Home » 'Junk DNA', Darwinism » Darwinist response to Wells’ junk DNA book: PZ Myers threatens to read it

Darwinist response to Wells’ junk DNA book: PZ Myers threatens to read it

The Myth of Junk DNAAs David Klinghoffer puts it at ENV:

Over the weekend, Jonathan Wells’s The Myth of Junk DNA broke into the top five on Amazon’s list of books dealing with genetics — a list normally dominated at its pinnacle by various editions of Richard Dawkins’ The Selfish Gene. Not bad, Jonathan.The juxtaposition with Dawkins’ Selfish Gene is appropriate, notwithstanding the demurrals of biochemist Larry Moran et al. Dawkins and other Darwinists, such as Jerry Coyne, have indeed posited that neo-Darwinian theory predicts that swaths of the genome will turn out to be functionless junk. The Junk DNA argument has been a pillar of the Darwin Lobby’s efforts to seduce public opinion and influence public policy. Professor Moran wants to imagine that Dawkins never held that neo-Darwinism predicts junk DNA. But that’s not how other Darwinists see it. (Compare, for example, Dennett’s Darwin’s Dangerous Idea, page 316.)

So far, with none of them having actually read the book (though P.Z. Myers threatens to do so), the Darwin apologists’ response to The Myth of Junk DNA has followed along four lines of defense.

1) The usual insults. In his blog Larry Moran of the Department of Biochemistry at the University of Toronto, a grown man and from the looks of him not a young one either, repetitively derides Jonathan as an “IDiot.” (How embarrassing for this mature gentleman, you might think. Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as “Larry Moron” or similar? The question is self-answering and tells you a lot about how desperation kindles anger among these people.)

- David Klinghoffer, “Junk DNA and the Darwinist Response so Far”ENV May 16, 2011 More.

UD News interview with Wells on his book, here.

Reb Moshe: PZ, What did you just say? You’re “thinking of picking up a copy of his book … well, hadn’t you better?” Or are you just a tourist around here? And haven’t we had this conversation already?

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86 Responses to Darwinist response to Wells’ junk DNA book: PZ Myers threatens to read it

  1. It’s important to understand that Well’s does not argue that most of the genome is not junk, but rather that the more we learn about it, the more we find what we previously assumed was junk turn out to serve some purpose or function after all.

    The “junk DNA” argument is turning out to be a “Darwinism of the gaps” fallacy, based not on what we do know, but rather on what we don’t know, and as science progresses, the junk appears to be in retreat.

  2. Perhaps if you can put your concerns with incivility to the side for a moment and focus on content, I wonder if you have actually read Larry Moran’s explanations for junk DNA? These reasons demonstrate with high levels of certainty that the genome bears large amounts of junk.

    i.e. this and this and this and this amongst many others. At least read the first link.

  3. Mung @ 1

    Sure – it is good that this is Well’s argument, but then isn’t the title misleading?

    Again, Larry Moran has addressed this point on several occasions. Sure, there are frequent discoveries of function in genomic parts previously thought to be junk. But, if you simply state that in words, it gives the false impression that we are progressing towards a 100% functional genome. We are not – such discoveries count for tiny parts of the genome.

  4. paulmc, defends, via Moran, the materialistic presupposition of ‘If we don’t understand its function then it probably doesn’t have any function’,,, Which reminds me exactly like the vestigial argument of neo-Darwinists of yore which has now, after much research and many years, been completely demolished ,,, be that as it may that the neo-Darwinists were completely, utterly, wrong on vestigial organs, are neo-Darwinists now justified in labeling the vast swaths of DNA, which they really have no firm understanding of, junk??? According to ENCODE (and common sense), NO they don’t!!!

    Concluding statement of the ENCODE study:
    “we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more ‘neutral’ view of many of the functions conferred by the genome.”
    http://www.genome.gov/Pages/Re.....e05874.pdf

    further notes,,,

    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

    Human Genome “Infinitely More Complex” Than Expected – April 2010
    Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said,,,, Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.”
    http://www.creationsafaris.com.....#20100405a

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

    ,,,Contrary to Darwinian expectations (requirement) for ‘junk DNA’, the complexity being uncovered in genomes keeps increasing dramatically as our resolution increases:

    Most Detailed Annotation of Fruit-Fly Genome Points Way to Understanding All Organisms’ Genomes – December 2010
    Excerpt: “We also found an order-of-magnitude increase in the ways that genes are spliced and edited to produce alternate forms of known proteins, thus significantly increasing the complexity of the proteome.”,,, Despite the scrutiny to which the Drosophila genome has been subjected, the researchers found new or altered exons or splice forms in almost three-quarters of Drosophila’s previously annotated genes,,,
    http://www.sciencedaily.com/re.....131131.htm

    This following study, that discovered a ‘Second Regulatory Code” on top of the protein coding DNA code, should have, by all reasonable accounts, completely stopped the neo-Darwinian claim for ‘Junk DNA’ dead in its tracks:

    Nature Reports Discovery of “Second Genetic Code” But Misses Intelligent Design Implications – May 2010
    Excerpt: Rebutting those who claim that much of our genome is useless, the article reports that “95% of the human genome is alternatively spliced, and that changes in this process accompany many diseases.” ,,,, the complexity of this “splicing code” is mind-boggling:,,, A summary of this article also titled “Breaking the Second Genetic Code” in the print edition of Nature summarized this research thusly: “At face value, it all sounds simple: DNA makes RNA, which then makes protein. But the reality is much more complex.,,, So what we’re finding in biology are:

    # “beautiful” genetic codes that use a biochemical language;
    # Deeper layers of codes within codes showing an “expanding realm of complexity”;
    # Information processing systems that are far more complex than previously thought (and we already knew they were complex), including “the appearance of features deeper into introns than previously appreciated”
    http://www.evolutionnews.org/2.....of_se.html

    This following paper highlights the regulatory role that the ‘second code’ has over the primary protein coding DNA code:

    Researchers Crack ‘Splicing Code,’ Solve a Mystery Underlying Biological Complexity
    Excerpt: “For example, three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain,” says Frey. “Previously, researchers couldn’t predict how the genetic messages would be rearranged, or spliced, within a living cell,” Frey said. “The splicing code that we discovered has been successfully used to predict how thousands of genetic messages are rearranged differently in many different tissues.
    http://www.sciencedaily.com/re.....133252.htm

    etc.. etc.. etc…

    ,,, neo-Darwinists think nothing of making such sweeping claims for vast swaths of Junk DNA, in the face of such apparent complexity. Claims which are clearly based on nothing more than their ‘religiously motivated’ atheistic/materialistic beliefs. But alas neo Darwinists arguing from a ‘theological’ basis, instead of a sober empirical basis, is how it has been from the beginning:

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species
    http://www.evolutionnews.org/2.....46391.html

  5. … but then isn’t the title misleading?

    No.

    Wells is also the author of Icons of Evolution and this is just another icon.

  6. No ba77 – honestly – I don’t have time nor energy to wade through your creation website links.

    Read some of the evidence for junk DNA and then try discussing it in your own words.

    For example, why not discuss Larry’s breakdown of the human genome (my first link above).

  7. Mung:

    No.

    Wells is also the author of Icons of Evolution and this is just another icon.

    The title of the book is The Myth of Junk DNA.

    The first post you wrote above states: “It’s important to understand that Well’s does not argue that most of the genome is not junk”

    …meaning junk DNA is not a myth. But ‘myth’ means the idea must be definitively wrong. Myth is the wrong word if your characterisation of the book is correct.

  8. Myth is the wrong word if your characterization of the book is correct.

    If I understand Wells correctly, the Myth is that “junk DNA” is evidence for Darwinism and evidence against Intelligent Design.

    So you’re reading the title as “Junk DNA is a Myth.” But that’s not the title.

