Thursday, September 13, 2012

Don't touch their junk

Yesterday I issued a challenge to the coterie of Darwinist commentors on this modest blog who are having a fit over the ENCODE data and the long-overdue implosion of "junk DNA".

Why the fit? Junk DNA is a cornerstone of Darwinist mythology, and among ideologues myths don't die easy.

How, you may ask, can Darwinists hope to deny such overwhelming scientific evidence-- 30 papers in the leading genetics journals written by 400 of the best molecular geneticists in the world-- that "junk DNA" is junk science?

Here's how: Darwinists are dissembling and spinning like tops on what constitutes "junk DNA" and what "functional" means with reference to DNA.

No reason for surprise. The rhetorical trademark of Darwinism is circumlocution. Darwinists are loathe to define things consistently and with precision. Think how many different ways 'evolution' is used, or 'selection' or 'random'. Darwinism is the creation myth of atheists, but it prevails in a scientific culture, which is ostensibly devoted to relentless testing of hypotheses. Darwinism would evaporate overnight if actually tested against evidence (do you really think that the genetic code came about because 'things changed and survivors survived?), so to maintain their creed Darwinists must keep it all vague. They are very careful about definitions-- not to make them, but to avoid them.

The only way Darwinism gets to survive as a scientific hypothesis is if Darwinists get to define the hypothesis anew with each challenge.

So on the junk DNA controversy I have asked my Darwinist interlocutors to define these terms:


1) Define "junk DNA". Precisely. When you claim that most of the genome is junk (and you have claimed that for decades), what do you mean. Exactly. No weasel words. What is junk. What is not junk.
 
2) Define "function", in terms of DNA. What does it mean for DNA to be functional?

3) What relation does "junk" bear to "function"? Be precise. Can DNA be functional (by your definition) and still be "junk"?

4) How much of the human genome is "junk"? How much is "functional"? Explain what you mean.

No one has taken up the challenge, or at least no one has taken it up well. No surprise. When you ask a Darwinist just what he means, he insults you, sneers, throws chaff, and, if all else fails, he runs. The first three have been used to no effect, so here it's number four.


Only bachfiend ventured into rhetorical clarity. He answered:

If you want a definition, I'd define 'junk' as having no current use, but isn't discarded, because it might turn out to have a use later (as an analogy, I have a lot of junk lying around the house, in contrast to garbage, which I discard immediately). 
Having a function means that if you delete the DNA, then it causes a change in the organism.

Bach's definition of "junk DNA" is nonsense. DNA that has "no current use" need not be junk. DNA that regulates embryological development may be turned off in maturity. But it's by no means "junk". DNA that regulates elaboration of a stress hormone may be turned off when you have no stress, but it's not junk. DNA that mediates ovulation may be turned off after menopause. But it's not junk.

Bach's definition of "function" is worse than nonsense. He asserts that if you delete (remove) the DNA and the organism changes, then it had a function. By corollary, if you delete the DNA and the organism doesn't change, it didn't have a function.

But that's hilarious nonsense. If you delete the DNA that regulated embryological development in an adult human cell, the cell might not change. But the embryological DNA certainly has a function. It's just that the function is not expressed at every moment.

And lack of cellular change after removal of DNA doesn't even mean that the DNA had no function at the time it was removed. Consider the analogy to human organs. You can remove a kidney, or half of the liver, or a lung, or a large part of the thyroid gland, or many feet of the intestine, or even major parts of the lobes of the brain (I do it regularly), and the function of the body doesn't change. You have normal excretion of urine with only one kidney, normal liver function with half your liver, normal respiration with only one lung, normal digestion with only part of your intestine, normal thyroid function with only part of your thyroid, and normal brain function even with parts of your brain removed.

That does not mean the your removed kidney or liver or lung or thyroid or brain tissue had no function. Each of those erstwhile organs had plenty of function.

Removal of a portion of DNA, just like removal of a portion of some organs, may or may not impair function. There is redundancy and adaptation in biology. Removal of DNA, without a change in the cell, is not evidence that the DNA had no function. 

You may ask yourself at this point: are Darwinists really that stupid?

Well...

So here's my answer to my own questions, as promised:


1) Define "junk DNA". Precisely. When you claim that most of the genome is junk (and you have claimed that for decades), what do you mean. Exactly. No weasel words. What is junk. What is not junk.

