Saturday, October 05, 2013

Barry Arrington, Junk DNA, and Why We Call Them Idiots

You're really not going to believe what's going on over at Uncommon Descent. Not only are we witnessing the meltdown of Barry Arrington, but we may also be witnessing the beginning of the end of Intelligent Design Creationism. The IDiots are manoeuvring themselves into such an extreme position that no intelligent person can possibly support them. Just read the comments.

I'm reminded of the word "pathos" but I had to look it up to make sure I got it right. It means something that causes people to feel pity, sadness, or even compassion. It's the right word to describe what's happening. It's also similar to the word "pathetic."

Here's what's happening.

As you know, Barry Arrington claimed that the IDiots made a prediction. They predicted that there's no such thing as junk DNA. They predicted that most of our genome would turn out to have a function [Let’s Put This One To Rest Please]. That's much is true. It makes perfect sense because an Intelligent Design Creator wouldn't create a genome that was 90% junk.

I'm happy that the IDiots made such a prediction because it is definitely falsifiable and if our genome turns out to be full of junk, which it is, it means that Intelligent Design Creationism has been refuted. It's practically impossible for them to argue their way out of the fact that the human genome does not look anything like something that was intelligently designed. Bacterial flagella are trivial in comparison.

I already blogged about this. It seems like only yesterday—wait ... it was only yesterday! [Intelligent Design Creationists Make a Prediction: How Did It Work Out?] Let me remind you what Barry Arrington said ...
For years Darwinists touted “junk DNA” as not just any evidence but powerful, practically irrefutable evidence for the Darwinian hypothesis. ID proponents disagreed and argued that the evidence would ultimately demonstrate function.

Not only did both hypotheses make testable predictions, the Darwinist prediction turned out to be false and the ID prediction turned out to be confirmed.
This was in response to a claim made by Elizabeth Liddle that Intelligent Design Creationists don't make predictions. She was wrong about this. I'm not going to defend her on that point.

However, there's several things wrong with what Barry Arrington said in his post. The first is that "Darwinists" never predicted junk DNA. There were evolutionary biologists who predicted that most of our genome would not have a function but that prediction was based on the genetic load argument and the argument was made by scientists who understood neutral theory and random genetic drift. They were not "Darwinists." Most Darwinists—believers in the power of natural selection—were opposed to the idea of junk DNA. Many still are.

I've covered this issue ad nauseum. There's a summary at: Educating an Intelligent Design Creationist: The Meaning of Darwinism. I don't really expect the IDiots to give up their rhetorical advantage by dropping the term "Darwinist" but I do expect them to acknowledge that they've been listening when problems over terminology arise.

The second thing that's wrong with Barry Arrington's statement is that, in fact, junk DNA is alive and well. When Dan Graur and I spoke at the Chicago evolution meeting last July, I expected that the audience of evolutionary biologists would be hostile in light of the ENCODE publicity fiasco. Turns out that the vast majority of evolutionary biologists at that meeting conclude that most of our genome is junk. In other words, they see the evidence and they accept it in spite of what the ENCODE Consortium said.

This is encouraging. We are reaching a consensus on the existence of junk DNA and the consensus is that most of our genome is junk. Some may disagree but that does not mean that Barry Arrington is correct when he says, "... the Darwinist prediction turned out to be false and the ID prediction turned out to be confirmed." That's just false.

Here comes the fun part. Elizabeth Liddle had the audacity to post a comment on Uncommon Descent where she said.
Sorry Barry that that example simply does not work.

Darwinian theory would only predict unused sequences of DNA were it to be the case that unused sequences had no metabolic or other cost . . .

And I will be first in line to cite Darwinian hypotheses that have been falsified. But not the “junk DNA” hypothesis.
What she meant, of course, is that Barry Arrington was wrong on two counts. "Darwinists" did not predict junk DNA and our genome is still mostly junk.

Barry Arrington was so shocked that he put up another post to deal specifically with Liddle's claims. You can see it at: Elizabeth Liddle’s Revisionism is Astonishingly Audacious!. Rather than do a it of investigation, lawyer Barry Arrington doubles down. I'm going to quote what he says. If any of you have irony meters, this is the time to turn them off.

Barry Arrington says,
Dr. Liddle, have you no shame? All I can say is your revisionist history is stunning in its scope and audacity.

Whole books were written by ID proponents about the Darwinist myth of junk DNA. See [The Myth of Junk DNA, by Jonathan Wells].

The ID position has now been largely vindicated and the Darwinist position debunked.

You know that. Therefore, I simply cannot imagine that you assert to the contrary in good faith. If I did not know better, charity would demand that I ascribe your statements to near invincible ignorance. Sadly, that option is not open to me. Therefore, I can only conclude that you are willfully and mendaciously misrepresenting the record.

You made a false statement in the prior post. I posted a second post calling you out. Instead of conceding or retracting you doubled down. Will you double down again or will you retract?
Wow! Can you believe that! Does anyone still wonder why we call them IDiots?

It gets even better. When Elizabeth Liddle posted a comment to this second post she was banned! That's right, she was banned from posting any more comments on Uncommon Descent [see Junk DNA on The Skeptical Zone]. Why is this amusing? See: Hypocrisy.

If you really want to see what Intelligent Design Creationists look like then you can do no better that read the rest of the comments on that post. It's a sorry sight. It reminds me of the word "pathos." It also brings to mind the word "pathetic."

I challenge Barry Arrington to take up this issue on Sandwalk where I promise not to ban him.


82 comments :

  1. I disagree with you that ID make falsifiable predictions, atleast if one adheres to skeptical theism per Michael Bergman which most theist do since they have to avoid the evidential problem of evil.

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    1. Well, yes: ID can either assume something about the Designer[s] and make predictions, or it can refuse to assume anything, and refrain from making predictions. Of course, in the latter case ID really isn't saying much, is it?

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    2. I found that confusing as well. Intelligent design creationism is not a scientific hypothesis. What possible predictions could it make?

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    3. Listen up punks: ID both does, and does not, lead to falsifiable predictions, as I'll now explain. Any pseudoscience consists of a subculture and a hypothesis. These are different and will produce different predictions, hence the confusion regarding falsifiability.

      The ID hypothesis leads to NO falsifiable predictions, but the authorities of the ID subculture can make any pronouncement they like, and call it a "prediction", even if it does not logically follow from the hypothesis. That's why ID is a pseudoscience.

      As I have repeatedly emphasized, the rules regarding 'falsifiability' and 'prediction' are different for pseudosciences.

      The hypothesis itself may logically lead to no testable predictions at all. In the case of ID, their God is all-powerful and can do anything he wants. If the purposes of ID's Intelligent Designer are unknown, then His purpose in creating humans may be that we're just a vector for carrying around dead, defective transposons. If we don't know the purposes of the Intelligent Designer, we cannot know how much DNA is junk, so the "bare ID hypothesis" logically makes no predictions regarding the matter.

      In order for the ID hypothesis to make predictions about the function in DNA, ID authorities must know the purposes of the Intelligent Designer, and knowledge of the purposes of God is inherently a religious belief.

      If and only if you have a religious belief that God's purpose in making the human genome is to add functionality to humans, then and only then can you predict no junk DNA.

      To sum up:

      1. Bare ID hypothesis --> No predictions about how much DNA is junk

      2. ID hypothesis + Religious beliefs about the purposes of God in creating humans --> Predictions that all DNA has a purpose to serve man somehow.

      In a pseudoscience, the authorities of the subculture (and the case of ID, Barry Arrington and the UDders count as such authorities) make phony predictions (fraudictions) which do not logically follow from the hypothesis.

      The "fraudictions" issued by the authorities don't logically follow from the hypothesis. They often, but not always include vague weasel words which enable equivocation to evade falsification when falsifying data is made widely known to the general public.

      Pseudosciences create the popular impression or illusion of falsifiability, while consistently attempting to evade falsifiability.

      To conclude: Larry Moran is quite wrong when he says that "ID" made a prediction that has been falsified. "ID" did no such thing.

      Rather, the bare ID hypothesis and the ID authorities, like Barry Arrington, produced different results. The bare ID hypothesis (without religious beliefs about the purposes of God) cannot produce any predictions to falsify.

      In contrast, the ID authorities, like Barry Arrington, Casey Luskin and Jonathan Wells made many predictions that never logically followed from the ID hypothesis, but that have been falsified. That discredits the authorities of ID, so Barry Arrington, Casey Luskin and Jonathan Wells are exposed as charlatans. The ID hypothesis, without religious assumptions added to it, continues to be non-falsifiable.

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  2. For those who don't want to click the links, here is the post that resulted in LIddle's being banned:

    Barry, can you cite a scientific paper that makes a prediction, derived from Darwinian theory, that large parts of the genome will be non-functional?

    Can you also find an ID paper that predicts that all DNA will be functional?

    Can you also find any paper that shows that all DNA is functional?


    Seriously, that's it.