  9. paulmc, what amazes me is that you neo-Darwinists have the audacity to pronounce vast swaths of the DNA, which you don’t even begin to have a firm clue as to its complete functionality, to be junk. Yet despite such deluded confidence to make such pronouncements, you guys cannot even account for the origination of a single functional gene within the genome;

    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

    (novel genes of which humans have over 1000 completely unique functional genes);,,

    ,,, nor can you guys even account for the origination of a single novel functional protein;

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

    “Blue Gene’s final product, due in four or five years, will be able to “fold” a protein made of 300 amino acids, but that job will take an entire year of full-time computing.” Paul Horn, senior vice president of IBM research, September 21, 2000
    http://www.news.com/2100-1001-233954.html

    Networking a few hundred thousand computers together has reduced the time to a few weeks for simulating the folding of a single protein molecule:

    A Few Hundred Thousand Computers vs. A Single Protein Molecule – video
    http://www.metacafe.com/watch/4018233

    Francis Collins on Making Life
    Excerpt: ‘We are so woefully ignorant about how biology really works. We still don’t understand how a particular DNA sequence—when we just stare at it—codes for a protein that has a particular function. We can’t even figure out how that protein would fold—into what kind of three-dimensional shape. And I would defy anybody who is going to tell me that they could, from first principles, predict not only the shape of the protein but also what it does.’ – Francis Collins – Former Director of the Human Genome Project
    http://www.pbs.org/wgbh/nova/t.....enome.html

    ,,,nor can you guys even account for the fixation of a single beneficial mutation within the human genome;

    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/

    ,,,yet despite the sheer, staggering, unmatched, complexity found in DNA;

    Do you believe Richard Dawkins exists?
    Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives.
    http://creation.com/does-dawkins-exist

    ,,,complexity that even makes our top engineers in quantum computing drool;

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

    ,,,you want to lecture me that I just don’t understand ‘junk DNA”???!!!??? EXCUSE ME paulmc, I have a much better idea, I suggest that you completely wipe the backboard of your mind clean of the only true ‘junk’ that is around this place, and that would each and every piece of neo-Darwinian garbage that you have swallowed through the years!!!

    further note:

    The ‘parallel’ complexity of genes is far, far beyond, human capability!!

    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

    etc.. etc.. etc..

  10. Mung says:

    If I understand Wells correctly, the Myth is that “junk DNA” is evidence for Darwinism and evidence against Intelligent Design.

    Sorry, but that is not correct. Read what Wells says in an interview with O’Leary on this very website:

    “If the Ming vase is a living cell and the leftover carpet nails are “junk DNA,” it turns out that the nails are not only made of gold, but they also make an essential contribution to the beauty of the vase….
    Like Haeckel’s faked embryo drawings and staged photos of peppered moths, junk DNA is not science, but myth.

    [Collins] and other promoters of the myth of junk DNA have put their faith in a “Darwin of the gaps” argument that must now retreat in the face of new advances in genome research.”

    This is a direct claim that “junk DNA” is not only potentially useful but essential. No scope is allowed for any of the genome to be junk in these quotations.

    Wells plainly claims that the existence of junk DNA is a myth.

  11. paulmc, how much of mouse DNA is junk in this test for functionality?

    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.....20011.html

    and paulmc, besides your preconceived philosophical bias for atheistic neo-Darwinism, what good reason would you have for ignoring such astonishing evidence for ‘whole’ functionality of DNA and to continue to argue that vast swaths of DNA are junk? This is science paulmc, this is not theology!!! The Evidence could care less about your feelings!!!

  12. semi OT: new podcast up at ‘ID The Future’;

    “An Insurmountable Problem for Darwinian Evolution”
    http://intelligentdesign.podom.....1_43-07_00

  13. what good reason would you have for ignoring such astonishing evidence for ‘whole’ functionality of DNA and to continue to argue that vast swaths of DNA are junk?

    Assuming you don’t mean that rhetorically, I have attempted to point you in the direction of (nice summaries of) this evidence. It is up to you to read it.

  14. paulmc, you are trying to force your philosophical bias against the evidence., I’m trying to point you in the CORRECT direction, yet you stubbornly choose to be misled despite the fact we are dealing with information processing that absolutely dwarfs our puny human capabilities. Perhaps you should write Bill Gates and tell him to stop spending money trying to cull programming secrets out of the programming of DNA since you are so convinced that DNA is for the most part junk????

    Bill Gates, in recognizing the superiority found in Genetic Coding compared to the best computer coding we now have, has now funded research into this area:

    Welcome to CoSBi – (Computational and Systems Biology)
    Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas.
    http://www.cosbi.eu/index.php/.....rticle/171

    ,,,Tell you what paulmc, I give you a chance to show me how commited you are to scientific integrity, falsify this, then you might have a leg to stand on in this first place scientifically, and you will have my attention;

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8 ) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    http://www.scitopics.com/The_L.....iency.html

  15. paulmc, you are trying to force your philosophical bias against the evidence., I’m trying to point you in the CORRECT direction

    Perhaps read the evidence before attempting to condescend to me.

    As for philosophical biases – why don’t you explain to me why each of the 1 million copies of Alu in the human genome is necessary.

    I happily accept that transposable elements are occasionally functional. But I don’t accept that this explains their copy numbers in the genome.

  16. 16

    I read the links that paulmc posted. I noticed this comment in the blogpost of the Moran fellow, in the oldest entry of the paulmc links.

    “The only way out of this box—without abandoning your assumption about humans
    being the most complex animals—is to make up some stories about the function of
    so-called junk DNA. If it turns out that there are lots of hidden genes in that
    junk then maybe it will
    rescue your assumption.”
    Mr. Moran 2007

    –How much does “lots” mean? Since this 2007 post, much info concerning the junky regions not being so junky has come to light (aside from the har-1 stinger). Does that mean the the assumptions of whomever the Moran nemesis was/is have been rescued?

  17. paulmc, you state;

    ‘why don’t you explain to me why each of the 1 million copies of Alu in the human genome is necessary.’

    Thus your philosophical/theological bias is, if we don’t know the function of it then it therefore has no function??? Is not this the same exact reasoning that led to the vestigial organ fiasco of neo-Darwinists???

    “The thyroid gland, pituitary gland, thymus, pineal gland, and coccyx, … once considered useless by evolutionists, are now known to have important functions. The list of 180 “vestigial” structures is practically down to zero. Unfortunately, earlier Darwinists assumed that if they were ignorant of an organ’s function, then it had no function.”
    “Tornado in a Junkyard” – book – by former atheist James Perloff

    ,, paulmc it is sheer arrogance for neo-Darwinists to assume that the parts of the DNA that we have not figured the function out for yet is ‘Junk’, ESPECIALLY considering the fact that from what we are able to grasp of DNA complexity we realize we are dealing with information processing that is orders of magnitude greater than anything we have yet devised in our most sophisticated computer programs. ,,, Indeed arrogance of a high order!!! Why such unreasonable arrogance paulmc, why do you let you atheism dictate your science instead of following the evidence where it leads???

  18. Moreover paulmc, you seem to completely miss the point of the null hypothesis I listed. Neo-Darwinists have NEVER demonstrated the generation of ANY functional information WHATSOEVER. Yet despite the FACT you have no evidence that neo-Darwinism can do anything that you claim that it can do, you act as if I should treat your opinions on other questions of information in DNA as if they mattered!!! Do you see the complete disconnect here paulmc??? Why in blue blazes should I treat your ‘scientific opinion’ with any more respect than someone who insisted perpetual motion machines are feasible???

  19. Okay 77 – perhaps you can manage a simpler question then:

    Considering that it is a retrotransposon, what do you think is the best current explanation for having more than a million copies of Alu in the human genome?

  20. 20

    the alu debacle seems to be divided, again by the junk, not-junk camps:

    Some scientists regard Alu as an example of “selfish DNA” – it encodes no protein and appears to exist only for its own replication. If one reduces the definition of life to “the perpetuation and amplification of a DNA sequence through time,” then Alu is an extremely successful life form. However, other scientists believe that transposable elements have played an important role in evolution by creating new mutations and gene combinations. Nobel laureate Barbara McClintock hypothesized that transposable elements provide a mechanism to rapidly reorganize the genome in response to environmental stress. Like Alu, the Ds transposable element discovered in corn by McClintock is a defective transposon and requires the help of a second element called Ac (activator).

    http://www.geneticorigins.org/pv92/aluframeset.htm

  21. paulmc, first quit playing stupid games and falsify the null hypothesis so that you have a ‘scientific leg to stand on!!! Second, you really are having a extremely hard time seeing your philosophical/atheistic bias in all this aren’t you. paulmc, JUST BECAUSE WE DO NOT KNOW THE FUNCTION DOES NOT MEAN IT HAS NO FUNCTION!!! moreover from what we can grasp of the information processing in the cell that far, far, surpasses anything we have ever accomplished in our most advanced programs, it is sheer arrogance for atheists to presuppose that simply because we do not understand the function therefore it is functionless. ESPECIALLY since the atheists have no scientific foundation to explain the information we find in the first place.