I like the Darwinian definition of junk DNA: junk DNA is archaic DNA that arose by mutation or similar event and that does not contribute to nor impair the functioning of the cell.

I like holding Darwinists to their own definitions, although they fight like cats getting a bath.

2) Define "function", in terms of DNA. What does it mean for DNA to be functional? 
Function, in terms of DNA, refers to DNA that contributes to the natural activities of the cell-- replication, nutrition, excretion, movement, etc. The function need not be continuous. The function may have been in the past, or in the future, or may even be only potential, in response to an environmental stimulus that may or may not occur. DNA that can make melanin is 'functional', even if you never get a tan.

3) What relation does "junk" bear to "function"? Be precise. Can DNA be functional (by your definition) and still be "junk"?

Junk means not contributing to function.  Junk DNA and functional DNA are mutually exclusive. Each 'unit' of DNA is either, but never both.

In working terms, I think that ENCODE criteria for function is reasonable: function is "specific biochemical activity" on one of several standard assays for "RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons."

4) How much of the human genome is "junk"? How much is "functional"? Explain what you mean.

I believe that nearly all DNA is functional. Vanishingly little is junk. I believe this for two reasons:

1) I believe that DNA is created by an intelligent Agent, who eschews 'junk'.
2) I believe the current state of the science favors the view that the vast majority of DNA is functional and not junk.

I think those are pretty good answers to my questions, but then, as you can see, we intelligent design folks don't have particularly impressive competitors.

31 comments:

  1. Yesterday I issued a challenge

    No, you asked for an explanation of terms you don't understand. If you really wanted to understand them, you could simply have read the blog posts you were directed to, written by actual biochemists. But you're too lazy, stupid, and dishonest to do that.

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  2. Michael,

    So how do you explain the thousands of broken genes (pseudogenes) within the human genome, including half of the genes for olfactory receptor proteins (like all mammals, humans have a suite of about 1000 genes for olfactory receptors. In whales, they're all broken)? And the broken gene for one enzyme in the pathway involved in synthesizing vitamin C so that humans are prone to scurvy?

    And how do you explain the fact that the size of the genome varies so much over species? In humans, it's 3 billion base pairs. In the marbled lungfish, it's 130 billion base pairs. In certain single-celled amoeba, it's even larger (no physiological restraints involved in embryological development there).

    My definition of junk DNA as being that, if you remove it, doesn't have any effect obviously refers to pluripotential cells, such as germ or stem cells. Admittedly, it's not a very good definition, because there's multiple copies of some genes, such as for lactase. But it's the standard definition, behind the idea of 'knockout mice' as a means of working out the function of genes.

    Comparing bodily organs to DNA is just silly. With bodily organs, there's excess tissue in relation to function (except with the brain - I hope that you as a neurosurgeon don't think that removing part of the brain will be without effect? It might have little effect or it may be compensated for, but it will have an effect, similar to that in patients with small strokes).

    What percentage do you regard as the 'vast majority' being functional? I wrote 3 comments to yesterday's thread which were apparently deleted after passing the spam filter in which I asked you this question. I commented that I thought that the percentage of junk DNA in humans will probably be at least 50%, and that it could be as much as 90%. Transposons ('jumping genes') would fit the ENCODE definition of functioning, but don't do much good to their human hosts. Dead broken transposons don't do any harm, but would be considered to be 'junk'.

    Also, how do you know that the Intelligent Designer eschews 'junk'? In which part of the Bible is this stated? God did something somewhere somewhen for unknown reasons and by unknown mechanisms isn't a theory. If God created the Universe, with its billions of galaxies each with billions of stars, just for humans (or so Christianity seems to imply), then why couldn't God have put say 95% junk DNA into the genome? That would be considerably less wasteful than creating a Universe as it is compared to one consisting of just the solar system and the few thousand stars visible to the naked eye.

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    1. bach:

      The spam filter had four of your comments. I don't know why. I freed them. If I could change it, I would. Sorry.

      Delete
  3. Bachfiend said:

    "I hope that you as a neurosurgeon don't think that removing part of the brain will be without effect?"

    Michael has said almost exactly that previosly on this blog. I believe he said something like large portions of the brain have no specific function and can be removed without negative effects.

