all the wonder and diversity we see in life on earth by Random Variations/Mutations of particles.,, Thus Larry, how can a quantum effect in biology be explained by a material cause when the quantum effect falsified material particles as its causation in the first place? Appealing to the probability of various configurations of material particles simply will not help since a cause must be supplied beyond material particles! Do you see the problem Larry?

  32. Larry Moran: “To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn’t make us look stupid?”

    No. I do not question your intelligence or that of the other prominent ID critics (although I’m not so sure about some of the commenters I have read in this and other blogs). Notice that in my post I (carefully and deliberately) said that your implication that ID proponents were stupid makes you LOOK stupid, not that you ARE stupid.

    My beef is with you and other ID critics attempting to win points in the debate by denigrating the intelligence of your opponents, when beyond any question people like Behe and Dembski and the others I mentioned above are anything but stupid. It goes beyond an intelligent discussion of the issues into personal attack and insult, and these men have done nothing to deserve such treatment. That’s why I say it does you no credit, and in fact damages your credibility.

  33. Bruce David says,

    My beef is with you and other ID critics attempting to win points in the debate by denigrating the intelligence of your opponents, when beyond any question people like Behe and Dembski and the others I mentioned above are anything but stupid. It goes beyond an intelligent discussion of the issues into personal attack and insult, and these men have done nothing to deserve such treatment.

    It would be really boring if the Intelligent Design Creationists started treating evolutionary biologist with respect and stopped insinuating that they are too stupid to understand their own discipline.

    It’s a lot more fun to have a real no-holds-barred fight.

    Don’t pretend that my side is the only side enjoying that kind of debate. It damages your credibility.

  34. 34

    Larry: ID Creationists are stupid.

    Bruce: I’m not so certain about that.

    Larry: Your’e stupid too.

    Bruce: What I’m saying is that neither of you is stupid.

    Larry: That’s boring.

  35. Thanks, Arthur (#13 & 14) – that gives a pretty good quantitative framework for my question in #9! Anybody else got anything quantitative and evidence-based to contribute?

  36. So when is the test going to hppen? The test that removes 90% of our genome and see if something can not only develop by survive and reproduce? Or is Larry blowing smoke?

    Larry Moran seems to think that essential means that which isn’t essential is junk- nonsense. As someone who has worked with redundant systems there is a reason for the extra parts to be there.

    And Larry, Intelligent design Creationists only exist in the minds of the willfully ignorant- and here you are.

    Ypu want a no-holds barred fight, Larry? I’m your hucklebrry. ;)

  37. Larry and Arthur:

    I welcome your comments on this PhysOrg article appearing today.

    Here’s a quote:

    For years, many biochemists were skeptical that lincRNA played any important role in a cell and considered the molecules just mere “noise,” perhaps vestigial protein-coding genes that had mutated to become nonfunctional. Chang’s group has been instrumental in proving that lincRNAs can play a critical regulatory role: determining what proteins a cell produces and, thereby, what identity it assumes.

    New, critical functionality now ascribed to what was formerly, for the most part, considered “junk”. When will this process end?

    Also, let’s never forget that DNA is a physical object, and that physical constraints might require stretches of DNA that will not have function, but will only act as a kind of physical ‘spacer’. Even this basic function is itself a function (whereas “junk DNA” is considered discarded and formerly functional DNA).

  38. 38

    Larry,

    Can you name even a single biological fact that ID theory contradicts?

    (fact= a documented, repeatable observation in biology)

  39. One more thing: I’d like to coin a phrase, if I may.

    As Dr. Cornelius Hunter continues to point out, Darwin’s argument is theological in character. The phrase I’d like to introduce is this: “The God of the Goofs”. This is typical Darwinian argumentation. A God who is all-knowing and all-powerful certainly couldn’t have done this, or that, or what have you. That is, God has “goofed up”.

    And then, of course, we find out that there is indeed a function, an important function, to it all. It is this “God of the Goofs” that the Darwinists rail against. (Sorry, Larry, but Darwin is the person who claimed that natural forces alone can explain life’s diversity and progression. The Neutral Theory is still a theory that invokes natural processes.)

    Finally, let us take note that the God of the Gaps is still there. Has science provided any credible intermediates? Can science document anything other than sudden emergence and sudden disappearance of species? As the power of microscopic techniques are enhanced, isn’t there more and more difficulty explaining (whether via directed evolution or neutral drift) the complexity that is unearthed?

    So we have the ‘God of the Goofs’ disappearing while the ‘God of the Gaps’ just won’t go away.

    I think I’m on the side of the trend-lines here.

  40. Dr. Moran,

    But not all people who believe in non-teleological evolution are non-believers. Some are full fledged theists.

    I’m just looking for a term to replace Darwinist that would exclude creationists, ID-ists and would combine the term Darwinist and whatever it is that you are. In essence, the majority of biologists are what? Please don’t say “biologists” because some biologists are ID-ists or creationists.

  41. Larry, not to drag you away from your important work of determining when and where to belittle people with the word stupid, idiot, ignorant, and what not,, but could you help me with another problem since you don’t seem to want to address the problem of quantum entanglement in molecular biology that can’t be reduced to a particle basis. Larry it has to do with Junk DNA,,,

    Junk DNA” is found to have purpose in an astonishing way in this following paper:

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.
    http://www.evolutionnews.org/2......html#more

    Thus Larry, since you hold that a vast majority of the human DNA is junk,,,

    I say that about 10% of our genome contains essential DNA that could not be removed without affecting the survivability of individuals.

    ,,, then how do you explain the fact that the entire nuclear genome of the mouse is transformed into a optical device??? If your conjecture for a large percentage of junk DNA was true should we not see discordance of some degree here??? Instead of tightly integrated functionality???

  42. You cleared that up by admitting that you made a mistake. The second quotation is from an article written 23 years later at a time when Dawkins has come to accept the existence of non-functional pseudogenes and degenerate transposons.

    I’m sorry you screwed up the original attribution but I appreciate the fact you admitted your mistake.

    Say what Dr. Moran? The attribution of those quotes is still to Richard Dawkins, the only mistake was one quote came from his Selfish Gene book and the other in his article years later where he said:

    creationist might spend some earnest time speculating on why the Creator should bother to litter genome with untranslated pseudogenes and junk tandem repeats.

    He is still making a mistaken claim and it is still at variance with your assertion Dawkins opposes the concept of Junk DNA. That’s indpendent of whether my citation was intially to the selfish gene book when it should have been to a later work. The fact that is in a later work by Dawkins is actually worse for you and him, and my attribution to the earlier work would have given you and him the excuse that it was when Dawkins was more ignorant of reality.

    So you can quibble that the quote came from two writing by Dawkins, rather than one writing by Dawkins, but it doesn’t change the fact it was by Dawkins, and the fact it was in a later work makes it less excusable for him, and less excusable for you to assert he some how opposes the notion of junk DNA!

    Your error is far more gigantic because you refuse to accept the implications what is evident in the record of Dawkins writings. The fact that I initially said both quotes came from his selfish gene book does not remove the fact Dawkins still made both those quotations, and that you keep asserting the same howler:

    Darwinists are the ones who OPPOSE the concept of junk DNA. Dawkins is a good example

    Hardly, he has been an advocate of the junk DNA hypothesis, and further he uses the junk claims against creationists:

    creationist might spend some earnest time speculating on why the Creator would bother to litter genome with untranslated pseudogenes and junk tandem repeats.

    Dawkins

    I respect the fact you’re sticking up for your friend, but his error in two published works is still there, and worse, in light of his taunting of creationists, it seems science is putting points in their favor, not his.

    In any case the next round of debate, my citations will be cleaned up, but I suspect you’ll still be asserting the same indefensible claims. Fine with me.

  43. I believe that the whole “junk dna” concept is an argument from ingorance. Just because we dont know the function of some dna, doesnt mean there isnt any.Similar to the whole vestigal organ argument.Its now seems there really arent any vestigal structures.And by the way the only reason vestigal structures were proposed was because the theory of evolution predicted it. It was a failed predicton. Same with junk dna. It wasnt because an observed portion of dna didnt exhibit obvious function, it was because the theory of evolution predicted it beforehand.

    http://creation.com/junk-dna-slow-death

    http://creation.com/images/pdf....._18-30.pdf

  44. Dr. Hunt,

    Just to be clear, what is your view of Junk DNA. Do you think most of non-coding DNA is functionless now?

    I’m actually unsure of what you’ve said.

    Thanks in advance.

    Sal

  45. Dr. Moran,

    For the sake of clairity, even though you’ve probably answered the question posed to Dr. Hunt, what is your view of junk DNA. Do you think most of the non-coding DNA is functionless for the organism that contains it?

    Thanks in advance.

    Sal

  46. Christians-

    For the sake of clarity, wouldn’t “the fall from Grace” explain the existence of non-coding, useless, junk DNA, excess baggage that may just explain why our lives are shorter than those depicted in Genesis? (Sanford’s genetic entropy?)