  22. I am more than happy to discuss other issues later – but one thing at a time. I will remind you that the topic of this thread is junk DNA, and you are going off topic by asking other questions. (I will respond to your other questions later but let’s at least stick to the task at hand for a moment.)

    So, please, answer my question:

    Considering that it is a retrotransposon, what do you think is the best current explanation for having more than a million copies of Alu in the human genome?

  23. paulmc believe whatever you want, you will anyway despite what the evidence says!!, If it trips your trigger to believe most of the DNA is functionless just because no one has figured out complete functionality of the DNA then go for it, It is your life to throw away as you wish on futile fantasies. Yet paulmc please carefully consider that the staggering complexity being dealt with, that we mere mortals may very well never figure out completely, has just begun to be looked at!! Should you not be a bit more humble in your opinion of yourself to say what is and is not functional at this point of investigation. And if you can’t find such humbleness in yourself in the face of such wondrous complexity, why do you insist that we also adopt the unwarranted arrogance to call it functionless at this point.

  24. 24

    Why the title of the “Myth of Junk DNA” is not misleading in the least.

    From New York times:

    “The human genome is riddled with dead genes, fossils of a sort, dating back hundreds of thousands of years — the genome’s equivalent of an attic full of broken and useless junk.”

    http://www.nytimes.com/2010/08.....0gene.html

    It is evident that the idea of “junk dna” has seeped into pop culture, media etc, and has worked well with the ideology that the NYT promotes, and ideology that generally utilizes, and possibly relies heavily on, the neo-darwinst perspective. (Most likely why “junk dna” has in fact reached legendary status within those circles.) Certainly held up like a trophy by the Dawkins types. Now with the initial findings of the newer research, the damage control has already started.

    The NYT excerpt was the lead-in. This article was written in 2010.

  25. What an odd response!

    All I asked was what you think the best explanation for an observed phenomenon – i.e. I tried to discuss the evidence that you claim I am avoiding. Yet, you baulk at the first question!

    Will you not answer the question at all? If not, you have no grounds to claim that I am the one avoiding the evidence.

    A final time – and I shall not respond to you if you refuse again – Considering that it is a retrotransposon, what do you think is the best current explanation for having more than a million copies of Alu in the human genome?

  26. …why don’t you explain to me why each of the 1 million copies of Alu in the human genome is necessary.

    It’s a trick question!

    Only 999,999 are actually necessary.

    When Jesus told the parable of the shephard leaving the 99 sheep, he was just rounding down.

    So here, in our own human DNA, we see the parable of the good shephard written. Yet more irrefutable evidence of Intelligent Design!

    Take that you doubting doubter!

  27. Mung – lovely parable. But where is the evidence for the claim that vast numbers of Alu repeats are ‘necessary’? Considering, in particular, that they are retrotransposons.

    Perhaps we have the reverse of your parable. 1 sheep remains and 99 sheep ran into the wilderness…

  28. paulmc, I hope you understand that what I wrote was humor. I’m not like BA77 and I don’t think he’s doing ID any favors.

    I have no idea whether there are 1, or 999,999, or 999,999 + 1 ALU repeats and I don’t intend to research the matter. I have other things I’m interested in right now that are taking up my attention.

    To answer your question, I could not possibly tell you how many are necessary or indeed if any at all are necessary.

    However, I do happen to be reading Wells’ book (among others).

    But right now I am at work and it is at home, so I can’t just now respond to you concerning what he may say specifically in the book about what he means in using the term “Myth” in the title.

  29. Mung – yes I’m aware that was lighthearted :)

    If I could say one thing, I really would recommend learning more about the genome before reading Wells’ book. It would surely give some valuable context to his writing.

  30. BA77 – even if paulmc is biased I don’t see why that stops you from answering the question. Science is about asking questions. Maybe some of them make no sense but . . . . shouldn’t we always try to test the boundaries of knowledge?

    I would also like to ponder the use of DNA testing for ‘relatedness’. In my understanding some bits of repeated genome are compared and if two individuals have the same number of repeats then they are most likely related. Which brings up the question: what possible function could the repeated sections have if different people have different number of repeats?

    I’m not trying to get at someone but you have to admit it’s an interesting question no matter what your assumptions.

  31. If I could say one thing, I really would recommend learning more about the genome before reading Wells’ book. It would surely give some valuable context to his writing.

    And I would recommend not making unwarranted assumptions.

  32. BA77 – also, looking at the evidence means ALL the evidence, paulmc’s included. He was just trying to make sure you had seen some of the evidence.

  33. Mung:

    And I would recommend not making unwarranted assumptions.

    I was responding to your statement that you “have no idea whether there are 1, or 999,999, or 999,999 + 1 ALU repeats“. This certainly has bearing on the validity of Wells’ thesis.

  34. ellazimm states:

    ‘BA77 – also, looking at the evidence means ALL the evidence, paulmc’s included. He was just trying to make sure you had seen some of the evidence.’

    Now let’s get this straight, neither paulmc, Moran, nor anyone else, has a firm clue as to complete functionality of DNA, and even though, from what little researchers have thus far gathered, we know that the programming of DNA is orders of magnitude greater than anything man has ever devised, we are to assume that most ALU repeats are junk because??? because??? well because by-golly atheists insist that if we don’t completely understand the function of a DNA sequence then it must be junk!!! Why do atheists insist that we do this unwarranted step??? Well because by-golly it is mandated by their number one piece of evidence for evolution,,, it is motivated by their a-priori philosophical/theological commitment that ‘God would not have done it that way’, and not by any reasoned look at ALL the evidence coming out of DNA research on their part,,,

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species
    http://www.evolutionnews.org/2.....46391.html

    notes:

    ,, Despite the fact the neo-Darwinists have not even generated a single novel functional protein or gene, much less any sophisticated functional information, by evolutionary processes we find stuff like this in the cell,,,

    10 Ways Darwin Got It Wrong
    Excerpt: As molecular biologist Jonathan Wells and mathematician William Dembski point out: “It’s true that eukaryotic cells are the most complicated cells we know. But the simplest life forms we know, the prokaryotic cells (such as bacteria, which lack a nucleus), are themselves immensely complex.,,, There is no evidence whatsoever of earlier, more primitive life forms from which prokaryotes might have evolved” (How to Be an Intellectually Fulfilled Atheist (or Not), 2008, p. 4). These authors then mention what these two types of cells share in terms of complexity:

    • Information processing, storage and retrieval.
    • Artificial languages and their decoding systems.
    • Error detection, correction and proofreading devices for quality control.
    • Digital data-embedding technology.
    • Transportation and distribution systems.
    • Automated parcel addressing (similar to zip codes and UPS labels).
    • Assembly processes employing pre-fabrication and modular construction.
    • Self-reproducing robotic manufacturing plants.
    So it turns out that cells are far more complex and sophisticated than Darwin could have conceived of. How did mere chance produce this, when even human planning and engineering cannot?
    http://www.gnmagazine.org/issu.....-wrong.htm

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

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

    Scientists’ 3-D View of Genes-at-Work Is Paradigm Shift in Genetics – Dec. 2009
    Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these ‘hot spots’. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
    http://www.sciencedaily.com/re.....160649.htm

    And if ALU sequences truly served no function, why in blue blazes does the cell take so much care to repair it from alteration/mutation:

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

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.arn.org/blogs/index....._contradic

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    ============

    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

  35. 35

    I’m with bornagain77!

    Evolutionists once again find themselves on a sinking island over junk DNA. Having previously enjoyed a vast landmass of ignorance, each passing month, the water level of knowledge is swallowing up the land and it’s starting to get very damp on the ground.

    BA77 is absolutely right to point out the similarity between evolutionists’ failed predictions about vestigial organs and evolutionists’ failed predictions about junk DNA. How many decades have those unscientific attitudes put us back? It is a wonderful thing that, amongst the many useful functions that an appendix provides, one of them is to provide a safe haven for ‘good’ bacteria in our body. But, thanks to the flawed evolutionary mindset, many still consider the appendix to be a useless piece of junk.