    I can't find it now on my phone but Steve Novella had a response to it at his blog on TheNESS. That was how I first came to find Egnor and his blog.

    -L

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    1. Here we are:

      "In fact, one can surgically remove much of the non-eloquent brain without significant discrete neurological deficit. Major portions of the frontal lobes, temporal lobes, parietal lobes, occipital lobes, and cerebellar hemispheres can be removed (and are removed, in operating rooms every day) without substantial specific loss of function."

      http://egnorance.blogspot.com/2011/08/dr-novella-inadvertently-highlights.html?m=1

      A distraction from the issue at hand. Fun to read never the less.

      -L

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    2. @L:

      I remove portions of the brain on a regular basis, and there generally is no discernable deficit as a consequence. It is routine knowledge among neurosurgeons.

      You are really a jerk, L.

      Delete
    3. In other words, Egnor has admitted that large portions of the brain are "junk", but that's not a problem for ID somehow, even though he seems convinced that lots of junk DNA is a problem for ID.

      Dishonesty, they name is Egnor.

      Delete
    4. mregnor,

      “You are really a jerk, L. ”

      I am completely baffled by your behavior.

      I directed bachfiend to the most likely answer to his question, a post from your own blog. You are responsible for its content, not me. I made no comment on the veracity of your claim.

      It seems you enjoy calling me things like bastard, liar, asshole, slimebag, and jerk. I forgive you for all all these minor transgressions. It usually happens when I correct you on what I believe is a factual error, ask a question you don't seem to want to answer, or include a quote with which you disagree. But this time I quoted ... you.

      And for that I am a jerk?

      -L

      Delete
    5. Ya know, L, for some reason I find your comments uncommonly annoying. Perhaps it's because I sense a disingenuousness, a pretense.

      Other commentors (bach, KW) are more straightforward.

      I admire candor, even if I strongly disagree with the content.

      I'm not your judge, but I'm being frank about my impression.

      Delete
  4. “I believe that DNA is created by an intelligent Agent, who eschews 'junk'.”

    Yes indeed and soon you will vote for a man who believes it’s a god that lives on or near the planet Kolob.

    As misguided as the ID movement is, it’s progress to see Christians’ tacit admission of the superiority of science over revelation. Only the dumbest Christians cling to literal belief in the bible, while the smart ones know they have to frame their arguments as science if they want to avoid looking stupid.

    -KW

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  5. Couldn't agree more with you, KW. This hilariously desperate Egnorian charade inadvertently highlights the triumph of the scientific method of inquiry when confronted with the new data over the "goddidit" stagnation embraced by ID creationists.

    I think that, in addition to the wonderful responses to this latest upwelling of Egnorance, it's worth pointing out that the term "junk DNA" has always been used as a tongue-in-cheek stand-in, not a definitive final assumption, by scientists when referring to the vast non-coding regions uncovered by the advent of whole-genome sequencing techonology. The term "junk DNA" was further popularized by media accounts during the heady days of early whole-genome sequencing, and of course the Egnors of the world now gleefully and disingenuously attack their latest straw man with ignorant brutality.

    In reality, we Biologists have never stopped working to annotate as much as we could of the massive amount of non-coding DNA (of all flavors) that we've encountered, because, quite simply, that's what we do. Unencumbered by the intellectual suffocation suffered by the ID-creationist, we've made incredible progress in a relatively short amount of time towards assigning functionality to most of this "junk," where applicable, and towards otherwise annotating the rest of it. We, as opposed to the hopeless creationist, revel in the fact that it appears we have much work ahead of us still. We argue, we disagree, but most importantly we experiment and let the data have the final say regardless of presupposition.

    Science progresses, while Egnor stagnates and whines piteously when his sad mischaracterizations find no quarter among the scientific community whose respect he and his ilk so desperately crave. It is the way of the modern world; quite satisfying to watch played out in these threads and elsewhere.

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    1. 'Goddidit' is an inadequate summary of ID. It should be 'God did something somewhere somewhen for unknown reasons and by unknown mechanisms' (I wish I could remember who came up with that formulation).

      Michael still hasn't answered as to what percentage of the human genome would be consistent with his belief that the amount of useless detritus would be very low. And why the thousands of broken genes aren't a problem for ID.