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    1. Well, asking an IDiot to produce factual support for an assertion is like .... um... er... asking.. an IDiot to produce factual support for an assertion. They can't handle it because they are used to their fellow pew-warmers simply accepting everything they are told.

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  3. Does anyone recall an actual example of an IDer predicting no junk? All the examples I know of came out after functional ncRNAs started turning up...so it wasn't a prediction...and I've been following ID arguments since the old talk.origins days. Back then IDers had a standard response the claim that junk DNA made an intelligent designer unlikely. They'd say no one can predict what a designer would or wouldn't do. Any such speculation was theology not science

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    1. How can you say that? Quoth Luskin:

      ID has quite naturally directed scientists to predict function for junk-DNA, leading to various types of research seeking function for non-coding "junk"-DNA, allowing us to understand development and cellular biology. (See Wells, 2004; McIntosh, 2009a); Seaman and Sanford, 2009.)

      http://www.evolutionnews.org/2011/03/a_closer_look_at_one_scientist045311.html

      Not only have they been predicting "no junk" all along, according to their own testimony, but they were also kind enough to altruistically direct other people's research (rather than do any of their own).

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  4. Larry wrote

    As you know, Barry Arrington claimed that the IDiots made a prediction. They predicted that there's no such thing as junk DNA. They predicted that most of our genome would turn out to have a function [Let’s Put This One To Rest Please]. That's much is true. It makes perfect sense because an Intelligent Design Creator wouldn't create a genome that was 90% junk.

    and then

    This was in response to a claim made by Elizabeth Liddle that Intelligent Design Creationists don't make predictions. She was wrong about this. I'm not going to defend her on that point.

    We need to distinguish between "intelligent design creationists"--the adherents--and "intelligent design creationism"--the so-called theory. What I suspect Elizabeth meant was that the latter, the so-called theory, doesn't make predictions. And it doesn't. I have read Behe, Dembski, Meyer, Luskin, Kenyon, Axe, and more, and I have yet to see a statement of intelligent design "theory" that has anything approaching the level of specificity that would allow one to derive predictions of observations.

    Even you, Larry, slip when you say that "...an Intelligent Design Creator wouldn't create a genome that was 90% junk." Sez who? Why not? What constrains agents with the power to design and manufacture biological systems to be economical? Nothing in intelligent design "theory." Don't forget that Dembski said that the "aesthetics problem" and the "intentionality problem" are both outside the purview of science: We can't know what the designer(s) consider beautiful nor whether the designer(s) intended to create economical structures. Maybe the designer(s) like wastage and surplus.

    In order to predict new observations based on some theory that theory has to put clear constraints on what is and is not 'permitted'--what we should and should not observe under some specified conditions. But Intelligent Design Creationism has no such constraints. Without a detailed characterization of relevant properties of the designing agent(s), IDC has nothing but ad hoc patches pasted on a core of ignorance.

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  5. In order to understand why Barry Arrington and the other UDders have had a mental melt-down, and why they accuse Lizzie Liddle of lying, you have to understand that they are the victims of their own quote-mining. The quote mines assembled by Jonathan Wells and Casey Luskin have created a false version of science and the history of science, so they go insane when Liddle (or I, or anyone else) accurately describes the history of scientific attitudes toward non-coding DNA, junk DNA, and genomic concepts.

    IDiots attempt to deliberately obliterate the distinction between these two concepts:

    1. Scientists say non-coding DNA is equal to junk DNA, or a subset of it.

    2. Scientists say junk DNA is a subset of non-coding DNA.

    The IDiots insist that scientists believed 1. In the actual history of science, which ID critics, like Lizzie Liddle, understand, scientists actually believed 2.

    The IDiots, particularly Wells and Luskin, back up their claim of 1 by accumulating a series of quote-mines in which scientists actually say 2-- either that, or else the scientists say some sentence with non-coding DNA in it, and "junk" or "no function" or something related, maybe in the same sentence or connected by a creationist-inserted ellipsis-- but never actually say non-coding DNA is equal to or a subset of junk DNA.

    The ID 'No Junk DNA' Hoax, among other deceptions, treats its audience as if they are too dumb to tell the difference between 1 and 2-- and the hard-core UDders don't want to know any difference. Plus most creationists have zero reading comprehension.

    The IDiots like Luskin back up their scurrilous accusation by copying a re-copying a core of about 12 or 14 quote-mines from various sources where some journalist or non-scientist says 2, or something else altogether, and they tell their readers it proves scientists said 1.

    So, and this is important, to argue with the IDiots you have to deal with their core of quote-mines.

    So I did, once, in a mini-debate with Luskin. Luskin tried this trick on me once, when ENV briefly opened comments-- I insisted that no geneticist nor molecular biologist had ever said 1, and Luskin dumped about 12 of their dishonest quote-mines on me. So I analyzed every one of Luskin's quote-mines and showed that in none of them, not one, had any geneticist nor molecular biologist ever said that he himself believed non-coding DNA is equal to or a subset of Junk DNA. If you want to argue with the IDiots on this topic, I recommend that you peruse my debunking of Luskin's quote-mines on Junk DNA over at ENV. The debate ended, as always, with an IDiot (in this case lying Jonathan McLatchie) getting in the last word and then closing comments.

    Real molecular biologists since the 1970's (or before) would be infuriated if you accused them of believing that all ncDNA is "junk". Luskin is a lawyer, he doesn't know how infuriating his accusations are.

    Just because IDiots like Luskin can emit English sentences does not mean they can understand English sentences.

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  6. I'm not quite sure what you think I was wrong about, Larry, and as Barry did not link to my statement, and I think that it was one that Kairosfocus had deleted, I'm not sure exactly what I did say, and in what context. However what I did say earlier, and is the context for whatever it was I said that Barry quoted:

    "
    djockovic, I’d say that neither of your hypotheses are what I’d call a hypothesis.

    I’d say that that the theory of ID is “certain features of the universe are best explained by a designing intelligence)” just as the theory Darwinian evolution is that “the distribution of features of organisms and their ability to survive in their habitat is best explained by descent with modification of all living things from a universal common ancestor and natural selection of those traits best suited for survival in the current environment”.

    In order to gain support for these theories, especially if one is seen as alternative to the other, hypotheses have to be derived that make differential predictions: what we will see if A is true that we would not see if B is true.

    That would be the classic empirical scientific method.

    The difficulty for ID is making a prediction other than “I don’t think the other hypothesis would predict this”.

    To be testable in classic empirical terms, it has to predict data better than the alternative, i.e. produce a model with a better fit.

    The only ID hypothesis that I’ve seen that started down this road was front-loading, which was interesting.

    All other ID inferences boil down to “the alternative model doesn’t have a good enough fit”.

    That is true of CSI, as well as Irreducible Complexity."


    http://www.uncommondescent.com/intelligent-design/infographic-the-science-of-id/#comment-474928

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    1. Lizzie writes: "I'm not quite sure what you think I was wrong about, Larry"

      Lizzie says, if I understand her, that the ID hypothesis does not logically lead to predictions about how much junk DNA there can or can't be.

      Larry says that the ID hypothesis does logically lead to the prediction that there can be no junk DNA.

      In my comment above, I pulled this apart, making the point that in pseudoscience, unlike in real science, there are two sets of predictions we must address, that are very different:

      1. The predictions that logically follow from the hypothesis (in ID's case, = NULL SET.)

      2. The predictions emitted by the authorities of the subculture (= no Junk DNA).

      Lizzie is talking about 1, and Larry is talking about 2. So there I would argue, they're not necessarily contradiction each other.

      However, I would add that Larry is wrong if he thinks that the "bare ID hypothesis", meaning that 'living things were created by an immaterial spirit of unknown purposes and unlimited abilities' leads to the prediction of No Junk. To get the 'No Junk' prediction, you must add to the 'bare ID hypothesis' certain religious beliefs about God's purposes in designing the human genome solely in order to add adaptive functionality to humans. Those are religious beliefs tacked onto the bare hypothesis.

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    2. Lizzie, how many times has Barry banned you from UD?

      I think all pro-evolution people have been banned from UD except Nick Matzke and Kantian Naturalist. Larry and I are both banned.

      You all recall about a year or so ago when Barry Arrington had his mental breakdown and purged everyone who accurately described quantum mechanics and quantum indeterminacy. He's having another melt-down and it won't be his last.

      Lizzie, I've wondered before, is your relationship to Barry kind of like the relationship between the sadistic dentist played by Steve Martin (who likes to induce suffering) and the masochistic patient played by Bill Murray (who likes to be made to suffer) in the move Little Shop of Horrors?

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    3. Elizabeth,

      Intelligent Design Creationists believe that God is responsible for life as we know it. They believe that life appears designed and that this is clear evidence of God's handiwork since evolution is incapable of creating such design.

      A human genome that consists of 90% junk DNA is inconsistent with the concept of design that they advocate so they predict that most of our genome will turn out to be functional in spite of what many evolutionary biologists are saying.