    When we discovered that human genes comprise only 2% of human DNA, evolutionists told us, with ‘scientific certainty’ that the remaining 98% of our DNA is just junk. This is exactly what the theory of evolution predicted, they told us. But then, we started to discover function in portions of that so-called junk. So, we were told that over 90% of our DNA is just junk. And that figure has been diminishing ever since as the waters of knowledge come flooding in. Now it’s, “Look, there is still a lot of junk in our DNA. Believe me, there is a (neo-darwinistic) scientific consensus here!”.

    BA77 is absolutely right to point out that this claim is absolutely ridiculous. Evolutionists were wrong about vestigial organs. They were wrong about 98% of our DNA being junk. And though that figure is diminishing as we learn more and more about the cell (we’re still just scratching the surface), evolutionists are still claiming that there is junk in our DNA. It’s just like a kid opening up some sort of electronic toy, putting it back together again but having screws and other components left over and then throwing them away because they’re “just junk”. If evolutionists were genuinely interested in scientific knowledge (rather than being, in truth, mere atheists with scientific pretensions) then they would withhold any further judgement on so-called junk DNA until at least another decade of well-funded and well-organised research had taken place. But they don’t. They must cling on to junk DNA because 21st century science has already destroyed the rest of their evidence for evolution.

    And there’s no sign of that rescue helicopter yet so I hope they can swim!

  36. of note to ALU functionality;

    On Not Reading Signature in the Cell: A Response to Francisco Ayala (Part 2) – Stephen Meyer
    Excerpt: Further, the Alu sequences that Ayala specifically cites as prime examples of widely and randomly distributed nonsense sequences in the human genome are NOT non-functional or “nonsense.” Short Interspersed Nuclear Element (SINE) sequences of which Alu is one member, perform numerous formatting and regulatory functions in the genomes of all organisms in which they have been found. It is simply factually incorrect for Ayala to claim otherwise.

    In general, SINEs (and thus Alus) allow genetic information to be retrieved in multiple different ways from the same DNA data files depending on the specific needs of different cell types or tissues (in different species-specific contexts). In particular, Alu sequences perform many taxon-specific lower-level genomic formatting functions such as: (1) providing alternative start sites for promoter modules in gene expression–somewhat like sectoring on a hard drive (Faulkner et al., 2009; Faulkner and Carninci, 2009); (2) suppressing or “silencing” RNA transcription (Trujillo et al., 2006); (3) dynamically partitioning one gene file from another on the chromosome (Lunyak et al., 2007); (4) providing DNA nodes for signal transduction pathways or binding sites for hormone receptors (Jacobsen et al., 2009; Laperriere et al., 2004); (5) encoding RNAs that modulate transcription (Allen et al., 2004; Espinoza et al., 2004; Walters et al., 2009); and (6) encoding or regulating microRNAs (Gu et al., 2009; Lehnert et al., 2009).

    In addition to these lower-level genomic formatting functions, SINEs (including Alus) also perform species-specific higher-level genomic formatting functions such as: (1) modulating the chromatin of classes of GC-rich housekeeping and signal transduction genes (Grover et al., 2003, 2004; Oei et al., 2004; see also Eller et al., 2007); (2) “bar coding” particular segments for chromatin looping between promoter and enhancer elements (Ford and Thanos, 2010); (3) augmenting recombination in sequences where Alus occur (Witherspoon et al., 2009); and (4) assisting in the formation of three-dimensional chromosome territories or “compartments” in the nucleus (Kaplan et al., 1993; see also Pai and Engelke, 2010).
    Moreover, Alu sequences also specify many species-specific RNA codes. In particular, they provide: (1) signals for alternative RNA splicing (i.e., they generate multiple messenger RNAs from the same type of precursor transcript) (Gal-Mark et al., 2008; Lei and Vorechovsky, 2005; Lev-Maor et al., 2008) and (2) alternative open-reading frames (exons) (Lev-Maor et al., 2007; Lin et al., 2008; Schwartz et al., 2009). Alu sequences also (3) specify the retention of select RNAs in the nucleus to silence expression (Chen et al., 2008; Walters et al., 2009); (4) regulate the RNA polymerase II machinery during transcription (Mariner et al., 2008; Yakovchuk et al., 2009; Walters et al., 2009); and (5) provide sites for Adenine-to-Inosine RNA editing, a function that is essential for both human development and species-specific brain development (Walters et al., 2009).
    Contrary to Ayala’s claim, Alu sequences (and other mammalian SINEs) are not distributed randomly but instead manifest a similar “bar-code” distribution pattern along their chromosomes (Chen and Manuelidis, 1989; Gibbs et al., 2004; Korenberg and Rykowski, 1988). Rather like the distribution of the backslashes, semi-colons and spaces involved in the formatting of software code, the “bar-code” distribution of Alu sequences (and other SINEs) reflects a clear functional logic, not sloppy editing or random mutational insertions. For example, Alu sequences are preferentially located in and around protein-coding genes as befits their role in regulating gene expression (Tsirigos and Rigoutsos, 2009). They occur mainly in promoter regions–the start sites for RNA production–and in introns, the segments that break up the protein-coding stretches. Outside of these areas, the numbers of Alu sequences sharply decline. Further, we now know that Alu sequences are directed to (or spliced into) certain preferential hotspots in the genome by the protein complexes or the “integrative machinery” of the cell’s information processing system (Levy et al., 2010). This directed distribution of Alu sequences enhances the semantic and syntactical organization of human DNA. It appears to have little to do with the occurrence of random insertional mutations, contrary to the implication of Ayala’s “sloppy editor” illustration and argument.

    Critics repeatedly claim that the theory of intelligent design is based on religion, not science. But in his response to my book, it is Ayala who relies on a theological argument and who repeatedly misrepresents the scientific literature in a vain attempt to support it. The human genome manifests nonsense sequences and sloppy editing ill-befitting of a deity or any truly intelligent designer, he argues. He also sees other aspects of the natural world that he thinks are inconsistent with the existence of a Deity. I’ll leave it to theologians to grapple with Ayala’s arguments about whether backaches in old age and other forms of generalized human suffering make the existence of God logically untenable. But on the specific scientific question of the organization of the human genome, I think the evidence is clear. It is Ayala who has been sloppy, and not only in his assessment of the human genome, but also, I must add, in his critique of my book.
    http://www.stephencmeyer.org/n.....art_2.html

    But paulmc, the amazing thing is that you will ignore all this and move on to some piece of neo-Darwinian tripe, merely to try to protect your atheistic religious belief! Why is this paulmc??? Why is it so important for you to deny God??? and Although you do you best to ignore the overwhelming evidence for God in this life, Do you think you will be able to hide from God when you die??? If so you are in for a VERY BIG surprise!!!

    It is also very interesting to point out that the ‘light at the end of the tunnel’, reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as an observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences:

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

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

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

  37. Interesting . . . from Wikipedia:

    In mammals, almost half the genome (45% to 48%) comprises transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons while DNA transposons account for about 2-3%.

    AND

    Short interspersed repetitive elements or Short interspersed elements are short DNA sequences (<500 bases) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, rRNA, and other small nuclear RNAs. SINEs do not encode a functional reverse transcriptase protein and rely on other mobile elements for transposition. The most common SINEs in primates are called Alu sequences. Alu elements are 280 base pairs long, do not contain any coding sequences, and can be recognized by the restriction enzyme AluI (hence the name). With about 1,500,000 copies, SINEs make up about 11% of the human genome. While historically viewed as "junk DNA", recent research suggests that in some rare cases both LINEs and SINEs were incorporated into novel genes, so as to evolve new functionality. The distribution of these elements has been implicated in some genetic diseases and cancers.

    AND

    Alu insertions are sometimes disruptive and can result in inherited disorders. However, most Alu insertions act as markers that segregate with the disease so the presence of a particular Alu allele does not mean that the carrier will definitely get the disease. The first report of Alu-mediated recombination causing a prevalent inherited predisposition to cancer was a 1995 report about hereditary nonpolyposis colorectal cancer.

    The following human diseases have been linked with Alu insertions: Breast cancer, Ewing's sarcoma, Familial hypercholesterolemia, Hemophilia, Neurofibromatosis, Diabetes mellitus type II.

    And the following diseases have been associated with single-nucleotide DNA variations in Alu elements impacting transcription levels: Alzheimer's disease, Lung cancer, Gastric cancer.

  38. So, I’m wondering . . . if the Alu sequences are purposeful and they’ve been linked to lots of nasty diseases then . . . is the designer malevolent?

    Is that a fair question? If there is a designer is the fact that there is so much death and pain and suffering an indication that the designer is actually evil?