    Thanks in advance.

    Joe

  47. Joseph:

    To follow up on your query, and to be a little provocative, let me ask this question: when Jesus healed the woman of her hemorrhaging, was it done through genetic alteration?

  48. Collin asks,

    I’m just looking for a term to replace Darwinist that would exclude creationists, ID-ists and would combine the term Darwinist and whatever it is that you are. In essence, the majority of biologists are what? Please don’t say “biologists” because some biologists are ID-ists or creationists.

    In most cases the term “Darwinist” is used as a pejorative synonym for “evolutionary biologist.”

    In some cases it’s used to describe those people who accept evolution as the best explanation of life even though they may not be experts. A better word would be “evolutionists.”

    The vast majority of practicing biologists (>99%) are evolutionists in this sense of the word.

    There are many people who believe in a Creator who also accept evolution. Ken Miller, Michael Denton, Francis Collins, and Michael Behe come to mind. These people are creationists AND evolutionists.

  49. scordova,

    For the sake of clarity, how much of the human genome do you think is junk? Please don’t say “zero” because that would indicate that you aren’t interested in a serious scientific discussion.

  50. I’m curious in how intelligent design can predict that most or at least large portion of the “junk DNA” should be functional. Or in other words: Why would the designer not design “junk”?

    And related to what Joseph said: Does ID not say that mutations can’t create any new functionalities but only alter or destroy information? Would one thus after these millions of years not expect the genome to be littered with deteriorated stuff?

  51. kuartus says,

    I believe that the whole “junk dna” concept is an argument from ingorance.

    Please explain how the genetic load argument is an argument from ignorance.

    Please explain how the experiment where large segments of mouse DNA were deleted is an argument from ignorance.

    Please explain how the existence of pseudogenes is an argument from ignorance.

    Please explain how our understanding of Alu sequences is an argument from ignorance.

    Please explain how the C-Value Paradox and the Onion Test are arguments from ignorance.

    Please explain how genome sequences are arguments from ignorance.

    Please explain how 50 years of discovery about the structure of genes and how they are regulated is an argument from ignorance.

    Please explain how the frequency of fixation of mutations in junk DNA s an argument from ignorance.

    You don’t know what you’re talking about, do you? Biochemists and molecular biologists are NOT ignorant about these things.

  52. Dr. Moran, you said, “Don’t pretend that my side is the only side enjoying that kind of debate. It damages your credibility.”

    I think, if you’ll read the books, articles, and blogs by the proponents I mentioned in my first comment (Behe, Dembski, Wells, etc.), and if you watch their public interviews and debates, you will find that without exception, their arguments are based entirely on the scientific issues and that they do not stoop to “enjoying that kind of debate”. In fact, in my opinion they are remarkably restrained, considering the ad hominem abuse that is heaped upon them by the likes of Coyne, Dawkins, and Myers (and apparently you as well).

    Of course, there will always be some supporters of any position who use less than stellar tactics to support it. However, to then use that as an excuse to attack others whose only guilt is by association is unjustified.

    And by the way, I think the scientific issues are fascinating in and of themselves, and an ongoing discussion that limited itself to them would not be boring at all.

  53. –Larry Moran: “Some years ago I made a deal with Bill Dembski. If he would stop using the incorrect term “Darwinist” and stop misrepresenting evolution then I would stop referring to him as an Intelligent Design Creationist and an IDiot.”

    There is no moral or intellectual equivalence between these terms.

    “The term “Darwinism” is used to CLARIFY. As anyone who cares knows, Darwinists falsely accuse ID supporters of being “anti-evolution,” when they know very well that it is the purposeless, unguided, and totally random variety of evolution that is being criticized. Thus, one can believe in “evolution” [emergence from a single cell or universal common descent] without believing in “Darwinism” [the claim that naturalistic forces alone could drive the process].

    The term ID/ Creationist is used to OBFUSCATE. As anyone who cares knows, “Creationists” conduct a Forward analysis, that is, they assume a Biblical world view and seek to make the scientific evidence harmonize with that assumption. ID advocates, on the other hand, conduct a Reverse analysis, that is, they begin with scientific evidence and allow the evidence to speak for itself, even if that evidence happens to be consistent with a Biblical world view.

    Thus, ID proponents seek to clarify the meanings of words because they know that the evidence is on their side. Darwinists seek to conflate terms and sow confusion because they know that the evidence is not on their side.

  54. Larry Moran:

    In most cases the term “Darwinist” is used as a pejorative synonym for “evolutionary biologist.”

    No. It is used to describe a specific type of evolutionary biologist- one who thinks chance and necessity explain life’s diversity-> the blind watchmaker, if you will.

    What do you call people who accept the change in allele frquency within a population, accept change, but go along with the observable genetic evidence which points to limited variation and some phenotypic plasticity?

    Are we called realists?

    Also do yu agree with Richard Dawkins when he says we wouldbe looking at a totally different given a biology given a creator/ designer? Dawkins begins around 14:30

  55. Larry Moran:

    Please explain how 50 years of discovery about the structure of genes and how they are regulated is an argument from ignorance.

    It takes knowledge to regulate genes. That is what we are saying. The more that is being uncovered the better Intelligent Design looks.

    Alternative gene splicing, overlapping genes-> evidence of planning.

    Thanks, keep up the good work!

  56. Dr. Moran: “In some cases it’s used to describe those people who accept evolution as the best explanation of life even though they may not be experts. A better word would be ‘evolutionists.’”

    My problem with the word “evolutionist” is that the evidence of the fossil record shows that life clearly evolved. The question between those who are ID proponents and the ones who are not is, “What was the mechanism?” The word “evolutionist” carries with it the implicit assumption that the fact that life evolved implies a Darwinian or other naturalistic mechanism, which it does not. And in fact, the fossil record supports ID as the “mechanism” better than any other that has been proposed.

  57. Larry at 50:
    “how the genetic load argument is an argument from ignorance”

    Never said it was

    “the experiment where large segments of mouse DNA were deleted is an argument from ignorance”

    Didnt say it was an argument from ignorance.But that could be explained by genetic redundancy in the sense of making the system more robust.

    “Please explain how our understanding of Alu sequences is an argument from ignorance”

    Again, never even mentioned it. Are you impying alu sequences are functionless?

    Again, blah blah blah. You kept metioning things that are irrelevant and somehow got the idea that I think they are arguments from silence.
    Okay?

  58. scordova says,

    So you can quibble that the quote came from two writing by Dawkins, rather than one writing by Dawkins, but it doesn’t change the fact it was by Dawkins, and the fact it was in a later work makes it less excusable for him, and less excusable for you to assert he some how opposes the notion of junk DNA!

    Let me try and explain this to you. Others have tried unsuccessfully but I still have hope that you can understand the concept of junk DNA.

    As I said earlier, no knowledgeable biologist would ever claim that junk DNA doesn’t exist. They all accept the examples of pseudogenes. That includes Richard Dawkins and other Darwinists.

    The scientific debate is over the amount of junk DNA in our genome. Is most of it junk or only a small percentage? In general, adaptationists (Darwinists) are skeptical of claims that most of our genome is junk and other evolutionary biologists are more comfortable with the idea.

    Here’s what Dawkins wrote in The Extended Phenoptype back in 1982.

    This does not mean, however, that the so-called junk DNA is not subject to natural selection. Various “functions” for it have been proposed, where “function” means adaptive benefit to the organism. The “function” of extra DNA may “simply be to separate the genes” (Cohen, 1977). Even if a stretch of DNA is not itself transcribed, it can increase the frequency of crossovers between genes simply by occupying space between them, and this is a kind of phenotypic expression. Spacer DNA might, therefore, in some sense be favoured by natural selection because of its effects on crossover frequencies….

    As far as I know, Dawkins still believes that a lot of what I call junk DNA has this kind of function. He does not believe that the majority of our genome is completely useless. At the same time, he understand that there are pseduogenes and degenerative transposons that represent real junk. He also talks about selfish DNA but that’s not the same as junk.

    Does this help you understand where he’s coming from? He oposes the concept of junk DNA where “concept” means huge amounts of junk in our genome. He and I have argued about this quite a few times.

    Why is it so important for you to show that Dawkins was a supporter of huge amounts of junk DNA? Will you turn into a pumpkin if you’re wrong?

  59. Bruce David says,

    The word “evolutionist” carries with it the implicit assumption that the fact that life evolved implies a Darwinian or other naturalistic mechanism, which it does not.

    Nonsense. When one describes someone as an evolutionist one clearly means that they accept evolution as the mechanism. That means natural selection, random genetic drift etc.etc.

    You can’t just re-define words to suit your personal preferences.

    And in fact, the fossil record supports ID as the “mechanism” better than any other that has been proposed.

    There are several reasonably intelligent arguments for ID. That’s not one of them.

  60. kuartus says (#42),

    I believe that the whole “junk dna” concept is an argument from ingorance. Just because we dont know the function of some dna, doesnt mean there isnt any.

    kuartus also says (#56),

    Again, blah blah blah. You kept metioning things that are irrelevant and somehow got the idea that I think they are arguments from silence.
    Okay?