      Delete
    2. @Biomedikal Gangsta:

      In reality, we Biologists have never stopped working...

      The capital 'B' in "Biologists" -- was that a typo? A Freudian slip? An indication that you're referring to a religious sect? Or what? ;)

      Incidentally, are you a professional biologist? Just curious...

      Delete
  6. @Kent D:

    I noticed the same thing. It's like a cult.

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    1. Yes, I am a Ph.D. candidate in Experimental Pathology, and as such very much a professional Biologist. We study chromatin dynamics in the context of transcriptional activation/inactivation at inducible genes in budding yeast.

      Capitalization of the "B" is a product of my own respect for the science, but in this case it serves to highlight your own hypocrisy: You capitalize "G" in "God" -- "It's like a cult."

      Incidentally, Kent D. and Michael Egnor, are either of you professional Biologists?

      Delete
    2. @Biomedikal Gangsta:

      Don't get me wrong -- I have great respect for science, properly so-called.

      You make a serious category error when you compare the collective wisdom of "Biologists" with the wisdom of God (yes, capital 'G' God). What He designed, brought into existence, and sustains, you all are still struggling to understand. The scientific endeavor of biology is a noble one, but the hubris, pretense, and religiosity of "Biologists" is merely tragicomedic.

      I am not a biologist; I am a software engineer.

      Delete
  7. ...we [Jurgen Brosius and Stephen Jay Gould] have long felt that the current disrespectful (in a vernacular sense) terminology of junk DNA and pseudogenes has been masking the central evolutionary concept that features of no current utility may hold crucial evolutionary importance as recruitable sources of future change. Indeed, such vital notions as evolutionary "breakthroughs," advances in complexification, etc., probably bear little relationship to conventional adaptation (as usually assumed up to now) but are crucially dependent upon the size and extent of currently nonaptive pools of potential exaptation--the very material that now receives derogatory names, thus leading to our inattention.

    (bolded emphases mine)

    This quote serves as an apt companion to a Klaus Scherrer excerpt I posted a couple of days ago. "Junk" is not a neutral word. And "derogatory names [like 'junk']" lead to scientists' "inattention".

    Decades ago, scientists like Scherrer, Brosius, and Gould were sounding warnings to their peers about prejudicial terminology and premature conclusions. Why is it that when past and present-day ID proponents point out the same obvious facts, they are excoriated? I think the shrilly vocal party within the materialistic evolutionist community is suffering from (willful?) collective amnesia. The level of vitriol and ad hominem they're spewing does almost as much to undermine their credibility as their defective logic does.

    =====

    J Brosius and S J Gould
    On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA"
    PNAS 1992 89 (22) 10706-10710
    Online here.

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    1. “Why is it that when past and present-day ID proponents point out the same obvious facts, they are excoriated?”


      Because, in their own words, they are doing it “to defeat scientific materialism and its destructive moral, cultural and political legacies, and to replace materialistic explanations with the theistic understanding that nature and human beings are created by God.”

      Kind of like the Taliban.

      -KW

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    2. Q: "Why is it that when past and present-day ID [creationist] proponents point out the same obvious facts, they are excoriated?"

      A: Because your ignorant regurgitation of cherry-picked commentary adds nothing to the "debate," such as it is.

      You are obviously not a Biologist. If you were, you'd understand that the cloning and categorization of putative novel genes was a non-trivial undertaking (to say the least) in 1992. Gould and Brosius' commentary completely undermines your hilariously stupid "they said the words 'junk DNA' once so all science stopped researching every aspect of it and we creationists were right all along" argument. By supplying us with a paragraph demonstrating that even way back in pre-genomic 1992 scientists were lamenting our inability to economically investigate the obviously important non-coding regions of the genome you inadvertently made my case! Your self-congratulatory ignorance is icing on the cake. Next time, make sure to put a cherry on top or I will taunt you a second time!

      As usual, the ID-creationist position arrives to us "[t]old by an idiot, full of sound and fury, signifying nothing."

      Out of curiosity, Senor Regnor, can you answer "...as to what percentage of the human genome would be consistent with his belief that the amount of useless detritus would be very low. And why the thousands of broken genes aren't a problem for ID[?]" H/T bachfiend

      Delete
    3. Damn Bio Gangsta, pat yourself on the back for delivering the comment smack down of the month. If Kent D is not totally embarrassed right now it’s only because he has faith, that mental illness that makes smart people come to incorrect conclusions.