      That prediction seems quite reasonable to me. I don't see any reason to quibble over whether it's a "real prediction" or not.

      You say that,

      ... the theory Darwinian evolution is that “the distribution of features of organisms and their ability to survive in their habitat is best explained by descent with modification of all living things from a universal common ancestor and natural selection of those traits best suited for survival in the current environment”.

      One of the important features of mammals is their large genomes that seems to be full of junk DNA. This is inconsistent with "Darwinian evolution" as you describe it above. Do you also predict that scientists will eventually find a function for this DNA?

      Or, do you favor a third option, one that's neither ID nor "Darwinian evolution," The third option is modern evolutionary theory. Most "Darwinists" predict that most of our genome is functional and junk DNA doesn't exist (or at least not very much junk). Are you a Darwinist?

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    4. Well, I won't quibble over what is a "real" prediction, but I will insist that what I meant was an actual predictive hypothesis!

      IDists are always scoffing at the idea that "Darwinists" reject ID because of "incompetent design". They can't have it both ways: say that ID predicts non-wasteful design, but that evidence of wasteful design isn't evidence against ID.

      So I simply don't buy that one. And in any case, I know of no place where any IDists actually predicted it. As I recall, the thing all started when some "Darwinists" started claiming that junk DNA was evidence against ID.

      Nor do I buy the idea that Darwinian evolution predicts junk DNA. It's perfectly consistent with it, and given that there is evidence for it, a Darwinian explanation isn't hard to find, and I do agree that broken genes will tend to be found in genomes if Darwinian evolution is true, but I don't know of anyone who predicted, a priori, from Darwinian principles that a large majority of the genome would be non-functional.

      It seems to me a bit like saying that because plate tectonics can account for earthquakes, that plate tectonics can predict earthquakes. Darwinian evolutionary theory broadly predicts that we will see tend to find vestigial structures in living things. But it doesn't predict a priori what those will be, because what gets rapidly eliminated, and what hangs on because it's harmless and what gets coopted for some other function depends on stochastic factors that are simply not predictable in specifics.

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    5. Elizabeth,

      The idea that most of the genome in species with high c-value has informational roles has been abandoned a long time ago, primarily based on evolutionary evidence (e.g. lack of sequence conservation). That’s why most scholars in the field of genome evolution, including Michael Bennett, Thomas Cavalier-Smith, Ford Doolittle and Ryan Gregory have focused on potential non-informational roles for the so called ‘junk DNA’ (jDNA).

      Here is an excerpt from a recent paper on jDNA by Ford Doolittle (Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE”; Proc Natl Acad Sci U S A. 110:5294-300):

      “Cavalier-Smith (13, 20) called DNA’s structural and cell biological roles “nucleoskeletal,” considering C-value to be optimized by organism-level natural selection (13, 20). Gregory, now the principal C-value theorist, embraces a more “pluralistic, hierarchical approach” to what he calls “nucleotypic” function (11, 12, 17)”.

      And here are 2 excerpts from Ryan Gregory’s papers:

      “Although some researchers continue to characterize much variation in genome size as a mere by-product of an intragenomic selfish DNA "free-for-all" there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates” (Gregory TR, Hebert PD. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res; 9(4):317-24).

      “These are the “nucleoskeletal” and “nucleotypic” theories which, though differing substantially in their specifics, both describe genome size variation as the outcome of selection via the intermediate of cell size” (Gregory TR. 2004. Insertion-deletion biases and the evolution of genome size. Gene, 324:15-34).

      Unfortunately, few people writing about jDNA are familiar with the work of these scientists. If they were, it is likely they would be sympathetic to Doolittle’s conclusion that: by developing a “larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon … much that we now call junk could then become functional.” (see reference above).

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    6. Just want to break in for a moment in regards to banning, both Joe G and bornagain77 have been temporally banned from UD, at different times in the past, then reinstated, as I suspect EL will be in the future...

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    7. Well that makes it all right then.

      For a minute there, I thought Arrington was only an asshole to people smarter than he is. Thanks for clarifying that.

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    8. Many ID proponents, including myself, did not agree with EL's ban, as stated on record @ UD..

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    9. rjop: Duly noted.

      Larry and I were banned from UD. Lizzie was banned twice. Dozens of other people were banned for offenses like asking the mod to provide evidence to back up his assertions, or contacting the scientist that the creationists were quote-mining.

      Arrington pulled a major dick move with Lizzie by posting a whole thread on her comment, thus luring her in, then allowing her one comment, and then banning her. Ironically, a few years back DaveScot, when he was moderator, pulled the same dick move with trrl: DaveScot posted a whole thread on trrll's comment, thus luring him in, then allowing him one comment, and then banning him. None of us are going over to UD so Arrington can insult us, lure us in, ban us, and insult us some more after we're banned.

      You tell Arrington this: If he has any evidence that most of the human genome has function that contributes to the fitness of the host organism and constrains DNA sequence, i.e. is not Junk, or that geneticists ever equated non-coding DNA = Junk, you tell him and all the Fellows of the Discovery Institute to meet us here. We'll take them all on.

      The UDders can't pretend they don't read this blog, because they talk about it at UD. If no senior fellow of the DI shows up here, they're conceding either defeat or cowardice.

      We'll squeeze those UDders.

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    10. @ Dio, And as I recall, you claimed to be banned from Shapiro's blog, which was not true according to Shapiro himself, and also stated, you've come close to being banned here at Sandwalk. The irony continues...

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    11. rjop: NO. You will not establish false equivalence, no flattening argument. Sandwalk has banned a total of about four people. UD has banned many dozens, so many that Arrington himself can't remember who he banned and who he didn't, as we saw in the case of Mark Frank cited below. Many, many of these bannings were for posters who:

      1. Asked for evidence/citations to back up an assertion

      2. Contacted a scientist who was quote-mined by creationists

      3. Criticized UD on another blog somewhere else on the internet, not UD

      4. Just disagreed with Jonathan Wells' book

      5. Accurately described quantum indeterminacy

      etc. etc. etc. No one has ever been banned from Sandwalk for such trivial bullshit reasons. UD has banned so many people for trivial bullshit reasons that Arrington can't tell them apart.

      No, you're trying to equate us with those irrational bullies. NO.

      Would you please inform Arrington to invite every one of the Discovery Institute fellows over here to UD to present their evidence that every there are no nucleotides in the human genome which are junk; and also their evidence that particular, named geneticists said all non-coding DNA = Junk. Three or four of us here at Sandwalk will dispatch all of the Discovery Institute fellows together.

      If they don't come here than they're conceding defeat or cowardice.

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  7. I have said before that UD exists expressly for the purpose of luring in evolutionists, insulting them, banning them, and then insulting them more and lying about what they wrote when they can no longer respond because they've been banned.

    Creationists on this forum got angry at me for writing that, and they would respond by saying, "Barry didn't ban Lizzie! So your claim is falsified!"

    Oh yeah? Who's right now?

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    1. really? because calling them IDiots is more insulting than anything i've ever seen on that site

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    2. really? because calling them IDiots is more insulting than anything i've ever seen on that site

      You can't have been looking very hard or very frequently.

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    3. "Unknown" says: "calling them IDiots is more insulting than anything i've ever seen on that site [Uncommon Descent]"

      God I hope you're being sarcastic. Every single post at UD is a long stream of ad hominems, insults and invective. That's all IDers have-- that and quote mines.

      Here's the moderator-- the MODERATOR!-- of Uncommon Descent, Barry Arrington, just the other day-- please note that the MODERATOR is supposed to be the mature, level-headed one, who "moderates"! And by UD standards, he is the mature, level-headed one, as most of the UDders are even bigger assholes, if you can believe that:

      Barry Arrington: "[Elizabeth Liddle] was not banned merely for asking questions. Those who would say that she was are either idiots or liars, probably the latter. The suggestion that EL was banned merely for asking questions is so obviously false as not to require rebuttal." [Barry Arrington, Comment #96 at UD of Oct. 5, 2013]

      Note that Barry uses insults as a substitute for evidence-- he constantly, again and again, throws out the "I don't have evidence, except my only evidence is that if you disagree you're an idiot" line:

      [Arrington To evolutionist Kantian Naturalist]: "Do you seriously think I banned EL merely because she asked a tough question? If so, I agree; you are an idiot." [Barry Arrington, Comment #101 at UD of Oct. 5, 2013]

      Let me emphasize that I'm not offended by Barry's endless insults, and all the ad hominems and personal attacks thrown out by the UDders. They're ID proponents; ID proponents have nothing but personal attacks and quote-mines. What bothers me is that they never have evidence that their opponents are wrong. I'd let them call Lizzie Liddle an "idiot" and "liar" after they had proved her wrong with evidence, but they didn't-- their evidence she's wrong is that they called Lizzie Liddle, and everyone who supported her, an "idiot" and "liar."