    Okay.

    Goodbye.

  61. Joseph says,

    Alternative gene splicing, overlapping genes-> evidence of planning.

    We’ve understood alternative splicing and overlapping genes for thirty years.

    How come all evolutionary biologists haven’t become believers in God?

    Is it because we’re stupid?

    Or is it because we know more than you do?

  62. StephenB says,

    The term ID/ Creationist is used to OBFUSCATE. As anyone who cares knows, “Creationists” conduct a Forward analysis, that is, they assume a Biblical world view and seek to make the scientific evidence harmonize with that assumption.

    Do you know who Phillip Johnson is? He’s one of the founders of the intelligent design movement. Here’s what he says in Darwin on Trial p. 113.

    The essential point of creation has nothing to do with the timing or the mechanisms the Creator chose to employ, but with the element of design or purpose. In the broadest sense, a “creationist” is simply a person who believes that the world (and especially mankind) was designed, and exists for a purpose.

    Are you a creationist in the sense that Johnson describes? Is Michael Behe? How about Bill Dembski?

  63. Dr.Moran: “When one describes someone as an evolutionist one clearly means that they accept evolution as the mechanism.”

    You have just proved my point. The meaning of the word “evolution” in a normal context is “change over time”, or “increasing complexity (or some other attribute) over time”. But you have just used it to mean “evolution by a Darwinian (or some other naturalistic) mechanism.” It is you who have co-opted the meaning to suit your purposes (you collectively, not individually).

  64. Larry Moran, as to the two posts you did not address at 31 and 40, which have foundational importance.

    http://www.uncommondescent.com.....ent-374560

    Please answer as to what is the exact transcendent ’cause’ of the quantum entanglement ‘effect’ in molecular biology, and please answer as to why the entire nuclear genome of the mouse is transformed into an optical device for aid in capturing photons if a great percentage of its genome is junk as you maintain?

    As to your supposed defense of Junk DNA:

    ‘Please explain how the genetic load argument is an argument from ignorance.’

    And Larry, exactly how does ‘genetic load’ help you establish evolution, when the whole overall concept actually supports Genetic Entropy in the first place?

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

    Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally – September 2010
    Excerpt: Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study).
    http://www.uncommondescent.com.....literally/

    Larry you then state;

    ‘Please explain how the experiment where large segments of mouse DNA were deleted is an argument from ignorance.’

    Yes Larry please do tell how finding large scale integrated redundancy helps you?

    The following study highlights the inherent fallacy in gene deletion/knockout experiments that have led many scientists astray in the past as to underestimating what the minimal genome for life (as as genomes for other life) should actually be:

    Minimal genome should be twice the size, study shows
    http://www.uncommondescent.com.....ent-349935

    Larry you then state:

    ‘Please explain how the existence of pseudogenes is an argument from ignorance.’

    Yes Larry please do explain how Darwinian ignorance helps us understand;

    Is “Pseudogene” a Misnomer?
    The term “pseudogene” may be as inappropriate as the term “junk DNA,” according to the entry on pseudogenes in the 2010 Encyclopedia of Life Sciences, published by prestigious the academic publisher John Wiley & Sons,,
    http://www.evolutionnews.org/2.....42301.html

    Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 5 – Fazale Rana
    Excerpt: In his critique, Venema does acknowledge that research shows some pseudogenes are functional, but he dismisses this point by claiming that such pseudogenes are rare. This assertion, however, is not supported by the latest work. In fact, two of the articles on our website discuss papers (published in peer-reviewed journals) that emphasize how widespread pseudogene function actually is.

    Researchers have discovered that the genesis of certain classes of junk DNA is not rare and random, but occurs frequently and in a repeatable manner. (Go here and here to read recent articles.) Scientists have also learned that the order of genes along a chromosome plays a functional role as well.
    http://www.reasons.org/pseudog.....del-part-5

    Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 7 – Vitamin C refutation
    Excerpt: Yet, as biologist Peter Borger points out, fifty percent of the mutations in the primate and guinea pig exon X sequence are identical. In addition, the guinea pig exon X region shows a mutation at position 97, the location in the primate genomes where a deletion took place. These shared features could not have resulted because guinea pigs and primates shared a common ancestor. Instead, they must reflect nonrandom, reproducible changes.
    http://www.reasons.org/pseudog.....del-part-7

    Daniel Fairbanks Cherry Picks Data On Pseudogenes To Prop Up Common Descent – March 2011
    http://www.uncommondescent.com.....n-descent/

    Evolutionary Thought in Action: The Subtlety of Metaphysics – Cornelius Hunter – July 2010
    Excerpt: In the above example, the crucial metaphysics is woven in here:

    but when the exact same pseudogene for Vitamin C is broken in the exact same place in humans and chimpanzees, indicating we inherited it from a common ancestor, what else do you say it is other than a fact that we evolved from that common ancestor?

    This shared-error argument is a good example of how the evolution lie depends on subtle misrepresentations of the science and unspoken metaphysical claims. Any scientific analysis of the evidence would come up empty handed. Pseudogenes reveal various patterns, some which can be employed to argue for common descent, others which violate common descent (they could be explained, for instance, by common mechanism). Furthermore pseudogenes reveal evidence of mutational hotspots.

    But such quandaries are left unmentioned. Evolutionists selectively present the evidence to make evolution appear to be well supported. The evolution lie corrupts scientific knowledge.
    http://darwins-god.blogspot.co.....tlety.html

    Endogenous Retroviruses (ERVs) – Page up for Pseudo-genes refutation
    http://www.detectingdesign.com.....Endogenous

  65. Larry Moran, as to the two posts you did not address at 31 and 40, which have foundational importance.

    Please answer as to what is the exact transcendent ’cause’ of the quantum entanglement ‘effect’ in molecular biology, and please answer as to why the entire nuclear genome of the mouse is transformed into an optical device for aid in capturing photons if a great percentage of its genome is junk as you maintain?

    As to your supposed defense of Junk DNA:

    ‘Please explain how the genetic load argument is an argument from ignorance.’

    And Larry, exactly how does ‘genetic load’ help you establish evolution, when the whole overall concept actually supports Genetic Entropy in the first place?

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

    Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally – September 2010
    Excerpt: Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study).

    Larry you then state;

    ‘Please explain how the experiment where large segments of mouse DNA were deleted is an argument from ignorance.’

    Yes Larry please do tell how finding large scale integrated redundancy helps you?

    The following study highlights the inherent fallacy in gene deletion/knockout experiments that have led many scientists astray in the past as to underestimating what the minimal genome for life (as as genomes for other life) should actually be:

    Minimal genome should be twice the size, study shows
    http://www.uncommondescent.com.....ent-349935

    Larry you then state:

    ‘Please explain how the existence of pseudogenes is an argument from ignorance.’

    Yes Larry please do explain how Darwinian ignorance helps us understand;

    Is “Pseudogene” a Misnomer?
    The term “pseudogene” may be as inappropriate as the term “junk DNA,” according to the entry on pseudogenes in the 2010 Encyclopedia of Life Sciences, published by prestigious the academic publisher John Wiley & Sons,,

    Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 5 – Fazale Rana
    Excerpt: In his critique, Venema does acknowledge that research shows some pseudogenes are functional, but he dismisses this point by claiming that such pseudogenes are rare. This assertion, however, is not supported by the latest work. In fact, two of the articles on our website discuss papers (published in peer-reviewed journals) that emphasize how widespread pseudogene function actually is.

    Researchers have discovered that the genesis of certain classes of junk DNA is not rare and random, but occurs frequently and in a repeatable manner. (Go here and here to read recent articles.) Scientists have also learned that the order of genes along a chromosome plays a functional role as well.

    Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 7 – Vitamin C refutation
    Excerpt: Yet, as biologist Peter Borger points out, fifty percent of the mutations in the primate and guinea pig exon X sequence are identical. In addition, the guinea pig exon X region shows a mutation at position 97, the location in the primate genomes where a deletion took place. These shared features could not have resulted because guinea pigs and primates shared a common ancestor. Instead, they must reflect nonrandom, reproducible changes.

    Daniel Fairbanks Cherry Picks Data On Pseudogenes To Prop Up Common Descent – March 2011

    Evolutionary Thought in Action: The Subtlety of Metaphysics – Cornelius Hunter – July 2010
    Excerpt: In the above example, the crucial metaphysics is woven in here:

    but when the exact same pseudogene for Vitamin C is broken in the exact same place in humans and chimpanzees, indicating we inherited it from a common ancestor, what else do you say it is other than a fact that we evolved from that common ancestor?

    This shared-error argument is a good example of how the evolution lie depends on subtle misrepresentations of the science and unspoken metaphysical claims. Any scientific analysis of the evidence would come up empty handed. Pseudogenes reveal various patterns, some which can be employed to argue for common descent, others which violate common descent (they could be explained, for instance, by common mechanism). Furthermore pseudogenes reveal evidence of mutational hotspots.