    Just a question. It’s fair to ask questions . . . yes?

  39. Is that a fair question? If there is a designer is the fact that there is so much death and pain and suffering an indication that the designer is actually evil?

    Sure. It’s just not an ID question.

  40. paulmc:

    I was responding to your statement that you “have no idea whether there are 1, or 999,999, or 999,999 + 1 ALU repeats“. This certainly has bearing on the validity of Wells’ thesis.

    wow. Could you read that any more literally? And then you extrapolate what I said about ALU repeats to the entire genome?

    Let me assure you that Wells’ book is not my first exposure to genetics or the genome or even ALU sequences.

    Sitting just a few books down on the shelf from the book by Wells is this book Inside the Human Genome: A Case for Non-Intelligent Design.

    And just a few books down from that book is this one Relics of Eden: The Powerful Evidence of Evolution in Human DNA.

    And then, Darwinian Detectives: Revealing the Natural History of Genes and Genomes

    And were you the won who asked BA77 if he’d read this book Evidence and Evolution? Because that one is just a few books further down.

    Please don’t worry about me. When you see me making bad arguments, either logically or on the facts, then perhaps you might be warranted in making some assumption about what I do or do not know. Thanks.

  41. nullasalus: I have never understood the reluctance to question the motivations, methods and timings of the intelligent designer.

    What questions can you ask past the existence of an intelligent designer? Does it matter, the nature of the designer? Does the nature of the designer help explain the design choices? A scientific theory must have explanatory power. Would a malevolent designer better explain more issues?

    If your hypothesis is that some aspects of the natural world are better explained as the result of the intervention of an intelligent designer AND if you think that proposition has been established beyond reasonable doubt (which I think some of you are saying) then what is wrong with pushing the inquiry on to further stages?

    ‘Cause that’s what science does . . . isn’t it? Ask questions. If the issue of a benevolent vs malevolent designer aren’t addressed here then where are they addressed? Outside of theological forums since I hope we’re still talking science here.

  42. If evolutionists were genuinely interested in scientific knowledge…

    Need I point out that it is “evolutionists” who are bringing all this information to light? We’re piggybacking on their findings. Let’s at least be honest about that.

  43. ellazimm, you’re looking for Intelligent Designer Theory.

    We’re Intelligent Design Theory.

  44. ellazimm asks;;

    ‘If the issue of a benevolent vs malevolent designer aren’t addressed here then where are they addressed?’

    Perhaps ‘Origin Of Species’ by Charles Darwin since it is far closer to a theological book than a science book!!!

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species
    http://www.evolutionnews.org/2.....46391.html

    ,,,Turns out that to be a very good neo-Darwinist you absolutely have to be a horrible theologian first and foremost!!! :)

  45. ellazimm,

    I have never understood the reluctance to question the motivations, methods and timings of the intelligent designer.

    What reluctance? I said, sure, good question. Behe if I recall correctly says that if, say… malaria shows signs of intelligence design, that’s that. We can’t just say “that’s not designed!” because malaria is harmful.

    I said such questions are not part of ID. But I agreed they’re valid questions.

    What exactly are you disagreeing with here?

  46. Mung: okay, but . . . if Intelligent Design Theory has been established then what? Where does it go from there? What further explanatory power can be generated? What’s the point of Intelligent Design Theory if not to explain, more fully, aspects of the material world?

    It seems to me that questions about the timing, methods and motivations of the designer are supporting rationales for Intelligent Design Theory. I cannot believe that all the people who have spent so much time arguing for the design inference here have not considered the nature of the designer. And if the design inference is a scientific issue then why isn’t the nature of the designer? Especially if, as I’ve heard, the design inference allows for corporeal, physical alien beings to be the designers. Surely it’s allowed to ask questions of their motives and methods if only to rule out some possibilities. Yes?

    If there is a place where Intelligent Designer Theory is discussed then I’d love to know about it.

  47. 47

    No Mung, scientists do the job they’re paid to do and then, if the results conflict with any pre-conceived evolutionist notions they might try and move the goalposts (or leave it to others to worry about because they’re sure their beliefs are corroborated by other scientific disciplines).

    Pointing out that many scientists are evolutionists in this context is like pointing out that many scientists are Democrats, fond of Tom Cruise or tend to be Virgos: in other words, irrelevant. I wonder why you don’t see this, Mung.

  48. nullasalus: It’s not so much a matter of disagreeing with anything . . . I’m just wondering why there is little discussion of what I’m seeing as some of the ramifications of some things being designed.

    Surely you’ve thought about it? You’re an intelligent person. You’ve wondered. You’ve thought. You’ve asked yourself: if malaria, whooping cough, measles, some cancers, plague, HIV, lupus, hermaphrodism, homosexuality, polio, tooth decay, dementia, arthritis, exzema, alopecia, hay fever, migranes, etc are part of the plan then who is making the plan? And why is it not a scientific question, that helps explain the reasons behind those things, regarding the motivations and methods of the designer? And if they’re not part of the plan then what power and influence does the designer have or choose to exert?

    In a court of law, where facts are at least attempted to be established, it’s fair to ask after motive and means. Why is that NOT part of the intelligent design inference? Why is it when a Darwinist says: well, that’s not the way an intelligent designer would do things you don’t say well it might be because of such and such reasons. And saying that design doesn’t have to be optimal continues to bring up the motive and method (and competency) of the designer. Surely. If a sub-optimal design has been implemented and suffering and pain are part of the results and if new and improved designs are implemented in an attempt to rectify some of the problems then surely that is arguing for either a fallible designer OR one that is intentionally making less than perfect designs. For some reason. And explaining those reason makes the design inference stronger and more explanatory.

  49. ellazimm so you want to talk ‘about’ the Designer now??? Does this now mean that you accept that neo-Darwinism is devoid of any rational foundation in science and you want to move on to Theology??? If so great, but if not, what would be the point since you would still hold blind, pitiless, chance of materialism as your ultimate creator and the discussion would not have any real meaning for you???

    By the way here is the falsification of reductive materialism (local realism);

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

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

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

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

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

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

  50. ellazimm,

    And why is it not a scientific question, that helps explain the reasons behind those things, regarding the motivations and methods of the designer?

    Who said it’s not a scientific question? I said it’s not part of ID. If you want to lay out the case that evaluating possible reasons for why the world is the way it is is a scientific question, let’s hear why. I’d be interested in hearing it.

    If a biologist tells me that fish eat plankton, and I ask where the carbon in the plankton came from, he may well tell me ‘That’s not a question for biology.’ It would be a question for, say.. cosmologists or physicists.

    And if they’re not part of the plan then what power and influence does the designer have or choose to exert?

    Good questions. Theology and philosophy deal with these. But you seem to be arguing that these questions are part of science. I’d love to hear why.

  51. BA77: I’m not here to find out about the materialist viewpoint. I’m here to find out why you are not discussing the nature, motivation and competence of the designer. I’m here to find out what you think about these issues. Why would I be asking the questions here otherwise?

    I’m quite sure you have all thought about the issues I’m bringing up. I don’t understand the reluctance to discuss them. Especially as, it seems to me, filling in those aspects of the design inference could strengthen you argument.

    For example: a malevolent designer would explain sub-optimal design and maybe aspects of pain and suffering. So, if you don’t think the designer is malevolent then how does a benevolent designer help explain aspects of the designed world?

    C’mon people! I know you’ve thought about this. This is your forum! I’m just asking questions. You can shut me up anytime you like. I’ve got no power or influence here. But, honestly, I’d like to know what you think. I can’t rectify some of what I see in the world with the notion of a designer but I bet some of you can.

    If Intelligent Design Theory is scientific then can withstand follow-on questions.

  52. 52

    I, for one, ellazimm don’t have a problem with the problem of evil… but it is strictly a theological matter. We are part of the ultimate scientific experiment and cannot get outside of it to report any scientific findings. Not in this life anyway.

    It is completely separate to the subject matter of Intelligent Design.

  53. BA77: I’m not here to convert or be converted. I’m just here to try and understand what you think. Okay?

    I think that if the existence of a designer is a scientific question then the designer’s methods, motivations and timing are also subject to scientific inquiry. How could it be otherwise?

    Clearly the designer has chosen or been obligated to intervene at certain moments in certain ways. We don’t see design implementation on an obvious and grand scale daily. So is this due to motivation or limitations? Can we find evidence for either of those? How is that not a scientific question? Even if the answer is: we’re not sure.