      Barry Arrington: "BTW, if you say the prominent Darwinists did not howl for years and years about junk DNA being a clincher for their theory, then you are either ignorant or a liar. I don’t know which you are." [Barry Arrington, Comment #38 at UD of Oct. 4, 2013]

      That's the MODERATOR! Can you even imagine what the other assholes say?

      Here's Upright Biped, who is one of the nicer UDders:

      "Elizabeth Liddle will say anything literally whatsoever, without the slightest sense of intellectual honesty." [Upright BiPed comment #13 at UD of Oct. 4, 2013]

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    4. Since our anonymous guest "Unknown" wishes to push the myth that UDders are "more civil" and don't use insults like us uncivil Darwinists, I will give you a brief summary of a typical UD thread I participated in.

      This is from the thread UB Sets it Out Step By Step, in which Upright Biped (UB) pushes his semiotic argument.

      I refute UB's semiotic argument, they don't understand math and can't admit they don't know math, so all they have to fall back on are insults.

      UB to me, comment #813: 'It’s because your entire counter-argument is deliberate, wholesale obfuscation (i.e. bullshit)...' [UB's Comment #813 at UD]

      Note UB can and does say "bullshit" and will never get banned. I never used language like that at UD, but my banning from UD is falsely claimed as being due to me allegedly talking like an ID proponent.

      Here are more typical comments from that thread. Mung does not address my argument; like UB, he just calls it bullshit:

      Mung wrote: "b.s. + bluster = diogenes"
      [Mung, comment #757 at UD]

      That's the whole comment. Mung expresses it as an equation because he was mocking me for trying to use mathematics.

      The use of foul language, "bullshit" and "bs", receives approval from UDders as long as it comes from ID proponents, who can barely spell, and who HATE and ridicule mathematics:

      Wateron1 wrote: "[Chuckle] Mungs analogy of bs + bolster [sic] = Diogenes seems to sum it up quite well" [Wateron1, comment #797 at UD]

      Later on, Mung develops his most intellectual refutation:

      Mung wrote: "what a maroon"
      [Mung, comment #793 at UD]

      That's his whole comment. He repeatedly ridiculed me for attempting to use mathematics.

      As for Joe "Security Clearance" Gallien, he was his usual self. I proved that he had misrepresented Stephen Meyer's false claims about biochemistry on page 303 of Signature in the Cell, in an attempt to protect Meyer. His response was deny, deny, deny. This is the kind of thing Security Clearance writes over and over and over, everywhere:

      Joe "Security Clearance" Gallien: "Face it diogenes, you are a demented lowlife liar- that is an observation, not an insult" [Joe Gallien, comment #782 at UD]

      It's "not an insult" only because it's coming from an ID proponent. It would be if it were directed at an ID proponent. Every comment Joe G writes to me is like that.

      For IDers, ad hominem attacks are facts, and facts are ad hominem attacks.

      Then after UD bans an evolutionist, the UDders make up fake stories about how he was banned for being "uncivil"! That's the REASON why UD exists. They're doing it right this minute to Lizzie Liddle.

      Delete
    5. As our anonymous guest "Unknown" has asserted that the UDders don't use insults over at UD, here's an UDder calling Larry Moran "Dr Moron."

      The topic is whether Larry should be invited to UD to squeeze the UDders. Axel, shockingly, is opposed:

      Axel at UD: "Ironical or what, that Dr Moron should have labelled dissenters, ‘IDiots?

      tee hee thither thither, as they used to chortle in the Beano and Dandy.
      Do I hear a squeaky, moronic little voice, wail, ‘Now who’s a moron?’ Stand to attention, when you’re speaking to me!"


      [Axel, Comment #8 at UD on Oct. 8, 2013]

      Hey that's Professor Moron to you!

      Delete
    6. The Wisdom of Upright Biped:

      “So if you are, perhaps, a slow learner or have difficulty with modest conceptualizations, then I simply did not pick up on it. More than likely I may have overlooked it given your pompous certainty…

      I apologize for not being more empathetic to any special needs you might have.…

      I simply assumed that you were just another materialist bigot…

      I am more than willing to slow down for you.”

      “As it becomes obvious, Diffaxial cannot allow himself the burden that he might be wrong – even to the extent of being able to have a reasoned conversation about the possibilities. He is a coward in this regard.”

      “This is an out and out lie. You are now lying to make your point.”

      “That was the most baited and sophmoric attempt witnessed since the recent talking donkey episodes (or perhaps watching Diffaxial’s laborious and repeated sholveling of the ground under his feet).”

      “I think that all regulars at this site have come to understand that Diffaxial cannot say anything in which he does not assume his conclusion. It is, apparently, a pathological trait from which he has chosen not to allay himself.”

      “Why would you ask such an ignorant and misplaced (dumbassed) question? Was it meaningful to you in some fashion personally?”

      “The glaring difference between our positions is that I rationally incorporate what we observe in nature, while you irrationally ignore it.”

      “In other words, his response was a nonsensical load of crap. Which was then immediately followed by a return to obfuscation.”

      “In Diffaxial’s case, he was simply a fool.”

      “Diffaxial, try to make sense – and try to be consistent as well.”

      “I am more than happy to consider you no more than highly-trained idiot. Moreover, if you think that I am impressed by the idea that (gasp) modern philosophers disagree with one another about a subject, then you are not even as smart as I might have given you credit for. You perhaps have the training, yet you lack the basic wisdom of a matured farm hand…”

      Delete
  8. This part of that UD thread is so hilarious, I have to share it. "Mark Frank" makes a comment about how Larry Moran and Lizzie Liddle would not be wise to respond to an invitation to debate at UD:

    Mark Frank: "It is an admirable idea [Moran at UD] but I do you think they would want to participate given the chances they would be banned if they asked the wrong questions?

    Perfectly reasonable question, considering that Arrington bans most evolution critics. But Arrington believes that he's got the perfect beat-down for the insolent Mark Frank:

    Arrington: "Ironic question coming from a person who has commented freely on this site since 2006." [Barry Arrington, Comment #102 at UD on Oct. 5, 2013]

    Oh SNAP! Barrry got 'im good that time! Ha ha! Mark Frank doesn't know how lucky he is to speak in the land of the free-- Uncommon Descent!

    So Mark expresses his gratitude to Barry:

    Mark Frank: "It appears you have got so used to banning people you forget who you have banned. You banned me last year for refusing to agree to certain statements (I forget exactly which). I recently found I could log on again." [Mark Frank comment #115 at UD on Oct. 5, 2013]

    Arrington has banned so many people now, he can't keep them all straight.

    Arrington has banned many people multiple times. He (or DaveScot) banned Lizzie Liddle twice now, Mercury twice, and Zachriel three times. Caligula was banned for asking for evidence to back up an assertion by DaveScot about natural selection. In Feb. 2012 Arrington freaked out and purged dozens of people for accurately describing quantum mechanics and quantum indeterminacy, and for not jumping when Barry says "jump."

    Arrington is like Stalin forgetting who he sent to the gulag.

    UD is so insane that some are now arguing that banning ALL evolutionists is justified by the principle of... free speech. Mapou and TheisticEvolutionist now demand that all "Darwinists" be banned "at the slightest provocation."

    Mapou: "...she [Liddle] is part of a group of people who will not allow the theory of evolution to be criticised in the schools... Banning free speech in education is one of the biggest affronts to my right to liberty that I know. It’s a Big Brother elitist mentality pure and simple... Dr. Liddle condones this stuff...

    This is why I say to IDists, ban them all. Ban them at the slightest provocation."
    [Mapou, Comment #38 at UD on Oct. 4, 2013]

    You see, by suppressing free speech, UDites are... uh... standing up for... free speech... sure. By enforcing a blanket policy to ban all evolutionists, they're fighting a Big Brother mentality. War is Peace, and Freedom is Slavery.

    ReplyDelete
  9. Elizabeth Liddle says,

    Well, I won't quibble over what is a "real" prediction, but I will insist that what I meant was an actual predictive hypothesis!

    I understand. We differ in what we count as a "prediction." You prefer a strict definition based on an explicit hypothesis while I opt for a loose definition based on a worldview. The IDiots say that their view of life leads them to predict that we will find function in most of our genome. I'm prepared to accept that this is a genuine prediction while you prefer to judge it against more traditional scientific predictions.

    Let's agree to disagree.

    ReplyDelete
    Replies
    1. But an informal prediction loosely based on a world-view is not even worth testing. The whole idea of falsification is that if the entailment H ⇒ P is correct and P turns out to be false (H = hypothesis, P = prediction), then H can't be true. If P is not the logical consequence of H but only the expression of somebody's wishful thinking, we can't refute anything worth refuting by demonstrating that P is false, so why bother?

      Delete
    2. @Piotr,

      The IDiots are saying that Intelligent Design Creationism predicts that most of our genome is functional. They are saying that their "theory" is inconsistent with junk DNA. It's they who are setting up the conditions where falsification of their prediction is damaging to their position.

      Let's encourage them to stake their reputations on the idea that most of our genome has to be functional.