    But such quandaries are left unmentioned. Evolutionists selectively present the evidence to make evolution appear to be well supported. The evolution lie corrupts scientific knowledge.

  66. Dr. Moran,

    I don’t know about many of those things you bring up, but as to the experiment where large segments of mouse DNA were deleted, I think I have an answer.

    Not all DNA is useful all of the time. It may have a function that only comes into play in certain stages of development, for example. Or perhaps it is triggered as a response to disease but is not active in day to day operations of the cell.

  67. Dr. Moran:

    “‘And in fact, the fossil record supports ID as the “mechanism” better than any other that has been proposed.’

    There are several reasonably intelligent arguments for ID. That’s not one of them.”

    (The first paragraph quotes me.)

    I beg to differ. If you look at the history of any human produced (ie., designed) technology, you will see a pattern of designs coming into being fully formed, existing for a while, and then disappearing (eg., aircraft designs, automobile designs, computer designs). As Gould pointed out, the “trade secret of paleontology” is that the fossil record shows exactly that pattern. Species come into existence suddenly, fully formed, persist unchanged for several million years, and then just as abruptly disappear.

    What one does not see, not in a single instance anywhere in the record, is a species slowly, step by incremental step, transform itself into an organism with any kind of novel feature. You do not see some rodent’s forelimbs incrementally elongating into bat’s wings, or reptilian scales slowly metamorphing into feathers, or fish fins step by incremental step becoming pentadactyl limbs, nor any other such transformation, as Darwin stated should actually be defining quality of the fossil record, given the truth of his theory.

    Can you demonstrate a theory to me that explains what is actually in the fossil record better than ID?

  68. Larry you then state;

    ‘Please explain how our understanding of Alu sequences is an argument from ignorance.’

    Yes Larry please do explain;

    Little-Understood DNA Elements Serve Important Purpose – February 2011
    excerpt: “Previously, no one knew what Alu elements and long noncoding RNAs did, whether they were junk or if they had any purpose. Now, we’ve shown that they actually have important roles in regulating protein production,” said Maquat, the J. Lowell Orbison Chair, professor of Biochemistry and Biophysics and director of the Center for RNA Biology at the University of Rochester Medical Center.
    http://www.sciencedaily.com/re.....131828.htm

    On Not Reading Signature in the Cell: A Response to Francisco Ayala
    Excerpt: This directed distribution of Alu (junk) sequences enhances the semantic and syntactical organization of human DNA. (page down for 33 references of ALU functionality)
    http://www.stephencmeyer.org/n.....art_2.html

    Larry you then state;

    Please explain how the C-Value Paradox and the Onion Test are arguments from ignorance.

    Yes Larry please do explain;

    ,,,The chimpanzee is found to have a 12% larger genome than humans. Thus, at first glance it would seem the chimpanzee is ‘more evolved’ than us humans, but this discrepancy is no anomaly of just chimps/humans. This disparity of genome sizes is found throughout life. There is no logical ‘evolutionary progression’ to be found for the amount of DNA in less complex animals to the size of genomes found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species despite their differences in complexity and this mystery is known as the c-value enigma:

    C-value enigma
    Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical;
    http://en.wikipedia.org/wiki/C-value_enigma

    Exactly how does that help you Larry? I want to know exactly why genomes are all over the place too, and Darwinian thinking certainly offers no meaningful insights into this ‘paradox’. In fact it is in reality unexpected from an evolutionary perspective since information is an suppose to be an ‘emergent’ property of a material basis and thus some overall correlation between complexity and genome sizes was expected, thus why it is called ‘paradox’!

    Larry you then state;

    ‘Please explain how the frequency of fixation of mutations in junk DNA s an argument from ignorance.’

    Yes Larry please do explain the fixation of even one beneficial mutation;

    Dr. Sanford calculates it would take 12 million years to “fix” a single base pair mutation into a population. He further calculates that to create a gene with 1000 base pairs, it would take 12 million x 1000 or 12 billion years. This is obviously too slow to support the creation of the human genome containing 3 billion base pairs.

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

    Simulating evolution by gene duplication of protein features that require multiple amino acid residues: Michael J. Behe and David W. Snoke
    Excerpt: The fact that very large population sizes—10^9 or greater—are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10^8 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.

    Further note; Larry you might want to look at this as well;

    Why The Chromosomal Fusion Argument Doesn’t Wash – Jonathan M – February 2011
    http://www.uncommondescent.com.....esnt-wash/

    Getting Over the Code Delusion – From Junk to Living Organism – November 2010
    Excerpt: So what’s going on? These puzzles turn out to be intimately related. As organisms rise on the evolutionary scale, they tend to have more “junk DNA.” Noncoding DNA accounts for some 10 percent of the genome in many one-celled organisms, 75 percent in roundworms, and 98 percent in humans. The ironic suspicion became too obvious to ignore: maybe it’s precisely our “junk” that differentiates us from water fleas. Maybe what counts most is not so much the genes themselves as the way they are regulated and expressed. Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.

    That suspicion has now become standard doctrine — though a still much-too-simplistic doctrine if one stops there. For noncoding as well as coding DNA sequences continue unchanged throughout the organism’s entire trajectory of differentiation, from single cell to maturity. Lillie’s point therefore remains: it is hardly possible for an unchanging complex to explain an ordered developmental stream. Constant things cannot by themselves explain dynamic processes.
    http://www.thenewatlantis.com/.....e-delusion

    The Origin at 150: is a new evolutionary synthesis in sight? – Koonin – Nov. 2009
    Excerpt: The edifice of the modern synthesis has crumbled, apparently, beyond repair.
    http://www.arn.org/blogs/index....._synthesis

    Modern Synthesis of Neo-Darwinism Is Dead – Paul Nelson – video
    http://www.metacafe.com/watch/5548184/

  69. Larry I would appreciate good solid scientific answers instead of handwaving. What kind of science do you practice, Larry, if you refuse to address the strongest points presented against you? Are you not just deluding yourself?

  70. 70

    Moran cannot show a single biological fact that ID Theory contradicts. So his use of the word “IDiot” to characterize ID proponents cannot be based upon their reasoning having any contradictions with scientific observation.

    So by sheer logical extension, his institutionalized demeaning of those who disagree with him can either be or based upon their reasoning (which doesn’t contradict scientific observation), or, based upon no scientific observation at all, Neither of these two remaining possibilities speak very highly of a person purporting to be scientific, but one or both must be true.

    Yet, Mr. Moran would have all believe that his word is the very testament to Science. This is dramatically evidenced by the fact that (in debate) he constantly refers back to ‘what he (and other biologists) know’ and that he (and these other biologists) are ‘not stupid’ about the issues

    But how can that be? If the conclusions (which drive his appetite to characterize people as IDiots) are a reliable reflection of scientific observation, then the average person might at least expect them to be based upon those scientific observations – but that’s not the case, as has been demonstrated.

    There are two realities that then unfold. Firstly, a scientist whose conclusions aren’t based upon observation is a pseudo-scientist, by definition. It hardly matters that it is a “scientist” who is doing the selling. And secondly, Larry Moran has a certain tone for those who don’t submit to his point of view. The fact is that he couldn’t care less about what the average person thinks on these issues – they are not his audience. His prized words have a very specific target, and it is unto that audience that he may indeed be considered “reliable”.

  71. —Larry Moran: “Do you know who Phillip Johnson is? He’s one of the founders of the intelligent design movement.”

    Of course.

    –”Here’s what he says in Darwin on Trial p. 113.

    –”The essential point of creation has nothing to do with the timing or the mechanisms the Creator chose to employ, but with the element of design or purpose. In the broadest sense, a “creationist” is simply a person who believes that the world (and especially mankind) was designed, and exists for a purpose.”

    Yes. As you will notice, he was talking about belief. He was not providing a formal definition about scientific methodology, which is an entirely different matter. That is why he used the phrase “in the broadest sense.” That is a hint for the reader to look for and be aware of a a more narrow sense and a more rigorous definition.

    From a research standpoint [not a faith standpoint], a Creationist is one who embraces “Creation Science” or Bible-first methodology, as opposed to one who embraces ID or data-first methodology. Darwinists seek to discredit the latter by placing them in the same category as the former.

    –”Are you a creationist in the sense that Johnson describes?”

    Yes, insofar as I “believe” that the universe was created and designed. However, what I believe has nothing at all to do with the scientific methodology I might choose to employ. As Johnson would be the first to tell you, his phrase does not qualify as an accurate descriptor of the ID method, which is the only thing that matters in a scientific context. When Darwinists use the term ID/Creationist, they are either unaware of the distinction (inexcusable) or they mean to mislead their readers into believing that both camps approach science the same way (also inexcusable).

    –”Is Michael Behe? How about Bill Dembski?”

    Here again, we must distinguish between belief and methodology. Neither are methodological “creationists” because neither presupposes Biblical truths as a starting point for their investigation.