    Even an all powerful, all knowing designer interacts with the world in ways that can be examine and scrutinised. I would think.

  54. Chris,

    Why is the question of evil theology when it has real world ramifications and results? If a designer is including suffering and pain then is it not fair to ask if that is part of the design? And is it not fair to ask if there is any evidence for it being part of the plan? And is it not fair to ask, scientifically, if a certain kind of designer would have more explanatory power than another kind?

    How can logic and the scientific method work and be applicable only up to a certain point? If we have the ability to think critically, ask questions, make inferences and filter results then why draw a line? When do we give up evidence and verification? And why.

    Who hasn’t had a ‘spiritual’ experience that they didn’t first examine with their sharpest critical skills? I know I have. Who hasn’t felt the presence of some greater power and not asked: is this real? How do I know? What evidence is there that convinces me I’m not delusional?

    And who hasn’t then had doubts and questions and had to look at it all again? And again? And who hasn’t wanted to have as much evidence and reasons as they could muster for their convictions?

    I do not believe that most of you have blind ‘faith’. I think most of you have really thought, long and hard, about your beliefs. I don’t think I agree with you but I’d like to understand where you are coming from. And I’d like to argue with you. :-) It’s part of the way I learn.

  55. Lovely discussion all but it’s late in England and I can see from the mistakes I made in my last reply that I really do need to call it a night.

    Thanks again for letting me ask my questions; I hope I haven’t offended anyone and that my intentions have not come across as manipulative or disingenuous. Because they’re not.

    Later then.

  56. 56

    Hi Ellazimm,

    Think of life like computer programming. Without any IT background, you can make some (very limited) progress using observation and experimentation alone (science). But if you really want to know what is going on, you need to read the flipping manual (theology)!

    There are no shortcuts when it comes to the best and important things in life. If you’re looking for answers you need to study the Book of Scripture as well as the Book of Nature.

  57. ellazimm you ask deep questions for one who refuses to closely examine his false view of reality i.e. materialism;

    ,,,To start, here is further falsification of your materialistic philosophy upon which your belief in neo-Darwinism is built;

    The following articles show that even atoms (Ions) are subject to teleportation:

    Of note: An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge.

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

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

    But ellazimm, though the preceding experiments conclusively falsify any claim your base materialistic philosophy had on being a complete description of reality, and indeed verifies the Christian Theistic postulate of John 1:1 (In The Beginning Was The Word,,) in the process, the results of quantum entanglement/teleportation have a far more devastating effect on falsifying neo-Darwinism directly! ellazimm this is because quantum entanglement/information has now been found in molecular biology on a massive scale!

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

    ellazimm, It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! Yet it is also very interesting to note, in Darwinism’s inability to explain this ‘transcendent quantum effect’ adequately, that Theism has always postulated a transcendent component to life that is not constrained by time and space, for Theism has always postulated that God, who is not limited by time or space, indeed He created time and space, has created all life on earth.

    Now ellazimm the only option you have to explain quantum entanglement, within molecular biology, and thus try to save some form of your neo-Darwinian belief system, is to appeal to a ‘non-reductive’ materialistic framework. This would include appealing to many-worlds-and/or appealing to multiverses. The crushing problem for that option for you is that you will destroy your ability to do science in a rational way since you will hold that anything can happen at any time;

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: The physical universe is causally incomplete and therefore neither self-originating nor self-sustaining. The world of space, time, matter and energy is dependent on a reality that transcends space, time, matter and energy. This transcendent reality cannot merely be a Platonic realm of mathematical descriptions, for such things are causally inert abstract entities that do not affect the material world. Neither is it the case that “nothing” is unstable, as Mr. Hawking and others maintain. Absolute nothing cannot have mathematical relationships predicated on it, not even quantum gravitational ones. Rather, the transcendent reality on which our universe depends must be something that can exhibit agency – a mind that can choose among the infinite variety of mathematical descriptions and bring into existence a reality that corresponds to a consistent subset of them. This is what “breathes fire into the equations and makes a universe for them to describe.,,, the evidence for string theory and its extension, M-theory, is nonexistent; and the idea that conjoining them demonstrates that we live in a multiverse of bubble universes with different laws and constants is a mathematical fantasy. What is worse, multiplying without limit the opportunities for any event to happen in the context of a multiverse – where it is alleged that anything can spontaneously jump into existence without cause – produces a situation in which no absurdity is beyond the pale.
    For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.

    Proof That God Exists – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    John Lennox – Science Is Impossible Without God – Quotes – video remix
    http://www.metacafe.com/watch/6287271/

    ellazimm, perhaps you would care to defend your now falsified philosophy?

  58. Mung:

    wow. Could you read that any more literally? And then you extrapolate what I said about ALU repeats to the entire genome?

    Let me assure you that Wells’ book is not my first exposure to genetics or the genome or even ALU sequences.

    I shall rest assured, then.

    When you see me making bad arguments, either logically or on the facts, then perhaps you might be warranted in making some assumption about what I do or do not know. Thanks.

    You mean, like regarding the title of the book in question?

  59. paulmc,

    What fact(s) did I get wrong, or what argument did I make that was not correct?

    What i recall is that I offered an opinion about what Wells meant by using the word “myth” in the title, and I also was sure to state that he made it clear that he was not saying there were no non-functional DNA.

    I felt free to offer my opinion for two reasons:

    1. I actually have the book and am reading it.

    2. I attended the book launching party in Seattle where I heard Dr. Wells speak and participated in the Q&A.

    That said, I think I have a more sound basis for my opinion than you have for yours. What say you?

  60. ellazimm, Hopefully you’ll see this tomorrow. Many of us agree that you are asking fine questions. Many of us would willingly discuss those issues.

    But why do you feel it necessary to tie them to intelligent design? If you were willing to demonstrate that you understand and accept that there is a difference, that the questions you are asking are not the sorts of questions that ID sets itself to answer, you might make more progress.

    I’m willing to wager that you reject the claim that the design in nature is real and is a result of an intelligent cause. So why should anyone bother to argue over hypotheticals with you about some designer or designers that you deny even exist?

    Say I agree that there is at least one malevolent designer running around out there. IS that all of a sudden somehow going to strengthen your conviction that there is real design in nature and that it has an intelligent cause, even though that cause may be malevolent?

    I seriously doubt it.

    ID is compatible with multiple designers.

    ID is compatible with all different kinds of designers with different motives and different skill set and different moralities.

    ID is compatible with non-supernatural designers.

    As such, your questions are truly misguided and display a profound misunderstanding of intelligent design. Is it willfull?

  61. p.s. ID is compatible with a designer or designers that no longer exist.

  62. Mung –

    In Post #1, you do not present your view as an opinion. You state with an apparent certainty what Wells’ intent is (which you later soften).

    I disagree with this interpretation because of Wells’ claims in the recent interview with Denyse O’Leary for this website. My assumption in doing so is that Wells is fairly representing his book in this interview.

    To reiterate, Wells says:
    “If the Ming vase is a living cell and the leftover carpet nails are “junk DNA,” it turns out that the nails are not only made of gold, but they also make an essential contribution to the beauty of the vase….
    Like Haeckel’s faked embryo drawings and staged photos of peppered moths, junk DNA is not science, but myth.”

    But as yet I have not had the chance to read more than small excerpts from the book. It may turn out that you are entirely right (leaving unresolved Wells’ apparent diningenuity in the above interview).

  63. 63

    spiritual experiences are not signs of delusion. This was empirically established by a couple of fellows who wrote a book called “How God changes the brain.” Apparently those who have had God type, or spiritual awaking hippy type experiences show brain scans with perfect function. They found also, that those who pray and meditate, not only have perfectly wonderful brains, but their brains actually show higher function in the regions associated with compassion and empathy etc.

    The guys that wrote the book were not religious. One says he believes only in the laws of nature, the other is an agnostic.

    So the notion that “religious characters are delusional” is more of a myth at this point.

    http://www.amazon.com/How-Chan.....0345503414

  64. Chris Doyle: well, as ID is a science independent of theology I think I’ll stick to more material evidence. But I appreciate your comment.

    BA77: As I said, I’m not her to promote or defend my views, I’m here to learn about yours, the collective yours. Please don’t waste your time attempting to argue against my assumed position. Perhaps I’m considering a change in my view . . . maybe that’s why I’m here?