      Delete
    3. I can see your point, but I don't think their position is really vulnerable to falsification. They may say that they "predict" the impossibility of junk DNA, but they are not committed to any explicit theory from which the prediction would logically follow. If the worst comes to the worst, they can easily retract their prediction (after all, the Intelligent Designer may be fond of useless redundancy -- they studiously avoid making any testable claims about her, so why not?). Their reputation as scientists is non-existent, so they don't have to worry about it.

      Delete
    4. Larry says: "Let's encourage them to stake their reputations on the idea that most of our genome has to be functional."

      But Larry, if ID predictions are defined as being whatever ID authorities say, then we have to deal with their equivocation. They will escape falsification by equivocating. Most ID "predictions" are carefully crafted, as sentences, to have at least two, maybe more, meanings. Casey Luskin very consciously and deliberately writes sentences with multiple interpretations: a "strong" interpretation that will be picked up by church audiences, and a "weak" interpretation that can mean nearly anything and is non-falsifiable.

      All ID concepts (Irreducible Complexity, Specified Complexity etc.) are full of weasel words that allow the IDiots to engage in equivocation.

      If we follow your method of saying the predictions of ID are whatever the IDiots say they are, then they'll change the meaning of everything on the fly. That means that we have to be prepared to deconstruct their texts and pick apart the multiple meanings in every sentence they write.

      Do you want to be a deconstructionist? You wanna try? Here's Dembski 1998, see if you can catch the weasel part:

      "Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. " [William Dembski, "Intelligent Science and Design," First Things, Vol. 86:21-27 (October 1998)]

      What does "as much as possible" above mean, Larry? It means whatever they want it to mean. They deliberately write sentences like this, with escape clauses. It's conscious and deliberate. How do you fight that?

      Delete
    5. They deliberately write sentences like this, with escape clauses.

      How else, with so many lawyers on board? And they have an experienced bancruptcy lawyer in charge of UD, just in case...

      Delete
  10. Elizabeth Liddle says,

    IDists are always scoffing at the idea that "Darwinists" reject ID because of "incompetent design". They can't have it both ways: say that ID predicts non-wasteful design, but that evidence of wasteful design isn't evidence against ID.

    But that's not what they are doing in this case, is it? They are staking out a claim against wastefulness. They are saying that junk DNA is wasteful design, therefore we will eventually find a function for all that junk.

    So I simply don't buy that one. And in any case, I know of no place where any IDists actually predicted it.

    There are lots of places where the IDiots make the claim that junk DNA is a myth.

    As I recall, the thing all started when some "Darwinists" started claiming that junk DNA was evidence against ID.

    We are going to have difficulty carrying on a conversation unless you clarify what you mean by "Darwinist" and by "Darwinism." In the sentence I just quoted it grates me to see you claim that Darwinists (with or without scary quotes) promoted the idea of massive amounts of junk DNA in our genome. Strictly speaking, Darwinists were opposed to that idea.

    Could you have used the term "evolutionary biologists" in your sentence? How about "evolutionary biologists who were not strict Darwinists or adaptationists"?

    Nor do I buy the idea that Darwinian evolution predicts junk DNA. It's perfectly consistent with it, and given that there is evidence for it, a Darwinian explanation isn't hard to find, and I do agree that broken genes will tend to be found in genomes if Darwinian evolution is true, but I don't know of anyone who predicted, a priori, from Darwinian principles that a large majority of the genome would be non-functional.

    That's because NOBODY predicted the existence of large amounts of junk DNA based on Darwinian evolution (e.g. natural selection). In spite of what you say, it is NOT easy to explain such a large amount of junk DNA using a Darwinian explanation. I've never seen such an explanation.

    Do you really believe what you say or are you using the term "Darwinian evolution" to include modern population genetics, Neutral Theory, and random genetic drift? If so, that's a non-standard definition and it's confusing.

    Darwinian evolutionary theory broadly predicts that we will see tend to find vestigial structures in living things. But it doesn't predict a priori what those will be, because what gets rapidly eliminated, and what hangs on because it's harmless and what gets coopted for some other function depends on stochastic factors that are simply not predictable in specifics.

    Exactly. That's why no Darwinist ever predicted the existence of junk DNA. The first predictions of junk DNA were based on genetic load arguments and the C-value paradox [see Five Things You Should Know if You Want to Participate in the Junk DNA Debate and Genetic Load, Neutral Theory, and Junk DNA].

    You should read Jukes & King (1969) [Science 164:788] where they discuss the possibility that much of our genome consists of superfluous DNA. They didn't call it "junk" but that's what they meant. The title of their long paper is significant. It is "Non-Darwinian evolution." It was published 44 years ago. Here's a PDF copy. If you haven't read it, it's definitely time to catch up on modern evolutionary theory and the history of junk DNA.

    ReplyDelete
  11. Larry, you're not being entirely forthcoming.

    Yes, Darwinists didn't 'predict' Junk-DNA. That's because NS was supposed to keep DNA rather tightly conserved.

    So, while you're correct in your assertion, you fail to point out that the high level of polymorphisms found in DNA during the sixties led to the notion of "Non-Darwnian Evolution." IOW, that Darwinian 'predictions' had failed.

    Where, then, did this leave evolutionary theory? It's historical foundation had just been swept away. And where does that leave us now, exactly?

    Then you fail to point out that this very same high level of polymorphisms led to Kimura's "Neutral Theory," and to biologists turning to random genetic drift in an effort to buttress up some kind of evolutionary theory.

    The reality is that if you accept ENCODE's findings, you're then forced, more or less, to abandon the notion of 'random genetic drift.' Is this perhaps the reason that at the conference you attended none of your confreres 'accepted' ENCODE's findings, despite its cutting edge character?

    I don't think it's Arrington that looks bad in all of this.

    ReplyDelete
    Replies
    1. @Lino Di Ischia,

      Thank-you. You should not ever worry about being banned on Sandwalk. Your posts are so amusing that I'd never think of depriving the other readers.

      Delete
    2. LDI: "The reality is that if you accept ENCODE's findings, you're then forced, more or less, to abandon the notion of 'random genetic drift.' Is this perhaps the reason that at the conference you attended none of your confreres 'accepted' ENCODE's findings, despite its cutting edge character?"

      Ho boy. We got a muggle.

      What, pray tell, do you think ENCODE's results were, precisely, and by what experimental means were they obtained?

      How many functional assays did ENCODE do, doya think?

      Delete
    3. Larry:

      Were you thinking of banning me because I disagree with you?

      You're amused; that's nice. However, you nevertheless remain unresponsive. Why? Are you running away from the issues?

      I've been looking around. It seems Graur's pointed criticism of the ENCODE project, one that partially relies on the criticism that many of the scientists in the project (which included 30 research teams, and 400 scientists overall) were computer scientists. And, yet, when Graur gets around to criticizing their results, as his very first criticism he challenges ENCODE's definition for "function" using a definition of "function" that comes, not from scientist working in a lab, but from a "philosopher of science" (Griffiths 2009). (Refresh my memory: isn't Steven Meyers a "philosopher of science"?)

      Tell me, should I take Graur's criticism seriously?

      I have a further question: Did anyone complain about ENCODE's definition for "function" PRIOR to their results? You see what I mean?

      Delete
    4. Lino,

      Yes, scientists complained about both ENCODE's redefinition of function, and ENCODE's acceptance of quite dubious results back when they published a first "test" with 1% of the human genome. Further, other articles besides Graur's have appeared criticizing ENCODE's "manoeuvre" that started by redefining function only to then claim that there's no junk DNA.

      Don't ask us if you should take Graur's criticism seriously. Read the proper articles and decide for yourself. Just make sure that you understand the science, the experiments, and therefore the significance of those results.

      Delete
    5. Neg is exactly right, about 5 years ago ENCODE published their pilot study on 1% of the genome and many scientists complained that their criteria-- basically, widespread transcription into RNA-- was a useless definition of "function" or at least, irrelevant to the Junk DNA hypothesis.

      Moreover, many of the ENCODE scientists themselves acknowledged that the 80% value mentioned in the abstract of the lead paper could ONLY be true if "function" is defined in a way that is irrelevant to the junk DNA hypothesis. Ewan Birney, who wrote that controversial abstract and chose that definition, has admitted several times since then that the human genome is really only 10 to 20% functional by the definition of function relevant to the Junk DNA hypothesis. He admitted this on his blog immediately after the paper was published, and reiterated the point multiple times, most recently in a BBC interview.

      Delete
    6. Negative Entropy:

      Yes, scientists complained about both ENCODE's redefinition of function, and ENCODE's acceptance of quite dubious results back when they published a first "test" with 1% of the human genome.

      I've done a Google search and don't find any articles where the definition they used in 2007 was criticized. Perhaps you can come up with a citation.

      Delete
    7. Larry:

      I'm still hoping you can give me some kind of substantial reply.

      It took you only 51 minutes to reply last Tuesday. It's been almost a day-and-a-half this time round.