  72. Larry,

    In many cases there is genuine scientific controversy about some evolutionary interpretation. Since the science can’t settle the issue right now, both sides have valid positions and neither side is stupid. (Although one side or the other might propose some stupid arguments to support their case.)

    Again, you’re not really responding to the point.

    There are “two sides” because one side is looking at the evidence and deciding that their interpretation is best. At the very least, it’s better than the other guy’s.

    A fair chunk of evolutionary biologists – perhaps the majority, I really don’t know – disagree with your interpretation of the data. They’re saying “Larry is wrong about this. He’s spent his whole life studying evolution, sure, but he’s wrong anyway.”

    Now, maybe you’re saying that the two sides are arbitrary: Taking either of the two (or more!) positions isn’t justified by the data. In which case it’s a game, and you’re telling me “This is what I think about the data, but really, I’m just pulling this out of my ass. The data’s inconclusive, but what the heck, I’m a betting man.” Which is tantamount to saying, “Ignore Larry and the others on this subject. None of them have a clue.”

    Or maybe the positions aren’t arbitrary: There is one best interpretation of the data, but not everyone has it. So there are a lot of guys out there who have “been studying evolution all their life” and still aren’t coming to the conclusion they should. Are they stupid? It seems if you were consistent in your standards, that’s the conclusion you’d arrive at.

    Or, hey, another possibility: Arriving at a conclusion distinct from one’s peers doesn’t imply those who disagree are stupid. So no, you’re not being called stupid just because people disagree with you.

    Oh, and again: Jerry Coyne and others define the belief in evolution devoid of teleology as the (only?) orthodox scientific view. Do you agree with him? It seems you wouldn’t, since you say people who believe evolution is devoid of teleology are atheists, agnostics, or (this seems wrong) Deists, which suggests their views on teleology are outside of science. But if that’s the case, you’re stating that Jerry Coyne – who’s been studying evolution all his life too – isn’t even clear on what he’s studying, or at least he doesn’t know the difference between what is science and what isn’t.

    So are you calling Jerry Coyne stupid? Beats me – I’m still trying to work out your standards here.

  73. PaV @ 37:

    I don’t think long non-coding RNAs have much a bearing, in a big-picture sort of way, on the perceptions and realities of junk DNA. Even if there are 10,000 of them and they are all 3000 nts long, we are speaking about a miniscule fraction of a mammalian genome (about one percent).

    The action (debate-speaking, that is), and the junk, lies in the massive tracts of highly-repetitive DNA.

    What new research does Wells describe that assigns function to all of this class of DNA? Can anyone who has a review copy give us a sneak preview?

    One aside – I’m pretty disappointed that no one has picked up on a glaring omission on my part (and Larry’s). Paul Nelson, if you’re following this, you especially have no excuse. You know why …

  74. Bruce David says,

    You have just proved my point. The meaning of the word “evolution” in a normal context is “change over time”, or “increasing complexity (or some other attribute) over time”. But you have just used it to mean “evolution by a Darwinian (or some other naturalistic) mechanism.” It is you who have co-opted the meaning to suit your purposes (you collectively, not individually).

    Evolution is defined as, “Evolution is a process that results in heritable changes in a population spread over many generations.” [What Is Evolution>]

    A person who describes themselves as an evolutionist will accept that this is the process that describes what we see around us and what we see when we study the history of life.

    Evolutionary theory concerns itself with the mechanisms of evolution. A typical evolutionist will also accept the modern consensus on evolutionary theory.

    You seem to imagine someone who could describe themselves as an evolutionist without accepting the basic premises of evolution.

    Don’t you think you’re being a bit obtuse? Do you have a point?

  75. Larry Moran:

    Evolution is defined as, “Evolution is a process that results in heritable changes in a population spread over many generations.” [What Is Evolution]

    Two points-

    1- That proves Intelligent Design is not anti-evolution

    2- Evolution is a “process”? It’s not the theory of evolution by means of natural selection, genetic drift- it’s the theory of evolution by means of evolution?

    Evolutionary theory concerns itself with the mechanisms of evolution.

    You just said that was evolution- a process is a mechanism, Larry.

    Here, please read the following:

    Biological Evolution, what is being debated

  76. molch @35 – thanks for the kind words.

  77. Larry Moran:

    We’ve understood alternative splicing and overlapping genes for thirty years.

    How come all evolutionary biologists haven’t become believers in God?

    Is it because we’re stupid?

    Or is it because we know more than you do

    1- Not God- I don’t hold that view, thanks

    2- It takes knowledge to be able to edit, splice, proof-read, repair, etc. This is the sort of thing we see software doing and designing agencies doing. There isn’t any evidence that just getting the right chemicals together and all that emerges.

    3- So what do you know Larry? That this stuff just happened- a fluke that just happened to work well enough to be kept around?

    Enlighten me, please.

  78. nullasalus

    Jerry Coyne and others define the belief in evolution devoid of teleology as the (only?) orthodox scientific view.

    What Jerry Coyne does is exactly what the ID proponents do. He conflates his atheism with science as the ID proponents conflate their theism with science. And the beauty about it is that both sides will equally vehemently deny doing so.

  79. Larry Moran:

    When one describes someone as an evolutionist one clearly means that they accept evolution as the mechanism. That means natural selection, random genetic drift etc.etc.

    Both ID and baraminology accept natural selection, genetic drift.

    That is what we have been trying to tell you.

    Natural selection is the result of three processes- (random) variation, heredity and differential reproduction. Nothing much has been observed to arise from that.

    (random) Genetic drift- never been observed to construct any useful multi-part systems.

    All known mechanims and all known mutations do not appear to be capable of the things you think they did.

    IOW evolutionist seems to be a synonym for “imagineer”.

    Just sayin’

  80. myname,

    What Jerry Coyne does is exactly what the ID proponents do. He conflates his atheism with science as the ID proponents conflate their theism with science. And the beauty about it is that both sides will equally vehemently deny doing so.

    When ID proponents (mistakenly in your view) say their beliefs are science, many people cry foul. The NCSE, Biologos, and others all scream about the violation being done to science.

    When Jerry Coyne, PZ Myers, Richard Dawkins and others do it, most of those same groups have little or nothing to say.

    Which is why when Michael Behe suggests that design – not “God’s design”, not even “supernatural design”, but “design of some sort” – can be inferred in nature, up go the cries of outrage.

    When Victor Stenger writes a book calling God a failed scientific hypothesis, and argues that science shows God does not exist, what happens? His book ends up on the NCSE recommended reading list.

  81. Bruce David says,

    As Gould pointed out, the “trade secret of paleontology” is that the fossil record shows exactly that pattern. Species come into existence suddenly, fully formed, persist unchanged for several million years, and then just as abruptly disappear.

    You don’t know what you’re talking about. I suggest you read the comments on Punctuated Equilibria in order to learn about real science.

    What is it with you guys? Do you just make things up? Do you even try to read the scientific literature?

  82. nullasalus says,

    All known mechanims and all known mutations do not appear to be capable of the things you think they did.

    Thanks for letting me know. Guess I’ll look for another line of work.

    What do you do? Do you have any openings for an ex-evolutionist?

  83. Larry,

    nullasalus says,

    Nope. Joseph, not myself.

  84. Larry Moran

    I was very interested in your earlier remark (#28):

    I say that about 10% of our genome contains essential DNA that could not be removed without affecting the survivability of individuals. It’s a much higher percentage in fruit flies and yeast and in bacteria it’s about 90%. (Emphases mine – VJT.)

    I’m curious about the 10% figure. If that’s true for humans then a similar figure is likely true for other mammals – e.g. mice. Here’s my question: if most of a mammal’s DNA is junk, then it should be possible to remove most of a mouse’s DNA without affecting its viability. Later on you state:

    Please explain how the experiment where large segments of mouse DNA were deleted is an argument from ignorance.

    Could I have some references to this experiment please? (I’m not a biologist.) Also, was the viability of the altered mouse’s descendants tracked (say, for about 10 generations)? Just curious.

  85. VJTorley,

    Could I have some references to this experiment please? (I’m not a biologist.) Also, was the viability of the altered mouse’s descendants tracked (say, for about 10 generations)? Just curious.

    Try here.

  86. Dr. Torley, I believe this is the experiment,

    Megabase deletions of gene deserts result in viable mice
    http://www.nature.com/nature/j.....03022.html

    As to ‘how much’ they removed;

    ‘We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length,’

    Yet, the mouse genome is almost as big as ours – 2.7 gigabases. Chopping 2.4 million bases out of it is less than one tenth of one percent or one-one-thousanths.

    they tested viability thus;

    Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice.,,, Some of the deleted sequences might encode for functions unidentified in our screen;

    Yet as scordova noted here;

    http://www.uncommondescent.com.....ent-349935

    Megabase deletions are a horrible way to gauge functionality in complex systems.

    See: Airplane Magnetos Contingency Designs and Reasons ID Will Prevail for the full treatment of that misunderstanding. Hopefully it will that discussion will help cure Darwinist perversions of reality.

