Monday, March 18, 2013

ENCODE & Junk and Why We Call Them IDiots

The Intelligent Design Creationists have been following the debate over the ENCODE results. For them this is a serious issue since they are committed to the idea that well-designed genomes should not be full of junk. You'd think that the IDiots would make an attempt to learn the real scientific issues at stake.

Let's see how andyjones does on Uncommon Descent: Function, the evolution-free gospel of ENCODE. He says,

Apparently, ENCODE are to be criticised for using an ‘evolution-free’ definition of function. Yep, you heard that right. You thought that function was function was function, but oh no, you must use a evolution-y definition or you will not get the ‘correct’ evolution-y answer. It seems awfully like you need to presuppose Darwinism or you will not find Darwinism. Can that be right?

The excuse for this is some interesting Darwinian philosophy (or do I mean sophistry? – make up your mind below): the authors believe that function means nothing (is purely subjective) unless it is selected for. For example, the heart causes the pericardium (the membrane around the heart) to not collapse by filling space, so we could call that a function, but it is selected for pumping blood.

....

Amongst other things the ENCODE authors are lambasted for not distinguishing between ‘Junk DNA’ and ‘Garbage DNA’. No seriously, ‘junk’ now means stuff that is functional, but not used very often, but could be used, like stuff in your attic is ‘junk’. It is different from ‘garbage’, which is the stuff that you would put straight in the bin. ‘junk’ is now a rather misleading word for ‘functional’. So our genome is full of ‘junk’ that is useful and functional, but to a Darwinian it does not count until it starts getting used so that natural selection can get the credit. How convenient! The possibility of design is sidestepped by careful choice of language. Welcome to 1984! A better word might be ‘archived’ rather than ‘junk’.

...

I, and many of us, hold to an ID worldview firstly and most securely because of what we know about prebiotic chemistry and thus the origin of the first life form. Based on that, because I know there has been a designer involved, I think probably a lot of ‘junk’ will turn out to be ‘brought down from the attic’ at various stages of an organisms life, especially in the developing stages. Time will tell.

Scientific means finding out what is actually there. ENCODE are to be praised for doing that. Darwinism has always been about telling creation myths from the point of view of naturalism (roughly, physics only), and shoehorning every fact into the story. ENCODE are now receiving scorn because they did not wait for the Darwinian imprimatur. Intelligent Design people and creationists (in fact everyone who is not a Darwinist) should take courage from this, jump in and start driving forward ordinary mainstream science, but just make sure they sidestep the attempts to sign them up to that cult.
Does anyone still wonder why I refer to Intelligent Design Creationists as IDiots?




26 comments :

  1. "Based on that, because I know there has been a designer involved, I think probably a lot of ‘junk’ will turn out to be ‘brought down from the attic’ at various stages of an organisms life, especially in the developing stages. Time will tell."

    Time has told, it's junk. Almost 10% of the snow you get on your TV screen is the cosmic microwave background radiation, but the rest is noise. ENCODE's redefinition of function is basically like saying "if I can see it on my TV, it's a real signal".

    No, it's noise ffs. The fact that you build an antennae that can pick it up and picture it doesn't make it all into a meaningful signal.

    Of course, getting an IDiot to even attempt to understand this is an exercise in futility. To these people there is no such thing as noise. Everything that happens in the entire universe, down to the random behavior of quantum systems, is the infallible plan of the omniscient creator of the universe. The plan is mysterious and we can't know it, but it's his plan dammit! We know because... well we just know because of personal experiences we had in our heads, and.. uhh.. because of ... the origin of life, we know nothing about it, therefore we know it was the result of non-random design(which we can't know, because it's mysterious). Something like that.

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  2. They certainly do seem to engage in large amounts of projection, to be sure.

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  3. This response is not surprising, of course. Misrepresenting scientific data is one of the ID creationists' main stocks in trade. In this case, the ENCODE consortium did the work for them.

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  4. Replies
    1. It is, isn't it. Almost makes one appreciate Behe's more sophisticated(this might not be the right word) approach.

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  5. I have difficulties in understanding why mos DNA is junk but almost all body and cell organs are functional

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    1. It's simple: Junk doesn't do anything. Including any harm.

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    2. 0fe681e6-90e1-11e2-b270-000bcdca4d7a asks a reasonable question.

      First, you're drawing an analogy between body organs and DNA. This analogy may not hold. Just because many (not all) anatomical structures have a function doesn't mean that every molecule must.

      Here are two different analogies you may consider.

      Analogy #1. Consider someone with permanant acne scars who had acne in their youth. Are the scars "functional"? In a sense, in that the person is better off with scar tissue than with holes in their face. However, it does not follow that someone with acne scars is better off than someone who never had bad acne to begin with.