    Mung: I am NOT wilfully mis-understanding ID. I’m asking why ID does not/will not extend into the questions I brought up for the reasons I gave. I think that the nature, methods and timing of the designer are science ESPECIALLY if the designer is non-trancendental. The presence of a malevolent designer I THINK might explain a lot of what we observe in the physical universe. So, in fact, contemplating that makes me MORE favourable to the notion of design in nature. I see much more pain, suffering and chaos than I see joy, kindness or reasons for existence. But if the designer is cruel and mean spirited . . .

    Anyway, I think we’ve pursued this as far as we can. I’m glad some of you think my questions are meaningful even if the only answer is: ID doesn’t go there. But I still wonder: if there is design in nature then what? Lots and lots of questions still to ask and answer I figure.

  65. But I still wonder: if there is design in nature then what? Lots and lots of questions still to ask and answer I figure

    Absolutely. So I take it you would disagree with those who claim that ID is a “science stopper”?

  66. Mung: well some interesting work was reported on the last two episodes of ID: the future; I’m interested in how those results are reviewed by others in the field. And to see if it can be replicated and enlarged upon. A single paper/experiment is interesting but it has to stand up to scrutiny. All scientific knowledge is provisional subject to verification and new data. Some recent work was done to confirm some of Einstein’s early work!! Scientists are a tough crowd to please.

    I would very much like to see some work done specifying the time and method of design intervention. If Dr Behe’s edge of evolution is correct then it should be possible to start to narrow down when design implementation was used to jump past the edge.

    But, as I’ve said, I’m here to ask questions and to listen to what you all think. So . . . what kind of research do you think ID should pursue? What hypotheses do you want to see tested? What ID predictions would you like to see established and how would you do it? If I won $20 million in the Euro Lottery and decided to spend it on ID research what do you think I should fund?

  67. If I won $20 million in the Euro Lottery and decided to spend it on ID research what do you think I should fund?

    1 million to me
    1 million to Uncommon Descent
    1 million for yourself
    17 million to Discovery Institute

  68. paulmc:

    In Post #1, you do not present your view as an opinion. You state with an apparent certainty what Wells’ intent is (which you later soften).

    Post #1 is there for all to read. I never mentioned anything about Wells’ intent.

    When I said I offered an opinion it was in reference to Wells choice of a title. That should have been clear from the context, as that is what we were debating.

    In fact, I stated that explicitly:

    What i recall is that I offered an opinion about what Wells meant by using the word “myth” in the title

    And you even acknowledge that fact:

    You mean, like regarding the title of the book in question?

    The question of the title did not come up until post #3:

    Sure – it is good that this is Well’s argument, but then isn’t the title misleading?

    So I ask again, what fact(s) did I get wrong, or what argument did I make that was not correct?

    Do you now disagree with my Post #1?

  69. Mung: :-)

    But seriously, what areas of research do YOU think should be pursued?

  70. Well, I think a good first project would be to look at human design and human designers and try to identify principles and patterns of design in general.

    I think that could give ID a lot of credibilty as a science.

    Then perhaps look to see whether any of those principle and patterns are present in the world apart from human design.

  71. So, for example, if we look at software engineering and come across some principle or pattern that we think might makse sense in a biological setting, we could say that we predict we’ll find cases in nature, and then we could actually test that hypothesis.

    ID call that real science, would you?

  72. Mung: Love the I’D pun.

    I’d pick different areas but thanks for answering the question. If I win the lottery I’ll let you know! :-)

    And now, one and all, it’s my bedtime here in England. Take care, do good, keep the faith.

  73. Mung

    Do you now disagree with my Post #1?

    At the risk of continuing a fairly trivial semantic argument, yes (although mostly with Wells, and less so with you).
    In Post #1, you state:

    It’s important to understand that Well’s does not argue that most of the genome is not junk, but rather that the more we learn about it, the more we find what we previously assumed was junk turn out to serve some purpose or function after all.

    This is different indeed than Wells’ argument that he makes – at least when describing the book (as above from his UD O’Leary interview) – hence the disagreement over the title.

    I take greater issue, however, with the second part of post #1:

    The “junk DNA” argument is turning out to be a “Darwinism of the gaps” fallacy, based not on what we do know, but rather on what we don’t know, and as science progresses, the junk appears to be in retreat.

    I disagree with this – and strongly – although I assume it is a continuation of Wells’ rather than your own position.

    There are two problems with this. Firstly, the term ‘Darwinism of the Gaps’ implies that Darwinian evolutionary theory is only a useful explanation for the non-functional ‘junk’ parts of the genome (in the same way that a ‘god of the gaps’ argument only seeks god in the unexplained)! Yet, nothing could be further from the truth. The functional genome is the bread and butter of classical neoDarwinian evolution, while junk has posed problems to classical neoDarwinian views.

    Secondly, there is a problem with the claim that ‘junk’ as a theory is in any sort of meaningful retreat. The amount of the genome where recent function has been found is miniscule. In total, there is only known function for 8% of the genome.

    This is problematic when you consider the mode of reproduction for the genomic elements being discussed. Retrotransposons are able to create DNA duplicates that reinsert themselves randomly into the nuclear genome. I will maintain that the best explanation we have for the large copy numbers of these transposable elements is that they are largely junk. Same with pseudogenes.

    Such things are occasionally functional. There is zero doubt that they have been essential to shaping the human genome and making us what we are. But only on fleeting occasions. And, of course, they are also the sometimes cause of disease. The bulk of them are best understood as relicts of old duplications that have mutated to the point of no longer functioning.

    Incidentally – a point of commonality, perhaps – I have already argued elsewhere that this shouldn’t be seen as an affront to ID. This would put me very much in line what you have stated is Wells’ position, but very much at odds with his claims in his UD interview.

  74. This would put me very much in line what you have stated is Wells’ position, but very much at odds with his claims in his UD interview.

    Well, hopefully you’ll read my first post as a cautionary tale to ID advocates to not take the “myth of junk DNA” argument too far. I began the post with “It’s important to understand …”

    An example of relying on an interview rather than the source can also be seen in Tom Schneider’s response to a James Gleick interview.

    http://www.ccrnp.ncifcrf.gov/~toms/Gleick2011.html

    Gleick claimed that Shannon originated the term ‘bit’.

    But when you actually read the book:

    Like the transistor, this development also involved a neologism: the word bit, chosen in this case not by committee but by the lone author, a thirty-two-year-old named Claude Shannon.

    With accompanying footnote:

    TRANSISTOR…BIT: The committee got transistor from John R. Pierce; Shannon got bit from John W. Tukey.

  75. Most of our DNA does not code for proteins; on that, everyone agrees. The question here is whether non-protein-coding DNA is nonfuncitonal “junk” that provides evidence for Darwinian evolution and against intelligent design.

    Evidence for the functionailty of non-protein-coding DNA falls into two broad categories: The first consists of evidence suggesting that such DNA is probably functional. Ths evidence comes from two sources; the first source is the transcription of most non-protein-coding DNA into various RNAs.

    A second source of evidence in the first category comes from comparisons of DNA sequences in different organisms. … As we have seen, many non-protein-coding DNA sequences are conserved, suggesting that they serve biological function.

    So in the first category, widespread transcription and sequence conservation suggest that much “junk” DNA is probably functional, though they do not tell us what the precise functions are. The second broad category consists of evidence for specific biological functions of non-protein-coding DNA.

  76. Mung – is #75 a quote from Wells’ book? (Hence the blockquote?)

    The idea that most of the genome is transcribed comes from microarray tiling expts, e.g. Johnson et al. (2005).

    However, more recent work has shown this to be more than likely a methodological artefact – see van Bakel et al. (2010).
    There may well be substantial amounts of non-coding RNA (e.g. Kapranov et al., 2010), but not a great deal of current support for a majority of the genome being transcribed. Further, those parts that are transcribed are only potentially functional.

    As far as the conservation argument goes, this sounds fine as a qualitative argument. But when we look at the proportion of conserved vs unconserved intragenic regions (e.g. here) we are still left with a situation where a majority of the genome is mostly likely to be junk.

    The most likely reason for the presence of such unconserved regions in the genome is duplication followed by genetic drift (i.e. the escape from purifying selection).

  77. ellazimm @72

    I’d pick different areas but thanks for answering the question.

    Would you mind telling me what those areas are and why you would pick them over the two that I specified?