    We see this Darwinist misperception played out in a small way:

    Minimal genome should be twice the size, study shows

    “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath.

    “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product.

    When you knock out one gene, the genome can compensate by using an alternative gene.

    But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead.

    Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.”

    That’s the problem with Darwinism. It defines functionality in terms of reproductive success. BAD idea. Andreas Wagner points out tis better to define in functionality in terms of integrated well-matched parts. Hmms sounds more like Behe!

  87. Thanks nullasalus, that was the one I was looking for;

    take home quote;

    Knowles cautions that the study doesn’t prove that non-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she says. “We don’t know if they have abnormalities that we don’t test for.”

    David Haussler of the University of California, Santa Cruz, who has investigated why genetic regions are conserved, says that Rubin’s study gives no hint that the deleted DNA has a function. But he also believes that non-coding regions may have an effect too subtle to be picked up in the tests to far.

    “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argues. “Darwinian selection is a tougher test.”
    http://www.nature.com/news/200.....018-7.html

  88. Dr. Moran,

    I would like to say first, that I can appreciate your position in this thread, because I have been in similar situations myself, although when I am answering numerous opponents coming at me from all sides, it is usually around some aspect of my particular brand of theism. I wouldn’t blame you if you got tired of responding to five different attackers.

    Now, to the point: you said, “Evolution is a process that results in heritable changes in a population spread over many generations.”

    My point (I do have a point) is that this is a very specialized definition of the word. If I said, for example, that my spiritual beliefs have undergone significant evolution since I was in college, or that there has been enormous evolution in the design of computers since the ’50s, in neither case would the definition you gave apply.

    So to call you an evolutionist (instead of a Darwinist) co-opts the normal meaning of the word. The effect of that is to subtly imply that people who are not “evolutionists” don’t accept that life evolved at all, reinforcing the lie that ID proponents are young earth creationists in disguise.

  89. Dr. Moran,

    Well, it looks like nullasalus and bornagain77 have supplied the references to the experiment you describe. Thanks to both of you.

    After reading the article in Nature News by Roxanne Khamsi, my own opinion is that it would be decidedly premature to label 90% of the mouse genome “junk”, especially in view of the fact that it is conserved so well.

  90. Larry Moran,

    I watched your video. I didn’t see any evidence of change. I saw things that were different abruptly. I saw an interpretation of evolution because of abrupt change, but no actual lineage of change. It’s awfully convenient when non-gradual, or abrupt, “change” is evidence of evolution, and so is the alternative of slow and gradual change also an evidence of evolution. So, according to evolutionists, stasis is evidence of evolution, and so is non-stasis, that doesn’t leave much room for an alternative, so what would stand to falsify evolution with regard to “changing” or staying the same? Hmmmm?

  91. Dr. Moran: “You don’t know what you’re talking about. I suggest you read the comments on Punctuated Equilibria in order to learn about real science.”

    Of course I’ve heard of Punctuated Equilibria, Gould’s largely discredited theory which he invented to solve the problem of the “traded secret”. It was the best he could come up with, given that he was PHILOSOPHICALLY, not scientifically, prevented from adopting the obvious solution: life was designed. I say philosophically because it was his commitment to methodological naturalism that was stopping him, not any scientific reasoning on his part.

    You have in no way demonstrated that there is a better solution to the problem of species stasis in the fossil record than ID.

  92. Correction: “trade secret”, not “traded secret” in my previous post.

  93. Larry Moran states;

    ‘I suggest you read the comments on Punctuated Equilibria in order to learn about real science.”

    Actually Larry the first time I read about the post hoc imposition of the punctuated equilibrium model onto the evidence, from Phillip Johnson’s ‘Darwin On Trial’, I was delighted, for it was then I realized that neo-Darwinists did not have anywhere near the evidence they needed to make their case. In fact Larry thanks for the video, I will reference it in the future to clearly illustrate to people how badly the evidence fits Darwinism!

  94. All known mechanims and all known mutations do not appear to be capable of the things you think they did.

    Larry oran:
    Thanks for letting me know. Guess I’ll look for another line of work.

    Thanks for agreeing with me. But no need to look for another line of work. I am sure you will keep getting paid doing what you are doing.

    BTW do you have any evidence of genetic changes accumulating in such a way as to give rise (ie construct) functional multi-protein systems?

    If not that helps my case don’t ya think?

  95. Hey Larry, I wrote this just for the theory of evolution:

    Poof, the magic Mutant (to the tune “Puff the Magic Dragon”)

    Poof the Magic Mutant, a-t-g-c
    And changed them just by randomness just to see what he could be.
    Little Richard Dawkins, loved that rascal Poof.
    And wrote him books to appease the kooks, oh what a silly goof!

    Oh Poof the Magic Mutant, a-t-g-c
    And changed them just by randomness just to see what he could be
    Poof the Magic Mutant, a-t-g-c
    And changed them just by randomness just to see what he could be

    Together they would mutate Poof into a beluga whale
    Richard kept a spectroscope trained on Poof’s mutating tail.
    Nobel things and atheists bowed whene’er they came
    Scientists would lower their flasks when Poof mutated a mane

    Oh Poof the Magic Mutant, a-t-g-c
    And changed them just by randomness just to see what he could be
    Poof the Magic Mutant, a-t-g-c
    And changed them just by randomness just to see what he could be

    Mutations can’t go on forever, just like little boys
    Antennaed wings and giant things doom nature’s mutant ploys
    One gray night it happened, natural selection said no more
    And Poof that Magic Mutant, mutated one last roar

    His head was bent in sorrow, his tears fell like rain
    Richard no longer went to write it gave him so much pain
    Without his life-long friend Dick could not be brave
    So Dick that evo-poofer sadly slipped in to his cave

    Oh Poof the Magic Mutant, a-t-g-c
    And changed them just by randomness just to see what he could be
    Poof the Magic Mutant, a-t-g-c
    And changed them just by randomness just to see what he could be

    (repeat chorus and fade…)

  96. Bruce David says,

    My point (I do have a point) is that this is a very specialized definition of the word. If I said, for example, that my spiritual beliefs have undergone significant evolution since I was in college, or that there has been enormous evolution in the design of computers since the ’50s, in neither case would the definition you gave apply.

    That is correct. The definition I gave is for “biological evolution.” I thought that was clear in context. What we were talking about was a scientific term so I gave a scientific definition.

    If you have a point, it still isn’t coming across. Do you honestly believe that the term “evolutionist” could refer to someone whose spiritual belief changed when they were in college? If you’re confused about that then we have a lot of ground to cover.

  97. vjtorely says,

    After reading the article in Nature News by Roxanne Khamsi, my own opinion is that it would be decidedly premature to label 90% of the mouse genome “junk”, especially in view of the fact that it is conserved so well.

    It would be “premature” to declare that it is a proven fact 90% of our DNA is junk. That’s my informed opinion. Other scientists disagree. This is a genuine scientific controversy.

    Did you happen to read about how much of our genome is evolutionary conserved? Perhaps you can inform the people reading this thread whether it is 90% of the genome or something a wee bit smaller?

    One other thing, I’m curious about your use of “evolutionary conservation.” Do you believe that different species (e.g. humans and chimps) evolved from common ancestors so that when they have identical sequences this is due to conservation? What about when they differ? Is this evidence of evolution?

    By the way, do you think it would be “premature” to declare that there is no junk DNA and thus the predictions of Intelligent Design Creationism have been upheld?

  98. Bruce David says,

    Of course I’ve heard of Punctuated Equilibria, Gould’s largely discredited theory which he invented to solve the problem of the “traded secret”.

    That’s a serious enough distortion of the truth that it labels you as either a liar or someone who is completely ignorant of evolutionary biology.

    Eldredge and Gould did NOT come up with punctuated equilibria to explain the lack of transition fossils. Punctuated equilibria was an observation in the fossil record and they explained it in terms of modern theories of speciation.

    One of the consequences of this observation/theory is that the small transitions between related species—think of the difference between African and Asian elephants—are difficult to observe because they happen rapidly. (Have you ever seen an elephant that’s half Asian and half African?)

    As Gould says in Evolution Is a Fact and a Theory (1983),

    Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists — whether through design or stupidity, I do not know — as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups.

    I find it extremely interesting that the intelligent design community has adopted many of the anti-evolution positions of the old-fashioned Young Earth Creationists. Do you find this interesting?

  99. Joseph asks,

    BTW do you have any evidence of genetic changes accumulating in such a way as to give rise (ie construct) functional multi-protein systems?

    Not sure what you are asking for here. If you’re asking for reasonable inferences based on what we know about molecular evolution then how about the evolution of hemoglobin?

    All the data point to a gene duplication event in an ancestor that only had a single myoglobin gene (one protein). Over time we see species with two different versions of globin genes (alpha and beta) and eventually they come together to form the multiprotein system we know as hemoglobin (two alpha subunits and two beta subunits).

    Will this do? I suspect not. I suspect that every time we come up with a possible answer you will demand more and more details before you accept it.