      The point of analogy #1 is that scars reflect a HISTORY. Even if scars have a "function" in that they're better than open wounds, we nevertheless know that they represent a history of damage and lesions, not that you're better off having scars than good skin.

      In the case of DNA, most of it is the result of well-understood "scarring" processes that we have observed happening. A lot of junk is stuff like transposons that copied themselves and got broken, retroviral DNA insertions, genes that got duplicated and then broken, and so on.

      Analogy #2. Chemical synthesis. When a chemical factory synthesizes some complicated chemical, many steps in the synthesis involve the production of unavoidable by-product chemicals that you don't need. Many steps in the synthesis produce more than one chemical results. Industrially, it may be necessary to purify the product or filter out the by-products.

      In a living cell, DNA is always being transcribed to make some RNA which may or may not go on to make protein, etc. This is a complicated multi-step process, and by analogy to industrial synthesis, we should expect there to be unwanted by-products. So if a stretch of DNA is (very rarely) transcribed into RNA, this RNA, which may occur in very small amounts, may be an "unwanted" by-product of the complicated synthesis, and not serving the host organism.

      However, anti-Junk people like IDiots and a few of the ENCODE scientists assume that every molecule in the cell must have "function", which is begging the question they need to prove.

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    3. It's simple: Junk doesn't do anything. Including any harm.

      Most of the time ... we hope. :)

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    4. I have difficulties in understanding why mos DNA is junk but almost all body and cell organs are functional

      You have to think about it in better terms. Example, do you have any doubt that many bacteria might live in our bodies just because they can live there and have no further effect? Do you have any doubt that some bacteria might live there and have positive consequences to our health? Do you have any doubt that some bacteria might be there and have negative consequences to our health? Well, why could there not be any DNA "living" in our bodies just because they can et cetera?

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  6. And because the small percentage that isn't junk does its job just fine.

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  7. It's quite pompous and condescending; someone put their rhetoric dial up to 11.

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  8. I'd be interested in finding out what exactly it is that IDiots know about prebiotic chemistry, what top tier, peer reviewed journals this has been published in and when we can expect to see life saving medicines and therapies emerge from this knowledge.

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    1. Yeah, what do IDiots know about prebiotic chemistry?

      That IDiot Stephen Meyer, in his book Signature in the Cell, insinuated that Jack Szostak was a crank and a crackpot-- Szostak won the Nobel the year Meyer's book came out.

      Meyer also idiotically argued that pyrimidines can never be synthesized in prebiotic conditions. IDiot went on and on about that point. But before Meyer's book even hit the bookshelves, that passage was disproven by Powner et al.

      Nature 459, 239-242 (14 May 2009) | doi:10.1038/nature08013; Received 11 December 2008; Accepted 24 March 2009. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Matthew W. Powner, Béatrice Gerland & John D. Sutherland.

      Wow, IDiots know a lot about prebiotic chemistry, huh.

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    2. Meyer also idiotically argued that pyrimidines can never be synthesized in prebiotic conditions. IDiot went on and on about that point.

      What are non-terrestrial pyrimidine derivatives (including uracil) doing in meteorites, then?

      http://astrobiology.gsfc.nasa.gov/analytical/PDF/Martinsetal2008.pdf

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    3. Pre-IDiotic Chemistry ?

      IDs know just as much as you do, which means nothing, because their speculations are worth just as much as yours—zero--both are based on faith.
      Here is proof: A couple of DEvoLUSIONISTS here talk about pre-idiotic chemistry and the origins of life as if it was a done deal. They believe that their theories are just as good as facts with just a couple of glitches to be worked out, and it is just a matter of time before they will be able to explain it; not to mention re-creating life. Right? Well, no…
      Let me bring you to out of your DEvoLUSIONS and back into coherence.
      1. Nobody can explain the origins of life and your so-called prebiotic chemistry was taken apart and buried six feet under by the famous chemist Dr. Robert Shapiro-now deceased. For details see the video on the older blog: http://sandwalk.blogspot.ca/2013/03/john-witton-will-pay-you-1000-to-answer.html
      2. No DEvoLUSIONIST, or any other scientist has been able to re-create even the simplest form of life. And yet, DEvoLUSIONISTS believe that life could have created itself by a blind chance. What that means is that blind chance is much more intelligent than all of the scientist in the world. Not only that, if DEvoLUSIONISTS one day recreate life--I doubt that very much) but if they were able to do that, what would that mean? Would that mean that life could spontaneously arise? Or, rather that it needs an intelligent DEvoLUSIONIST or a scienitst? In other words, DEvoLUSIONISTS believe that if one day they are successful at recreating life, they can be considered as intelligent as blind chance + billions of years. For now, they can’t be considered equal to blind chance because they have not had chance to re-create what the blind evolution has done by chance. But, when they do, they are going to be just as intelligent as a slot machine for the lack of better example of DEvoLUSIONISTS’ stupidity.