      Delete
    8. Lino,

      If you search Larry's blog you will find some references questioning that first paper by ENCODE and their pervasive transcription results. ENCODE back then did not mention that as "function" though. They left it to be guessed, thought they tried to imply so, if that was functional or not. Only later did they change function to mean almost anything but replication.

      So, no complains before the big fiasco because they had not redefined function yet. My mistake. After all, how could anybody criticize their definition of function if they had not given that definition yet?

      Delete
    9. Lino,

      As per your questions. I insist that you should understand the science before going on. For example, Darwin is about natural selection. That scientists found that most changes in protein sequence were not due to natural selection does not mean that natural selection does not happen. It does not mean that evolution does not happen either. You have to learn to be able to distinguish between evolutionary theory, the facts of evolution, and the mechanisms of evolution. In a safer environment, like gravitation, nobody would complain that gravitation is unfalsifiable because Newton's take failed to predict some gravitational phenomena. Those phenomena were later explained within Einstein's take at the problem. Therefore the theory of gravitation was modified. That it is no longer Newtonian does not make gravitation false. Newton's take is still helpful to solve some problems, while the more complicated Einstenian stuff can be used to the most complex behaviours. None of that invalidates gravitational facts. None of that makes gravitation "unfalsifiable." The same goes for evolution. There's facts, there's things that natural selection can explain, there's points where natural selection does not work, but genetic drift does. Nothing about "salvaging" anything. All about complementing what we knew after observing evolutionary facts that were not predicted by natural selection. Understanding these things might require some study.

      While I don't speak for Larry, I would venture that he is not very inspired to answer you because you come across as a mere ideologist who does not know one thing about evolution or science. As an ideologist who does not care one bit about the answers. Maybe you are no such thing, but, after lots of experience with people using your particular style of discourse, that's an easy conclusion to make (most often correct). Besides, Larry has written extensively about these issues in his blog. If you were authentically interested you would have figured it out already. Take a look. Search the blog. Maybe you'll find those answers. Again, if you do care. If not, then I tried, and the rest is up to you. As I said, It's not about my word, Larry's, Graur's, whatever. It's up to you to learn.

      See ya.

      Delete
    10. I'm still hoping you can give me some kind of substantial reply.

      What do you want me to reply to? Someone else has already explained that the ENCODE Consortium only defined "function" when they published their slew of papers. They were challenged within 24 hours.

      Delete
    11. The ENCODE project chose to use and define "functional elements" instead of defining "function" itself. But biological function is rather obvious, is it not?

      So what, then, is the problem here?

      Delete
    12. Negative Entropy:

      Dear NE: It is unwise to assume an air of superiority. What science is there that I'm not up to speed on?

      You wrote this: [My remarks interspersed.]

      As per your questions. I insist that you should understand the science before going on. For example, Darwin is about natural selection. That scientists found that most changes in protein sequence were not due to natural selection does not mean that natural selection does not happen. [No, but it means that the "predictions' of neo-Darwinism---i.e., the population genetics version of it---proved to be wrong. That should count for something. You blithely swat it away as a complete nothing. Why?] It does not mean that evolution does not happen either. [Well, if NS doesn't account for evolution, then per Dawkins, there's absolutely no way to "climb Mt. Improbable. This is a problem. You simply swat it away. Why?] You have to learn to be able to distinguish between evolutionary theory, the facts of evolution, and the mechanisms of evolution. [I try to do that. Do you? When the "mechanisms" of evolution prove to be astronomically improbable--meaning it couldn't possibly have happened that way---then what does that say about "evolutionary theory"? It says something is wrong with "evolutionary theory". You are then left not with the "fact of evolution", which are scant, but with the giant FACT of EVOLUTION: i.e., that the fossil record clearly tells us that organic forms changed over time, and sometimes quite dramatically. But this "fact of evolution" does not belong to Darwinism, nor to neo-Darwinism, nor to Neutral Drift. It's simply a fact, regardless of the theory and mechanisms posited as an explanation.]

      You then wrote:
      In a safer environment, like gravitation, nobody would complain that gravitation is unfalsifiable because Newton's take failed to predict some gravitational phenomena.

      Your interpretation of this misses the mark.

      First, Darwinism isn't "unfalsifiable" because it fails to predict. It's failure to predict makes it wrong. What makes it "unfalsifiable" is that ex post facto some "just--so" story is always invented to make this failure seemingly go away. The comparison here would be to the "epicycles" constructed by the Ptolomeans to explain this deviation from their theory and that deviation over there, etc. etc.

      Second, that my analysis in the above paragraph holds water is demonstrated by what you write about Einstein. He was able to account for Mercury's precession accurately, and not approximately, like Newton's. You see, the "failure" of Newton's Theory led to the development of Einsteins's Theory, and science moved forward. With Darwinian "just-so" stories, there is NOTHING that fails, so there is no reason to move forward, and so biology is stuck in the 19th Century. It simply remains, in the hands of its practicioners, "unfalsifiable".

      The reaction to the ENCODE project is emblematic of this "unfalsifiability," isn't it? neo-Darwinism predicts lots of "junk-DNA", and when an experiment (on the grandest of scales and probably one of the most sophisticated to date) contradicts this prediction, the authors of the study are bludgeoned. Maybe you should try re-thinking things.

      Look, science has to sort of "drag their feet" a bit, or else no one would know where things stand. But in the case of Darwinism, there is such intransigence that it can be described as nothing else but being "reactionary."

      Delete
    13. Lino,

      You just confirmed my "sense" of "superiority," since, rather than understanding what I was saying, you lead towards some pretty damning signs of ignorance (or pretence thereof).

      [Well, if NS doesn't account for evolution,

      Are you paying any attention? NS does not account for all the changes that we see in evolution. That does not mean that it does not account for any events in evolution.

      then per Dawkins, there's absolutely no way to "climb Mt. Improbable.

      Since your premise is flat out wrong, there is indeed way to climb Mt. Improbable.

      This is a problem. You simply swat it away. Why?]

      Because this problem only exist in a mind that ignores the most basic of science and logic. Neutral and semi-neutral evolution means that DNA and protein sequences have plenty of options for change that are impervious to natural selection. That does not mean that NS never happens. Simple logic.

      [I try to do that. Do you? When the "mechanisms" of evolution prove to be astronomically improbable--meaning it couldn't possibly have happened that way ...

      Well, since this is a huge jump taken on behalf of unsurmountable ignorance on your part, I see no reason to try and translate what you might mean. Sense of superiority? What next? Am I been condescending for stating the obvious about your knowledge of science in general and evolution in particular? Do you even understand the difference between DNA sequences, protein sequences, neutral and semi-neutral changes, phenotypes, and then natural selection? I mean, if the fact that proteins can change a lot without phenotypic consequences means to you that natural selection does not happen, there's something seriously wrong with your understanding and logic.

      You see, the "failure" of Newton's Theory led to the development of Einsteins's Theory, and science moved forward

      Sure. The development of neutral and semi-neutral theories lead to better understanding, and application, of population genetics, and also advanced our understanding of such things as how complexity evolves. Lots of new avenues were open, and much better understanding developed and is still under development (hot scientific debates in this very blog attest to that). So, sure. That natural selection did not explain everything allowed for further development of evolutionary theory. Science moved forward. Therefore I am quite far from missing the mark when I compare gravitation with evolution.

      The reaction to the ENCODE project is emblematic of this "unfalsifiability," isn't it?

      It isn't. If ENCODE had to change the definition for function in order to "debunk" the concept of junk DNA, then the problem is ENCODE, not the concept of junk DNA. It does not matter how many and how expensive the technologies involved.

      neo-Darwinism predicts lots of "junk-DNA" ...

      Curious that just a few comments ago you admitted that Darwinism did not predict lots of junk DNA. Now you contradict yourself. Should I assume, as I was guessing, that you are nothing but an ideologue with no interest in answers?

      Delete
    14. Negative Entropy:

      Since your premise is flat out wrong, there is indeed way to climb Mt. Improbable.

      Have you read Climbing Mt. Improbable? I haven't read it, but am somewhat aware of Dawkin's argument. His argument--since "Blind Watchmaker"--is that NS is what accumulates complexity, NS alone. Things happen in the cell in random fashion, but NS is non-random, thus empowering the accumulation of beneficial effects, leading to increased complexity. The argument is bogus and unsubstantiated. But if you abandon NS, then you're left with absolutely nothing.

      Further, if you look at the criticism of ENCODE by Doolittle, you'll see that some leading evolutionary biologists are still pan-selectionists. IOW, Doolittle does not much credence to random genetic drift, etc.