    If not that helps my case don’t ya think?

    Perhaps. Maybe you could do something for me? Give me a detailed intelligent design explanation for hemoglobin. Please give the same level of detail that you demand from evolutionary biologists and back it up with the same amount of supporting evidence that you expect of an evolutionary explanation.

    If Intelligent Design Creationism is really a scientific theory then you should have no trouble fulfilling this simple request. On the other hand ….

    Waiting …..

  100. La Moran:

    It would be “premature” to declare that it is a proven fact 90% of our DNA is junk. That’s my informed opinion. Other scientists disagree. This is a genuine scientific controversy.

    So two or more cientists who hold differing opinions is a “genuine scientific controversy”? Doesn’t such a thing require genuine scientific data?

    I find it extremely interesting that the intelligent design community has adopted many of the anti-evolution positions of the old-fashioned Young Earth Creationists.

    1- The arguments are anti blind watchmaker, not anti-evolution- how many tims do we have to go over that?

    2- It order to reach a design inference it is mandated that chance and necessity be eliminated first. Meaning both Creation and Intelligent Design have to deal with and eliminate chance and necessity.

  101. Larry Moran:

    If you’re asking for reasonable inferences based on what we know about molecular evolution then how about the evolution of hemoglobin?

    Evolved how? By design or culled willy-nilly?

    Larry Moran:

    All the data point to a gene duplication event in an ancestor that only had a single myoglobin gene (one protein).

    And gene duplication (along with the required regulatory networks) has been determined to be a blind watchmaker process, how?

    Have you read “Not By Chance” by Dr Lee Spetner?

    Larry Moran:

    Will this do? I suspect not. I suspect that every time we come up with a possible answer you will demand more and more details before you accept it.

    It’s OK, for what it is.

    Larry Moran:

    Maybe you could do something for me? Give me a detailed intelligent design explanation for hemoglobin. Please give the same level of detail that you demand from evolutionary biologists and back it up with the same amount of supporting evidence that you expect of an evolutionary explanation.

    I will work on it but for now I ill say that ID is OK with Common Descent- ID says it happens by design.

  102. Larry Moran:

    All the data point to a gene duplication event in an ancestor that only had a single myoglobin gene (one protein).

    Only if you start with there being a common ancestor- that is if you already assume universal common descent.

    The issue being is that it is not verifiable- some duplication event followed by diversification of the duplicated gene did this.

  103. 103

    Larry Moran: “Eldredge and Gould did NOT come up with punctuated equilibria to explain the lack of transition fossils. Punctuated equilibria was an observation in the fossil record and they explained it in terms of modern theories of speciation.”

    I never said that Gould came up with punctuated equilibria to explain “the lack of transition fossils” I said that he invented it to explain the lack of what Darwin claimed should be in the record and what is not, not in one single instance, and which I carefully defined in #67.

    And in addition, punctuated equilibrium is generally NOT accepted by the Darwinist community. (Do YOU accept it as a correct theory?)

    So I challenged you to come up with a theory that explains what is actually observed in the fossil record better than ID. That you have not done.

  104. Dr. Moran,

    ID-ers do not have to explain how the design happen because they are more humble in their theory. They state that some elements of biology and the cosmos exhibit evidence of design. That’s IT! Intelligent design is a much more humble and narrow theory than evolution.

    But evolutinists state that EVERYTHING in biology comes about by naturalistic means. We are right to put them to their proof. Yet when ID-ers point out that many things in life seem to follow the same kinds of patterns of design that we see in human design, they get labled as pseudo-scientists, creationists etc.

    By the way, what would you call Michael Behe who believes in common descent but thinks that there are aspects of life that exhibit design? Is he not an evolutionist? Can you think of a non-insulting label for him?

  105. Larry Moran:

    Perhaps. Maybe you could do something for me? Give me a detailed intelligent design explanation for hemoglobin.

    Use a targeted search starting from a known oxygen carrying macromolecule. As Richard Dawkins and others have demonstrated cumulative selection towards a target is a powerful design tool.

    So we have this primitive globin and we have several targets. Targets which can be used as inputs to find other targets.

    The reason for targets being used to generate more targets is because sometimes all it takes is a subtle tweak to what you already have to get you what you need.

    So the targets would be the monomeric myoglobin and the tetrameric hemoglobins and both were generated from a common input.

  106. —Larry Moran: “By the way, do you think it would be “premature” to declare that there is no junk DNA and thus the predictions of Intelligent Design Creationism have been upheld?”

    In an earlier post, I patiently and courteously [I hope] explained the difference between a belief and a methodology. I also marked the critical distinction between Bible-first methodology [Creationism] and data-first methodology [Intelligent Design]. Even so, you continue to use the term “Intelligent Design Creationism” as if the two methodologies were one and the same. Is this an oversight on your part?

  107. StephenB asks,

    Even so, you continue to use the term “Intelligent Design Creationism” as if the two methodologies were one and the same. Is this an oversight on your part?

    Nope. I reject your premise. I agree with Phillip Johnson that anyone who believes in a creator is a creationist (small “c”). There are various forms of creationism depending on the role of the creator. Young Earth Creationism is one kind and so is Old Earth Creationism. Intelligent Design Creationism is a rather nebulous kind of creationism that encompasses all the others but it nevertheless postulates a creator. (That’s who the intelligent designer is, don’t you know?)

    Theistic Evolution Creationism is another form of creationism.

    Intelligent Design Creationism grew out of Scientific Creationism when it’s leaders decided they needed a new word to try and disguise the religious basis of their agenda. Like its parent, the main activity is attacking evolution and evolutionary biologists. Just look at the comments and the postings on Uncommon Descent if you don’t believe me.

  108. —Larry Moran: “Nope. I reject your premise.”

    But I wasn’t offering you a premise, I was presenting you with a fact. Creationism = Bible first methodology; Intelligent Design = data first methodology. (Stay tuned for an abbreviated history below)

    –”I agree with Phillip Johnson that anyone who believes in a creator is a creationist (small “c”).”

    Johnson was speaking about a belief. Most of us here likely believe that God was the designer. Science, on the other hand, is about methodologies. ID methodologies cannot address the identity of the designer. This is very easy to prove as it is impossible to extract religion from such paradigms as “irreducible complexity” or “specified complexity.” It simply cannot be done.

    –”There are various forms of creationism depending on the role of the creator.”

    There are various forms of creationism with respect to belief, but there is only one form of creationism with respect to methodology. We are talking about scientific methodology, not belief.

    —”Young Earth Creationism is one kind and so is Old Earth Creationism.”

    Same error as above–attributing methodology to a belief system.

    –”Intelligent Design Creationism is a rather nebulous kind of creationism that encompasses all the others but it nevertheless postulates a creator.”

    The phrase is nebulous because it is self contradictory. A methodology cannot begin both with the Bible and with data. As is evident from the law of non-contradiction, a thing cannot be true and false at the same time under the same formal circumstances.

    —”(That’s who the intelligent designer is, don’t you know?)”

    ID paradigms cannot establish the identity of the designer, though its proponents may certainly believe that the designer is the God of the Bible. There is a big difference between believing in an article of faith and making a design inference to the best explanation. It’s another one of those intellectual distinctions which, once grasped, will illuminate the subject matter for anyone who has a modicum of intellectual curiosity.

    —”Theistic Evolution Creationism is another form of creationism.”

    Theistic Evolution is simply an irrational attempt to integrate the guided evolution of Christianity with the unguided evolution of Darwinism. As such, it is just another form of belief. There is no such thing as TE methodology.

    –”Intelligent Design Creationism grew out of Scientific Creationism when it’s leaders decided they needed a new word to try and disguise the religious basis of their agenda.”]

    No, actually that is not the case. I know that Barbara Forrest has become famous for her mindless conspiracy theories, but they are founded solely on her imagination. She knows almost nothing about the subject.

    Let me give you an overview:

    Creationism moves forward: that is, it assumes, asserts or accepts something about God and what he has to say about origins; then interprets nature in that context.

    Intelligent design moves backward: that is, it observes something interesting in nature (complex, specified information) and then theorises and tests possible ways how that might have come to be. Creationism is faith-based; Intelligent Design is empirically-based.

    Each approach has a pedigree that goes back over two thousand years. We notice the “forward” approach in Tertullian, Bonaventure, and Anselm. Augustine described it best with the phrase, “faith seeking understanding.” With these thinkers, the investigation was faith-based.

    By contrast, we discover the “backward” orientation in Justin Martyr, Aristotle, Aquinas, and Paley. Aristotle’s argument, which begins with “motion in nature” and reasons BACK to a “prime mover” — i.e. from effect to its “best” causal explanation — is obviously empirically based.

    So, you can see that the backward method did not grow out of the forward method. They have both been with us all along.

    —”Like its parent, the main activity is attacking evolution and evolutionary biologists.”