      -KW

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    4. Kent,

      Actually 'junk' isn't a derogatory word. 'One man's junk is another man's treasure' and all that. I have plenty of junk lying around the house. I'm a fairly typical liberal in that regard. Conservatives tend to be ordered and conscientious. Liberals tend to like mementos and a cluttered existence.

      'Garbage' on the other hand is derogatory. I don't tolerate garbage around the house. Unpaired shoe laces could come in handy sometime. Banana skins never will, unless I decide to build a compost heap.

      Junk DNA is just the DNA without a function but not causing much harm, like the thousands of broken genes in the human genome. Garbage DNA would be positively harmful DNA such as the multiple repeats at the end of the Huntington gene, the more repeats (and they tend to multiply with generations) the more likely is the person to come down with Huntington disease, at a younger age and more severe.

      Delete
    5. @Biomedikal Gangsta:

      Because your ignorant regurgitation of cherry-picked commentary adds nothing to the "debate," such as it is.

      I used the excerpts from Scherrer, and from Brosius & Gould, because their observations are directly relevant to the present discussion. Why not respond to their assertions? I've not taken them out of context, nor have I portrayed their conclusions inconsistently with the full context of their respective articles.

      I've taken care not to make any claims about biology that are beyond my rudimentary knowledge of the field. In fact, I don't think, in this present discussion, that I've made any claims about biological details at all. One need not have a profound grasp of biology to understand the excerpts I quoted; the language of the scientists is clear enough.

      ...your hilariously stupid "they said the words 'junk DNA' once so all science stopped researching every aspect of it and we creationists were right all along" argument.

      For a professionally trained scientist, you have abysmal reading skills. Your caricature of what I wrote is just that--a caricature. I challenge you to find anything I wrote that bears any resemblance to your portrayal.

      Instead of setting up a phantasmal straw man, try answering directly to the assertions that Scherrer, Grosius, and Gould make. Was the phrase "junk DNA", on average, a good one for science? They (at the time they wrote) say no. Was that prejudicial phraseology an impediment to scientific progress? They say yes. Respond to them.

      All ad hominem argument is logically fallacious. It remains fallacious regardless of repetition, and regardless of the intellectual pedigree of the taunter. (Indeed, taunting smacks more of desperation than of confidence.) Ad hominem is fallacious even when originating from a professional Biologist. Surely you have something more valuable to contribute to this discussion?

      Delete
    6. @KW:

      If Kent D is not totally embarrassed right now...

      I'm not embarrassed for myself. I'm embarrassed at the level of discourse demonstrated by certain professional folk like Biomedikal Gangsta. I live next door to an elementary school playground. The kinds of argumentation I hear through the fence bear an eerie similarity to BG's.

      KW, please refer to the last paragraph in my response to Biomedikal Gangsta on the merits of ad hominem argumentation.

      Delete
  8. @bachfiend:

    Actually 'junk' isn't a derogatory word.
    ...'Garbage' on the other hand is derogatory.


    I grant your distinction. But your disagreement would be more with Brosius & Gould than with me.

    Junk DNA is just the DNA without a function but not causing much harm...

    Did you mean to say, "DNA without a known function"? Isn't function the primary issue in question? Do scientists know with certainty that "junk DNA" is indeed non-functional in all respects, and at all times? -- that it serves no useful purpose under any circumstance?

    When I read the back-and-forth between the two sides of the current junk DNA debate, David Berlinski's incisive question from The Deniable Darwin keeps coming to mind:

    ...could a system we do not completely understand be constructed by means of a process we cannot completely specify?

    The intellectually responsible answer to this question is that we do not know -- we have no way of knowing. But that is not the answer evolutionary theorists accept.


    Berlinski was discussing the purported evolution of an eye. But his remarks apply, at least on some level, to DNA too.

    There is so much we don't know about DNA. Our relative ignorance need not be an impediment to continued investigation, or to the proposal and validation of new hypotheses or theories. But given science's current state of knowledge, the "junk DNA assertion" is merely a hypothesis. Pending validation, its epistemological status should not be presumed to be anything more.