      Now your position might be that evolution is a combination of these various mechanisms: NS, random genetic drift, neutral drift. But if NS is let go of---IOW, if randomness is allowed in via neutral drift/random genetic drift--then there is no sensible way of expecting that complexity--Dawkin tells us that organisms are amazingly complex--will increase in time. This is the Achilles Heel of purely materialistic evolutionary theories

      The idea that a use of a "little NS, a dash of neutral drift, and smidgen of random genetic drift plus stochastic processes" will get you macro-evolution (or, even, micro-evolution for the most part) amounts to no more than a "just-so" story. Where are the experimental data supporting this view? It's nowhere to be found. That's why evolutionary theory remains problematic.

      You wrote:Curious that just a few comments ago you admitted that Darwinism did not predict lots of junk DNA. Now you contradict yourself. Should I assume, as I was guessing, that you are nothing but an ideologue with no interest in answers?

      Why don't you go back and look at what I actually said, instead of what you said I wrote. You're wrong about this as well.

      Delete
    15. Larry:

      Cat have your tongue?

      Here's what was said in 2007:

      Nature Article--"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project" June 2007

      Here's the link.


      Unconstrained experimentally identified functional elements

      We believe there is a considerable proportion of neutral biochemically active elements that do not confer a selective advantage or disadvantage to the organism. This neutral pool of sequence elements may turn over during evolutionary time, emerging via certain mutations and disappearing by others. The size of the neutral pool would largely be determined by the rate of emergence and extinction through chance events; low information-content elements, such as transcription factor-binding sites110 will have larger neutral pools. Second, from this neutral pool, some elements might occasionally acquire a biological role and so come under evolutionary selection. The acquisition of a new biological role would then create a lineage-specific element. Finally, a neutral element from the general pool could also become a peer of an existing selected functional element and either of the two elements could then be removed by chance. If the older element is removed, the newer element has, in essence, been conserved without using orthologous bases, providing a conserved function in the absence of constrained sequences. For example, a common HNF4A binding site in the human and mouse genomes may not reflect orthologous human and mouse bases, though the presence of an HNF4A site in that region was evolutionarily selected for in both lineages. Note that both the neutral turnover of elements and the 'functional peering' of elements has been suggested for cis-acting regulatory elements in Drosophila115, 116 and mammals110. Our data support these hypotheses, and we have generalized this idea over many different functional elements. The presence of conserved function encoded by conserved orthologous bases is a commonplace assumption in comparative genomics; our findings indicate that there could be a sizable set of functionally conserved but non-orthologous elements in the human genome, and that these seem unconstrained across mammals. Functional data akin to the ENCODE Project on other related species, such as mouse, would be critical to understanding the rate of such functionally conserved but non-orthologous elements.


      Conclusion:

      . . . At the outset of the ENCODE Project, many believed that the broad collection of experimental data would nicely dovetail with the detailed evolutionary information derived from comparing multiple mammalian sequences to provide a neat 'dictionary' of conserved genomic elements, each with a growing annotation about their biochemical function(s). In one sense, this was achieved; the majority of constrained bases in the ENCODE regions are now associated with at least some experimentally derived information about function. However, 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.


      So, you see, six years ago they were already using the "functional element" terminology, and already they suspected large portions of FE in non-coding sections of the genome. It's only after the headlines that annoyed evolutionary biologists that the scrutiny began. Or, should we say, the bludgeoning began?

      Delete
    16. Lino,

      Please pay close attention to what I said. You are doing nothing but keep showing that you have no idea what you're talking about. Had you paid attention you would not come back with more nonsense. As per your claim that you did not admit that Darwinism did not predict lots of junk DNA, here what you said:

      Yes, Darwinists didn't 'predict' Junk-DNA. That's because NS was supposed to keep DNA rather tightly conserved.

      You keep conflating evolution with Darwinism, and you keep mistaking the huge accumulation of neutral and semi-neutral changes for a complete lack of NS. The only way you will ever understand what I'm saying is if you do two things: pay much better attention to what I wrote, and get a much better education.

      See ya.

      Delete
    17. In other words, Lino, I doubt that what I write to you gets into your mind because you lack the most basic knowledge to be able to process what I say. Your lack of understanding cannot be explained any other way, but as being a problem with your foundational knowledge. Get an education, then we can talk.

      See ya.

      Delete
    18. Negative Entropy:

      It is you who don't understand what you propose. You simply propose it, and then wave your hands: "abra cadabra". And so it was. Why should I accept nonsense simply because you propose it, or supposed authorities "believe" something to be true (without being able to actually demonstrate that it is true).

      Did you notice that I said "Darwinists 'predicted'". I didn't say "neo-Darwinism predicted", nor did I say, "neo-Darwinism predicts".

      We're dealing with two completely different moments in time. When I said "predicted", this was in the 1960's. Science didn't yet know about the huge level of polymorphisms that would soon be discovered. Neo-Darwinism predicted that the only things of importance are kept in check by negative selection. Nor did they suspect that "genes", i.e., protein-coding sequences, were so small a proportion of the genome. Coupled together, the whole idea of "junk-DNA" didn't even enter the mind of a committed neo-Darwinists--the only species of evolutionary biologist that existed at the time.

      When the limited scope of positive and negative selection was discovered, Kimura proposed his Neutral Theory, and so greater thought and relevance was given to neutral drift and random genetic drift as evolutionary mechanisms. Ohta, a colleague of Kimura, then put forth the notion of "junk-DNA". This was back in 1972.

      Then, when the limited amount of DNA that actually "codes" for proteins was determined (around the turn of the century), and this then linked to the notion of NS keeping 'coding sequence' "conserved', led to the idea of the genome being full of "junk-DNA." All of this was then touted as "proof" that notions of 'design' like ID were patently wrong.

      But the IDists didn't budge from their convictions. So, when in 2013 the ENCODE project loudly declares that "junk-DNA" is a misnomer, and that "non-coding" DNA is both transcribed and functional, all hell breaks loose. Why? Well, it's obvious, isn't it.

      So, be as smug as you want; your conception of evolutionary theory is being proven insufficient while we speak.

      Get an education! Really. I have three degrees, two advanced, in completely unrelated fields. I'm currently studying in a fourth, unrelated field.

      Delete
    19. NE, I suggest you start your education over at Lino's fine blog, Darwin's Demise, where I'm sure all your misconceptions about evolutionary theory will be corrected, and what better teacher than one who has "three degrees, two advanced, in completely unrelated fields" and who is "currently studying in a fourth, unrelated field".

      Oh wait, there are no posts there.

      Delete
    20. Lino,

      Your little attempt at appearing knowledgeable only come to confirm, as if that was needed, that you don't know what you're talking about. Your logic and reading comprehension seem quite lacking too, because, so far, I have not proposed anything. I have just been attempting to clarify your misconceptions. Vain effort because I was not expecting such basic gaps in your knowledge and understanding of the science involved, nor was I expecting your gaps in logical thought. After all, you seemed to have a rather good grasp of English (curious that you can write, but you can't read).

      As per you trying to get away with your contradictions, you just did it again. You started with:

      Yes, Darwinists didn't 'predict' Junk-DNA

      Then you said:

      neo-Darwinism predicts lots of "junk-DNA" ...

      And now you say:

      Coupled together, the whole idea of "junk-DNA" didn't even enter the mind of a committed neo-Darwinists

      Seems like three degrees in completely unrelated fields, plus your "studying" towards a fourth one, have not improved your mind or your logic one bit. Maybe you need to actually do some work, and think carefully, instead of accumulating degrees.

      Delete
    21. Hey Steve,

      Yes! Three degrees in completely unrelated fields! One more coming soon! Let's go get some of those!

      Delete
    22. Larry:

      Thanks for the links. I found your first article on the first ENCODE results the most informative.

      At least you've been complaining since 2007. So my criticism certainly doesn't apply to you.

      From your first link on the definition of the gene post-ENCODE:

      The importance of the ENCODE project is that a significant fraction of the human genome has been analyzed in detail (1%) and that the group made some serious attempts to find out whether the transcripts really represent functional RNAs.

      My initial impression is that they have failed to demonstrate that the rare transcripts of junk DNA are anything other than artifacts or accidents. It's still an open question as far as I'm concerned. . . .

      The real problem here is that the ENCODE project predicts that alternative splicing is abundant and complex. They claim to have discovered many examples of splice variants that include exons from adjacent genes as shown in the figure from their paper. . . .

      If this represents the true picture of gene expression in the human genome, then it would require a radical rethinking of what we know about molecular biology and evolution. On the other hand, if it's mostly artifact then there's no revolution under way.


      You raise two issues. As to the first, Ewan Birney had this to say in a conversation with BBC:

      It’s interesting to reflect back on this. For me, the big important thing of ENCODE is that we found that a lot of the genome had some kind of biochemical activity. And we do describe that as “biochemical function”, but that word “function” in the phrase “biochemical function”is the thing which gets confusing. If we use the phrase “biochemical activity”, that’s precisely what we did, we find that the different parts of the genome, [??] 80% have some specific biochemical event we can attach to it. I was often asked whether that 80% goes to 100%, and that’s what I believe it will do.

      100% biochemical function/activity? Doesn't this demolish "junk-DNA"? Why continue to maintain these results are "artifacts"?