    ID proponents do often attack the Darwinist’s proposed mechanism of evolution, [I know I do] but they do not typically attack evolution. Whatever your perception of ID’s “main activity,” or motives, that perception has nothing to do with ID’s scientific methods.

  109. Dr. Moran (#97)

    Thank you for your reply. As regards humans and chimps: I happen to believe that they diverged from a common ancestor six million years ago, and I also believe in common descent. Quite a few ID advocates do. The key point at issue between ID theory and evolutionary biology is not common descent, but whether the vast amount of functional information that we observe in living things required an intelligent source.

    As regards conservation of parts of the genome: I am inclined to think that when two species that diverged tens (or hundreds) of millions of years ago both exhibit the same highly conserved sections of their genome, it would be prudent to regard these regions as having some sort of function. Can these regions then be used to support the thesis of common ancestry? Only if they show additional similarities which are manifestly non-functional – e.g. pseudogenes.

    Finally, as regards the percentage of junk DNA in the genome: Intelligent Design theory does not predict that it should be zero. What I would expect, however, is that any junk DNA which appeared in the human genome (or the genome of any other organism) would be relatively short-lived (disappearing within a few million years), and that the percentage of the genome which is composed of junk would be relatively small (less than 10%).

  110. vjtorley says,

    Finally, as regards the percentage of junk DNA in the genome: Intelligent Design theory does not predict that it should be zero. What I would expect, however, is that any junk DNA which appeared in the human genome (or the genome of any other organism) would be relatively short-lived (disappearing within a few million years), and that the percentage of the genome which is composed of junk would be relatively small (less than 10%).

    Thank-you for your civil reply. I’m a bit confused about Intelligent Design theory, as you describe it.

    Can you explain to me how you arrive at your predictions using this theory? Pluralistic evolution is consistent with the persistence of junk DNA in the genome. Why does Intelligent Design theory say it can exist but will be eliminated in a few million years?

    Your expectation seems to be about the same as a Darwinist (adaptationist). What’s the difference between you and a Darwinist?

  111. StephenB [108], excellent points on ID and methodology!

    This brings to mind a question: after ID identifies design, what’s the next step? ID theorists have identified design many times. Do they keep doing it until their critics accept it? Well, then they’ll keep doing it forever, because their critics are never going to accept it. What can ID scientists do to show the consequences of this discovery? To date, the consequences have mainly been explored philosophically and spiritually. These may be more important in the long run, but what’s the second phase, experimentally? And is anybody going to that second phase?

  112. Larry Moran:
    Intelligent Design Creationism grew out of Scientific Creationism..

    Nope, that is a lie. Intelligent Design has been around since Aristotle.

    And srange how scientifc creationism is still around.

    And by Larry’s logic Darwin was a Creationist and the theory of evolution is a Creationist theory.

    Other people have also weighed in on this- including John Morris, the president of the Institute for Creation Research:

    “The differences between Biblical creationism and the IDM should become clear. As an unashamedly Christian/creationist organization, ICR is concerned with the reputation of our God and desires to point all men back to Him. We are not in this work merely to do good science, although this is of great importance to us. We care that students and society are brainwashed away from a relationship with their Creator/Savior. While all creationists necessarily believe in intelligent design, not all ID proponents believe in God. ID is strictly a non-Christian movement, and while ICR values and supports their work, we cannot join them.”

    In the end it is the failure of Larry and other eolutionary biologists to support the claims of their position that has allowed ID to persist.

  113. QuietID

    after ID identifies design, what’s the next step?

    Study it so we can understand it.

    And as Dawkins said we are looking at a totally different type of biology- meaning there is a lot of work to do.

    It is the difference between geologists studying Stonehenge as a natural rock formaion and archaeologists studying Stonehenge as an artifact.

  114. Stonehenge is a good analogy for the first step of ID, but I think it’s limited for what I’m talking about. Once we know Stonehenge is designed, every question about it becomes either about the designers (“who were they?”) or about the material mechanisms (“how did they build it?”). If the whole point is to separate geologists from archeologists, that’s a pretty narrow task.

  115. QuietID,

    Intelligent Design is about the detection and understanding of (the) design.

    And the only possible way to make any scientific determination about the designer(s) or the specific processes used, in the absence of direct observation or designer input, is by studying the design in question.

    That said look at it from this perspective- say a native Amazon tribe who never saw any modern technology came across an abandoned campsite and found television monitor.

    That is the level we are dealig with as obviously the design we are trying to understand is way above our capabilities to produce.

  116. The point being is that it is easier to understand technology that we are capable of producing, that is of equal or lesser “value” than we already have.

  117. Arthur Hunt [73]:

    The action (debate-speaking, that is), and the junk, lies in the massive tracts of highly-repetitive DNA.

    Arthur, I’d ask you to consider this:

    Think of a car. It has a bumper. Why? To protect the main frame of the car. What is the length of the bumper as compares to the main frame from midpoint forward? Maybe 10%?

    But the bumper, AND, the main frame of the car are meant to protect the driver and passengers. What is the length of the distance between driver and front bumper as a measure of the person’s chest diameter? What? 500%? 600%? And safer cars would have higher percentages.

    Now, applying that to the genome, if parts of the genome are as critical to life as is the human chest containing the heart and other vital organs, then, “STRUCTURALLY”, wouldn’t it make sense to protect that material from excessive compression and elongation, and from the effects of recombination?

    And when the introns are highly-functional, i.e., they are involved in, a part of, the construction of much more than one protein molecule, then they need to be protected even more.

    Per this thesis, based on the “structural strength” and structural needs of the DNA molecule, then as introns do more and more, inter-intronic lengths should increase more and more.

    Is that not what we see?

    So, e.g., how much structural shock absorption does DNA need on ‘each side’ of an intron? Well, three times its length? Four times? Five times?

    If you figure on four times its length, then, pretty much, you have your human genome.

    Any thoughts, reactions?

  118. PaV says,

    So, e.g., how much structural shock absorption does DNA need on ‘each side’ of an intron? Well, three times its length? Four times? Five times?

    If you figure on four times its length, then, pretty much, you have your human genome.

    Exons make up about 2% of the human genome. Introns account for about 35% of the human genome.

    I’m not sure I understand your argument. Are you saying that all of the intron sequences are essential in every gene?

    If that’s true then why do intron lengths vary so much from species to species. Does Intelligent Design Creationism have an explanation for that observation?

    What about species, like yeast, where the amount of intron sequence is less than the amount of coding sequence? Do you have a general theory of intelligent design that accounts for such a fact?

  119. Larry,

    Your position doesn’t have any explanation for introns and exons and alternative gene splicing. All you can say is “it just is”.

    Yes ID has an explanation for introns- alternative gene splicing- that is getting more than one protein product out of the same sequence. This gives the design a great deal of flexibility.

    But Intelligent Design Creationism can’t explain it because Intelligent Design Creationism only exists in the minds of the willfuly ignorant, and here you are, again.

  120. Joseph says,

    Yes ID has an explanation for introns- alternative gene splicing- that is getting more than one protein product out of the same sequence. This gives the design a great deal of flexibility.

    In other words, there’s no difference between an “ID” explanation and an adaptive explanation, right?

    So, why do you refer to your explanation as “intelligent design”? Why don’t you just accept the fact that adaptive evolution provides a perfectly good explanation for introns and alternative spicing?

  121. Larry Moran:

    In other words, there’s no difference between an “ID” explanation and an adaptive explanation, right?

    Wrong again. ID is the only explanation for the planning required for alternative gene splicing. ID is the only explanation for the knowledge required to edit, splice, proof-read and error correction.

    So, why do you refer to your explanation as “intelligent design”?

    Because ID is the only feasible explanation.

    Why don’t you just accept the fact that adaptive evolution provides a perfectly good explanation for introns and alternative spicing?

    What is the evidence that adaptive evolution can produce a plan?

  122. Larry:

    I’m just now noticing your question.

    I was not thinking in the least about exons. Rather, I was thinking about the distal ends of the intron region (which also contains the exons) which, quite possibly, require some ‘insulation’ from the mechanical processes taking place during replication and transcription.

    As to this rant of yours:

    If that’s true then why do intron lengths vary so much from species to species. Does Intelligent Design Creationism have an explanation for that observation?

    What about species, like yeast, where the amount of intron sequence is less than the amount of coding sequence? Do you have a general theory of intelligent design that accounts for such a fact?

    First, how should I know why the intron lengths vary? Isn’t that what science is supposed to find out?

    Here’s the difference: when it is found out why it is “BETTER” that intron lengths vary, Darwinists will say: “Evolution brought about this variation in the intron length because ____________________ (and fill in the blank; i.e., whatever reason it is that varied length is BETTER), while IDers will say that there was a ‘design reason’ for varying the length of introns.

    Same science; different interpretations. Here’s the IMPORTANT difference: which of the two ‘interpretations’ is more plausible; i.e., has greater ‘explanatory power’?

    Darwinists, no matter what is found in nature, simply presume that EVOLUTION can do anything. But, you see, it’s a “presumption”, not a “proof”.

Leave a Reply