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    4. IDs know just as much as you do, which means nothing

      No. Stephen Meyer said pyrimidines could never be synthesized in prebiotic conditions. His shit book was disproved by the time it hit the bookstores. You IDiots know nothing.

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  9. Larry: You know it’s kind of ironic that you continue to insist on this “junk DNA’ garbage and each time I open my hair-stylist mags, there is a new evidence of non-coding-DNA being a major player in some major disorders and diseases of the skin and hair, like melanoma and baldness. This is a perfect example:

    "Evidence for two independent functional variantsfor androgenetic alopecia around the androgenreceptor gene."
    http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0625.2010.01132.x/pdf

    Just to let you know Larry, in our hair-styling business we call baldness--androgenic alopecia….

    BTW: I’m sure you knew that Junk DNA had a “function” that triggered your baldness and then it went to the attic to spend the rest of its life as junk…
    No doubt you were going to mention it in our contest… Too bad it did not work out…but no worries… I will eventually get it my way, like I always do… They say money is power, but I don't view it that way... It's just a tool for good...

    BTW: Professor Behe declined the offer and I don’t personally blame him… I mean what can he expect from the willing, true and honest man like Larry? He probably has heard that they are going to rename the “Honest Ed” store in Torono to “Honest Larry” just to commemorate your virtues of honesty and truth…” I have a buddy on the board of directors…I’m sure you will make it Larry You have the charisma...

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    1. Witless,

      have you sent your $1,000 check to Denton yet?

      Larry: You know it’s kind of ironic that you continue to insist on this “junk DNA’ garbage and each time I open my hair-stylist mags, there is a new evidence of non-coding-DNA being a major player in some major disorders and diseases

      Strange... this is not a description of you sending your $1,000 check to Denton. Why should we care what comes out of your lie-hole, you lying fuck?

      And for the ten millionth time, Junk DNA is not non-coding DNA. Junk DNA is not "DNA whose function we don't know yet" and it is not non-coding DNA.

      Jesus you people really are IDiots.

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    2. It has gone up! Your faith is on the line....,.

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    3. Diogenes:
      "And for the ten millionth time, Junk DNA is not non-coding DNA"
      Really?It's been know since Larry began to lose his hair and drinking his favorite beer..

      Junk DNA is not "DNA whose function we don't know yet" and it is not non-coding DNA.
      I'm not going to comment on this because obviously you are either drunk or a moron...I'm not surprise though..

      BTW: I will be able to find Larry in 2-3 years to tell him he was an IDiot but you? I don't care about...You have serious issues more important than this shit

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    4. I'm not going to comment on this because obviously you are either drunk or a moron

      You welched on your bet and you've never made even one valid scientific point, troll and pussy.

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    5. Diogenes,

      You can't expect someone like John, who needed six persons to send a single e-mail, to be able to follow the discussion enough to understand what we are talking about. John is simply that much of an ass-hole. Not deserving of much more than the odd insult when he comes and talks as if he knows something only to make the most spectacularly imbecilic/ignorant blunders. I would enjoy it were it not because it shows John to be at such level of self-inflicted stupidity that it hurts to imagine that he's a human being.

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    6. I beg to differ, John isn't so much an asshole as he just suffers from clear, subnormal encephalization. This, of course as so often demonstrated, begets a lot of confidence on his part.

      You have to really wonder how much of a case you have to make when your "allies", Luther Flint, Andyboerger and Andre gross et al. occasionally have to drop in and tell you to stop making a fool of yourself or something similar.

      Witton is the slightly more literate but extremely arrogant Rober Beyers. Slightly better spelling and grammar, still no content or thought. Oh well..

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  10. I gotta admit that I really enjoy all the name calling I receive here... I always get that when so-called scientists have no arguments...

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    1. It's more that you are a steriotype troll. As such, the best recourse is to ignore you until you go inflate your ego somewhere else.

      For the others reading JW's comments, we don't feel like repeat stuff that is freely available in print, and get annoyed when those who we've asked to read do not. There is little point in talking to a plant. Likewise...

      The real points are freely available at;

      http://gbe.oxfordjournals.org/content/early/2013/02/20/gbe.evt028.short?rss=1
      http://www.pnas.org/content/early/2013/03/06/1221376110.abstract

      PZ Myer translates the first to common speak at...
      http://scienceblogs.com/pharyngula/2013/02/22/encode-gets-a-public-reaming/

      If JW would read, and come back with an informed comment, and if certain promises he has made regarding challenges are actually followed though on, maybe we would respond. Until then, just assume we are ignoring him.

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