      Of course, I know we're right back where we started from. You can define it away by using a particular definition of "function", which is what Draur did. But that risks 'missing the forest for the trees.' Something important might be happening here.

      Delete
    23. Random DNA sequences possess "biochemical activity" of the sort that ENCODE assayed. Which means that mere "biochemical activity" is not evidence of function in any useful sense. You might want to redefine "function" so as to mean "the sort of thing that random sequences have", but wouldn't that mean that junk would have function by definition, even if it were evolving neutrally?

      Delete
    24. John,

      I doubt that Lino understands what you're saying. I guess that we will see what his three almost four degrees help him get from your comment.

      Delete
  12. The reality is that if you accept ENCODE's findings...

    ENCODE findings must be distinguished from ENCODE's overhyped press releases.

    ReplyDelete
    Replies
    1. Piotr:

      Is that like when it comes to Global Warming (I'm not going to let the hysterics conveniently change the terms) are we going to distinguish the actual findings from the "overhyped press releases"?

      Delete
    2. Yes Lino, by all means, let us distinguish the actual findings from the "overhyped press releases". The actual findings are that the Earth is getting warmer and that humans are responsible for much of that warming.

      Super-storms? Florida underwater in 20 years? Maybe not.

      But a much hotter planet caused by humans and the die-off of all coral reefs in a hundred years? Probably.

      Delete
    3. One problem is that scientists who strongly believe they are on to something really cool too often can't resist the urge to issue a press release and start giving interviews before their results are replicated and verified. Thus we get PR factoids like cold fusion in a test-tube, arsenic-based life, faster-than-light neutrinos, etc. Another problem is that journalists need sensational headings, no matter how stupid: DARWIN WAS WRONG (New Scientist); EINSTEIN'S LAWS QUESTIONED AS SPEED OF LIGHT IS BROKEN AGAIN (The Independent); JOURNEY TO THE GENETIC INTERIOR: WHAT WAS ONCE KNOWN AS JUNK DNA TURNS OUT TO HOLD HIDDEN TREASURES, SAYS COMPUTATIONAL BIOLOGIST EWAN BIRNEY (Scientific American).

      Delete
    4. Piotr:

      You gave a sagacious reply. I both appreciate it and concur---for the most part.

      (!) I think Darwin is wrong---very, very, very wrong about almost everything.
      (2) The faster-than-light stuff and the cold-fusion stuff were both head-scratchers. I couldn't see how they could possibly be right (although there are still unexplained phenomena associated with cold-fusion; but this could simply be that no one wants to take the time to track them down.)
      (3) The Arsenic-based life story struck me as a bit incredulous; and, upon doing a little searching around, was clearly bogus (as we've seen proven since.)
      (4) As to ENCODE: yes, maybe the PR was a bit overblown. However, to my mind, it's more likely that evolutionary biologists feel threatened by it and simply strike back harshly at the claims.

      Again, Druar uses a definition for "causal function" that traces itself back to an article by Cummins in 1975---Cummins who is also a philosopher of science.

      In the 2007 study, they distinguish between having a "function" and having a "functional role" in biochemistry. It seems to me that if you raise the bar on what 'function' consists high enough, then you'll end up with whatever percentage of function you think is right. But that is no longer science, but simply playing with words and numbers to arrive at a preconceived conclusion. IOW, it's scientists fooling themselves. That's why I asked about what criticism there was in 2007, when only 1% of the genome was explored, a low enough percentage to make the claims of Ewan Birney impossible at the time.

      To me this is the cardinal sin of Darwinism/evolutionary biology: it's almost completely ex post facto. And, hence, unfalsifiable.

      Delete
    5. Diogenes:

      But a much hotter planet caused by humans and the die-off of all coral reefs in a hundred years? Probably.

      Try your hand at this---no one, so far, has succeeded in providing an explanation:

      The "warming trend" that we are living through--a "warming trend," I might add, increasomg faster before1945 than after---started around 1835. What caused the "warming" in 1835 until the huge increase in man-made CO2 beginning in about the 1960's?

      For clarity's sake, please give an explanation for the "warming" between 1835 and 1910.

      Delete
    6. The "warming trend" that we are living through--a "warming trend," I might add, increasomg faster before1945 than after---started around 1835. What caused the "warming" in 1835 until the huge increase in man-made CO2 beginning in about the 1960's?

      Can you document that? I mean in particular the following claims:

      1. A clear warming trend starting around 1835 and distinguishable from earlier fluctuations.

      2. Temperatures increasing faster before 1945 than since.

      Delete
    7. Piotr:

      Just look at temperature charts that go back to the 1800's. You will see a flattening (very, very slight, but nonetheless there) right around 1945-1950 period. That's partly why they were predicting "global cooling" in the 1970's.

      I'll try to link: Here.

      You'll see the part of the graph where all the fluctuations in blue begin: this is where global alarmists choose to begin their "history" of global temperatures. You'll note that it results in a "hockey stick".

      So, now, what are your thoughts about the warming between 1830 and 1890?

      Delete
    8. What I see in temperature chats is: (1) insignificant fluctuations until ca. 1910; (2) a slight warming trend between 1910 and 1940; no warming, or even a slight drop between 1940 and the mid-1970s; a sharp rise since. There's absolutely no evidence EITHER of a significant rise in the 19th century OR the rise before 1945 having been faster than that of the last four decades.

      See here and here

      Delete
    9. Piotr:

      The temperature rose just as much from 1830 to 1890 as from 1945 to the present. So, does that make the current rise, as you say, "insignificant"?

      Using the 'red' curve on my chart, from 1913 to 1932, the temperature rose 0.4 degrees. From 1971 to 2004 (we're lower now), it rose 0.61 degrees. That's 0.021 degrees/yr for 1913 to 1932, and 0.0185 degrees/yr from 1971 to 2004. Numbers don't lie.

      I expected more from you.

      Delete
    10. What is the sourse of "your chart"? What research was it based on? It seems to me that, typically, you have no idea what you are showing as evidence. The legend, such as there is, calls the red line a "reconstruction/prediction". It surely does not represent real measurements (or it wouldn't extend into the future!). Why scrape up such crap from obscure corners of the Internet if reliable research articles, containing real data as opposed to someone's fantasies, are not hard to find?

      And no, 2012 was not cooler than 2004. It was 0.02 °C warmer (despite a drop from the record-breaking maximum of 2010), and it was 45 ± 0.10 °C above the 1961-1990 global average.

      I didn't expect anything better from you, though.

      Delete
    11. Self-correction: ... 0.45 ± 0.10 °C above the 1961-1990 global average.

      http://www.metoffice.gov.uk/news/releases/archive/2012/global-temperatures-2012

      Delete
  13. Off topic - but I sometimes get the feeling that Upright Biped is actually David Abel. I observed that after 'derwood' brought up Abel's scam of re-listing his publications over and over under different headings to make it look like he had a huge publication list to Upright Biped, that within a few days, Abel had altered his publication list so as not to be so embellished.

    http://theskepticalzone.com/wp/?p=212

    ReplyDelete
  14. Sorry for the side show - see Upright in action a bit over a year ago - same old arguments, same old condescension, same old dubious nonsense...

    http://www.politicalbullpen.com/philosophy-religion-34/materialist-forum-ignore-empirical-evidence-2143/

    ReplyDelete
  15. If he did clean up his publication list, it wasn't a particularly thorough job.

    http://davidlabel.blogspot.com/

    Some of the papers still appear as more than one avatars:

    "The First Gene: The Birth of Programming, Messaging and Formal Control"
    "The Universal Plausibility Metric (UPM) & Principle (UPP)"
    "The Genetic Selection (GS) Principle" (three times!)
    "The Capabilities of Chaos and Complexity"
    "Is Life Reducible to Complexity?"

    And since when do conference abstracts and Internet self-reviews like this one count as "peer-reviewed publications" (not that many of the others should qualify either).

    Pathetic, for such an upright biped.

    ReplyDelete
    Replies
    1. PS Alternative hypothesis: David L. Abel = Kairosfocus

      Delete
    2. You're kidding right? We know Kairosfocus is Gordon Mullings who lives in the Caribbean.

      They're both nuts, but nuts in different ways.

      Delete
    3. If any of us have not yet been banned at Uncommon Descent, someone please ask Upright Biped how he feels about a person (generic) citing himself and praising his own work anonymously.

      Because Upright Biped at UD often praises and cites the work of David L. Abel. If UB = Abel, he's complimenting himself.

      Don't say anything accusatory. We don't know for sure UB = Abel. But just ask how he feels, in general, about a person citing himself and praising himself while pretending not to be himself.

      Several creationists have pulled that trick, e.g. Jan Peczis = John Woodmorappe.

      Delete
    4. We know Kairosfocus is Gordon Mullings

      Thanks, I didn't know. They share some stylistic habits, for example they number their lists in a similar way. But it's the kind of thing you can easily borrow from a fellow sect member.

      Delete