    My recommendations began with:

    I think a good first project would be to look at human design and human designers and try to identify principles and patterns of design in general.

    Any general theory of design ought to be able to say what design is, what it looks like, and offer generalities that go beyond specific instance.

    Wouldn’t you agree?

    So why would that not be a fundamental necessity for design theory if it truly hopes to be accepted as science?

    Do you have any reasons why what I have described cannot be included in the category of science?

  78. Mung – is #75 a quote from Wells’ book? (Hence the blockquote?)

    Absolutely. Apologies for not including the appropriate cite.

    Chapter 9. pp 89 and 90

    The idea that most of the genome is transcribed comes from microarray tiling expts, e.g. Johnson et al. (2005).

    Are you claiming that the idea that most of the genome is transcribed is false?

    Are you claiming that the idea that most the genome is transcribed has not been arrived at by other independent researchers?

    Chapter 9 is a summary chapter. But in Chapter 10 Wells cites the ENCODE project, from 2007.

    First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another.
    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

    From your source:

    Finally, results from the ENCODE pilot project have suggested a highly interleaved structure of the human transcriptome, with an estimate that as much as 93% of the human genome may give rise to primary transcripts [9]. Though this estimate was based on a combination of sources that included rapid amplification of cDNA ends coupled to detection on tiling arrays (RACE-tiling), manually curated GENCODE annotations, and paired-end sequencing of long cDNAs (GIS-PET), it was dominated by the results of RACE-tiling experiments that alone found 80% genome coverage, compared to 64.6% and 66.4% for GENCODE annotations and GIS-PET, respectively.

    Don’t even ask me to interpret that, lol.

    64.6 and 66.4?

    The GENCODE project was not thorough enough before they came to their conclusions?

    Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded novel mechanistic and evolutionary insights about the functional landscape of the human genome. Together, these studies are defining a path forward to pursue a more-comprehensive characterisation of human genome function

  79. As far as the conservation argument goes, this sounds fine as a qualitative argument.

    I’m more interested in what it says about common descent.

    Can one accept the findings of these comparisons, reject common descent, and then reason that these sequences are indeed conserved, in a coherent manner?

    I’m not one dimensional :)

    I have the impression that Wells does not accept common descent. i could of course be mistaken.

    But as far as I am concerned it makes no sense to speak of a “conserved” sequence apart from common descent. So how can one use it as an argument against “junk DNA” unless one accepts common descent?

  80. Mung:

    Are you claiming that the idea that most of the genome is transcribed is false?

    Are you claiming that the idea that most the genome is transcribed has not been arrived at by other independent researchers?

    I am stating that more recent methods (RNA-seq) produce rather different results than tiling array experiments do, and that tiling arrays are understood to have a high false positive rate.

    I wouldn’t like anyone to take the reading that simply because a more recent (2010) study contradicts an earlier study, the earlier study must be wrong, however the technology is improving and there are reasons to suspect the earlier results.

    A false positive in a tiling array can come from occasional transcriptional errors and so are noise, rather than a genuine part of the transcriptome.

    There is of course still the further step that they need to actually function (i.e. they need to predictably affect the proteome), otherwise they are junk RNA.

    I think it is important for ID advocates to consider the more recent results rather than preferentially accepting the earlier results simply because they suit their world view (not directed at you, Mung).

  81. Me:

    As far as the conservation argument goes, this sounds fine as a qualitative argument

    Mung:

    Can one accept the findings of these comparisons, reject common descent, and then reason that these sequences are indeed conserved, in a coherent manner?

    OK. An interesting proposition.

    To do so, you must reject quite a large part of established theory, but for a moment let’s do so. As I see it, there are two parts to this idea: the first is why are apparently ‘conserved’ sequences similar?, and the second is why are apparently ‘non-conserved’ sequences dissimilar?

    Rejecting common descent, I guess you would have to argue that the conservation reflects some sort of shared function. Of course, between more apparently similar species you would expect more shared function, so you would expect the pattern of similarities even in the absence of common descent.

    Rejecting common descent, the non-conserved regions could either represent functional differences or variation due to noise/mutation (i.e. in true junk). The former is a rejection of junk, and would be consistent with the rejection of junk DNA also. The latter is more problematic.

    Under the latter, the question arises: why do species share patterns in their junk more often when they also share patterns in the non-junk? This implies common descent.

    I suppose then, on reflection, it is perhaps difficult to accept junk DNA while rejecting common descent provided differences and similarities are scrutinised.

    Do you agree, or would you propose a different way of looking at this?

  82. Mung: I think your ideas are fine; I didn’t mean they shouldn’t be included in ID research. Personally, I’m not optimistic that detecting design is going to be easy so . . .

    I’d spend money testing the ability of DNA to generate new features. LIke what Lenski is doing but more so. For example: after carefully sequencing the genome of a base population of a given species (flies? worms? whatever) see if it’s possible to generate novel features with really strong environmental input. I”m not explaining this well ’cause I’m trying to be concise. I’d take the base population and split them into different stressful environments, let them breed for hundreds of generations and see what happens.

  83. ellazimm you state:

    ‘I’d spend money testing the ability of DNA to generate new features. LIke what Lenski is doing but more so. For example: after carefully sequencing the genome of a base population of a given species (flies? worms? whatever)’

    which reminded me of this recent experiment;

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

    and also reminded me of this recent paper:

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

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

  84. BA77: I heard about the fruit fly result. Still, worth more time just in case . . .

    One paper/result is suggestive, it matters. But lots of results over years and years becomes consensus. Which is why I’d recommend the ID community to do the same kind of thing. A lot.

  85. ellazimm, in case you didn’t notice, I also listed a paper in which Dr. Behe did a survey of ALL the major papers of laboratory evolution experiments of microbes going back four decades and found a stunning failure for the neo-Darwinian paradigm to extrapolate micro-evolutionary events, which all come at a cost of degrading the genome, to macro-evolution conjectures. I would maintain that is ‘lots of results’ that consistently undermine the current ‘consensus’! Moreover ellazimm, even working from when we thought that ‘some’ mutations might be beneficial to the genome, the fact is that the overwhelming majority of detrimental mutations, which neo-Darwinists already admitted to, was already crushing to the neo-Darwinian paradigm as illustrated by Dr. Sanford in his book “Genetic Entropy and The Mystery of the Genome”:

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

    The foundational rule for explaining the diversification of all life on earth, of Genetic Entropy, a rule which draws its foundation in science from the twin pillars of the Second Law of Thermodynamics and from the Law of Conservation of Information (Dembski, Marks, Abel), can be stated something like this:

    “All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment, will always come at a loss of the optimal functional information that was originally created in the parent species genome.”

    further notes;

    In fact, trying to narrow down an actual hard number for the truly beneficial mutation rate, that would actually explain the massively integrated machine-like complexity of proteins we find in life, is what Dr. Behe did in this following book:

    “The Edge of Evolution: The Search for the Limits of Darwinism”
    http://www.amazon.com/Edge-Evo.....0743296206

    Dr. Behe, in his book examined the largest ‘real world’ tests that could be preformed on evolution to see what he could find and found,,

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

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

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

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

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

    The Edge Of Evolution – Michael Behe – Video Lecture
    http://www.c-spanvideo.org/program/199326-1

    Thus ellazimm, why is this consistent and overwhelming evidence against neo-Darwinism not sufficient for you? Perhaps you will wait for the ‘consensus’ to change? But what does consensus have to do with empirical science ellazimm? It matters not one iota what triple PhD scientists say if they don’t have the evidence to back them up!!!

  86. BA77: Yes I did notice that. I haven’t had a chance to read it yet. I’ll try and find the time before I mouth off again. :-)

    As you know, however, Dr Behe’s premises are heavily criticised and his conclusions are generally dismissed by ‘mainstream’ science and I will keep those opinions in mind as well. Not because they agree with me but because I consider it important to consider all the evidence and interpretations.

    I do not consider myself to have a materialistic or atheistic bias but I do think, at this point IN MY OPINION, the other side has a better case. Which doesn’t mean I’m not interested in yours or that I’m here to show you the error of your ways or make you look foolish. That would be rude and juvenile and I don’t think understanding and respect come from an attitude like that.

    Anyway, thanks for the info! I got the lawn all mowed (whew! three hours + of work) and now I’ve got to get ready to take my son to a swimming birthday party.

    And no sign of the Rapture yet here in England.

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