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    1. Kent,

      Broken genes (of which there are thousands in the human genome) are junk DNA. They have no function (not just no known function) and also are doing no harm.

      I don't take any notice of anything David Berlinski says or writes. He's an intellectual whore. At one ID debate he announced that he doesn't believe in ID, doesn't have a theory to replace it and later admitted that he debates on the side of ID for the money. To me, that sounds as though he's a moral vacuum (to use the terminology from 'Yes, Minister').

      Delete
    2. @bachfiend:

      I don't take any notice of anything David Berlinski says or writes.

      Genetic fallacy.

      He's an intellectual whore.

      Ad hominem.

      At one ID debate he announced that he doesn't believe in ID...

      Wholly irrelevant. If Kurt Gödel denied that goats are mammals, his denial would not affect the logical validity of his Incompleteness Theorem in the least. Berlinski's agnostic stance with respect to ID doesn't affect the validity or invalidity of his critiques of evolution.

      ...[Berlinski] doesn't have a theory to replace [ID]...

      Also wholly irrelevant. So, Berlinski doesn't have an alternative theory to replace ID. How does that validate or invalidate his critique of evolution? Not at all.

      ...[Berlisnki] admitted that he debates on the side of ID for the money.

      "Appeal to motive" fallacy. As Oxford's Professor for Public Understanding of Science, Richard Dawkins was quite literally paid to evangelize for evolution. Does that income stream logically validate or invalidate his pro-evolutionary message?

      Is it so difficult to engage the real issues, bachfiend? Respond to Berlinski's question, and to his assertions.

      Delete
    3. Kent,

      Richard Dawkins accepted money for publicizing things that he accepts as true. David Berlinski is on record as staing that he doesn't believe in what he's paid to sprout.

      Not an inconsiderable difference.

      Delete
    4. Kent,

      And also you haven't addressed the main point of my comment - the many thousands broken genes within the human genome. They're definitely junk DNA. No function but not much harm.

      Delete
  9. @KW:

    You equate faith with "that mental illness that makes smart people come to incorrect conclusions".

    Rational thought is, of course, totally and absolutely impossible without faith. The fundamental premises of any rational system are taken on faith. With all due respect, if you think as a non-Christian you're occupying some sort of epistemological high ground, you're deluded. You either exercise faith at some starting point, or you are irrational--in the most literal sense of that word. Either faith, or irrationality; there is no middle ground.

    The fatal contradiction inherent in any materialistic world view is that, when its erroneous fundamental premises (which the materialist takes on faith) are carried to their logical conclusions, the possibility of rationality is excluded. So whatever logic the atheist employs is parasitic on theism, without which rationality is impossible. To even argue his case, the materialist must implicitly assent to theistic assumptions.

    That doesn't seem like high ground to me. It seems more like an airline passenger waxing eloquent to his traveling companion about the impossibility of aerodynamic lift, all the while cruising at 30,000 feet.

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    1. Gangsta:

      Kent D is right. Your rhetoric is a discredit to the scientific profession.

      There is a backlash coming against materialist thugs in science. The ENCODE publications are evidence for it. What's really remarkable is the extent to which the ENCODE scientists, Nature Genetics itself, and science journalists are defying Darwinist thugs like you.

      Keep up the public arrogance and anti-science rhetoric. You help our cause-- the cause of objective science-- immeasurably.

      Delete
  10. Kent,

    I've thought about Berlinski's question. The answer is obviously 'yes'. Just because we don't completely understand something today, and how it came to be, doesn't mean that we won't be able to eventually work it out. Something still exists even if we don't understand it completely.

    As an analogy, consider stars. We don't even have a good model for the nearest one, the Sun, so thinking that we understand how all the stars in the Universe of varying size, composition and age formed and evolve, all 10^22 of them in the visible Universe alone, is completely false.

    But the stars don't stop existing despite that.

    Junk DNA, if it has any real meaning, is just DNA that doesn't have any function at all, doesn't have any benefit to its host, but also doesn't cause any harm. It's still a robust hypothesis. The many thousands of broken genes in the human genome and the wide variation in genome size across similar species prove that.

    Points that Michael continues to refuse to address. And continues to throw abuse at materialists when it was materialistic scientists who did the ENCODE research.

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