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Why Kissing the Wall is the Worst Possible Heuristic for Biological Discovery

And would be the worst, whether one is an ID proponent or not.

Many UD readers know the Australian molecular biologist John Mattick as a leader in thinking about functional roles for so-called ‘junk DNA.’ Mattick has earned the implacable ire of ID critics such as Larry Moran and T. Ryan Gregory, although not because Mattick is an ID proponent. He’s not — see the opening sections of this interview, which is also available as a video. (Scroll to the Supplementary Material at the end; SIZE WARNING: 46M.]

It’s a fascinating exchange, although I think Mattick greatly underestimates the significance of clade- or taxon-specific novel proteins in eukaryotes.

If nothing else, however, empirical discovery itself stands entirely on Mattick’s side. In biology, the claim “structure x has no function” can only topple in one direction, namely, towards the discovery of functions. “No function” represents a brick wall of infinite extent, from which one can only fall backwards, into the waiting arms of a function one didn’t see, or overlooked.

Because one was kissing the wall, so to speak.

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21 Responses to Why Kissing the Wall is the Worst Possible Heuristic for Biological Discovery

  1. I’m curious what makes ID proponents assert that mainstream biologists don’t think about these issues.

    It is widely believed that the most evolutionarily conserved DNA sequences in the human genome have been preserved because of their functional importance and that their removal would thus have a devastating effect on the organism. To ascertain this we removed from the mouse genome four ultraconserved elements—sequences of 200 base pairs or longer that are 100% identical among human, mouse, and rat. To our surprise, we found that the mice lacking these elements are viable, fertile, and show no apparent abnormalities. This completely unexpected finding indicates that extreme levels of DNA sequence conservation are not necessarily indicative of an indispensable functional nature.

    Based on the compelling evidence that ultraconserved elements are conserved due to functional constraint, it has been proposed that their removal in vivo would lead to a significant phenotypic impact [7,8]. Accordingly, our results were unexpected. It is possible that our assays were not able to detect dramatic phenotypes that under a different setting, for instance, outside the controlled laboratory setting, would become evident. Moreover, possible phenotypes might become evident only on a longer timescale, such as longer generation time. It is also possible that subtler genetic manipulations of the ultraconserved elements might lead to an evident phenotype due to a gain-of-function-type mechanism.

    http://www.plosbiology.org/art.....io.0050234

  2. Who knows what goes through the minds of ID proponents, Petrushka.

    Perhaps they can, you know, read.

  3. Petrushka,

    Your example is an old one that everyone is aware of here, been commented on before if not Posted.

    Your comment ignores the post was aimed at Darwinist Zealots, not practical scientist.

    If anything, your point clarify’s Nelson’s post. That practical science about JUNK DNA is not limited by the Dogma of Moran, PZ Meyers and crew.

    There are hard core Darwinian zealots that for decades up until just the last few years argued for vestigial organs. They were critical of Design Theorist, insulting and in the end, wrong.

    Vestigial organs were all clearly labeled a FACT. As must as a FACT as macro evolution. Oh my how the Darwinian Dogmatist laughed hardily anytime someone questioned their “FACTS” of vestigial evolution.

    This is the problem with Darwinian Dogmatic Statist. Only they are allowed to control scientific discourse – or so – they think.

    Well, so to was Junk DNA thought to be vestigial. Design Theorist said, be careful, don’t jump so fast without more research.

    Oh my how the Zealots laughed, insulted and attacked those who dare question their evolutionary dogma. Their evolutionary predictions appear to be crumbling once again.

    Scientific studies are finding that there is indeed function where yet again, hard core zealots said there was none.

    From the quote you posted:

    “This completely unexpected finding indicates that extreme levels of DNA sequence conservation are not necessarily indicative of an indispensable functional nature.”

    Keyword = “indispensable”

    “Indispensable” does not automatically lead to a narrow interpretation of being afunctional sequences. The function(s) may as of yet been undiscovered, which goes back to the point of scientific discovery.

    Simply chopping and slicing is not enough.

    Ironically, what this study ultimately shows is scientist do not have a clue what they’re doing. That they are far away from engineering sciences and are blindly hacking. In fact, hacking is to much of a compliment in todays culture. Hacking implies that they know what they’re looking for and have a strategy to break the code. In this study, they’re like klumsy ATM thieves, hooking up a chain to an ATM to a pickup truck and yanking it out. The store survives, business is still open and customers still buy the products, they simply cannot get quick cash. At least the ATM theives know their is a function for the ATM. It is not “indispensable” to the stores business, but it still has a function.

    That evolutionist were “surprised” is the first indication yet another failed prediction by neo-Darwinian theory.

    That they used blind “evolution” as their blind guide to their blind predictions is the most important indication of a failed theory.

    However, people like Moran and PZ Meyers and their Darwinist dogmatic dogbot followers will continue to insult, sneer, attack those that rightly question their religion.

  4. In his remarks about C. elegans (the 1,000 cell worm) and the sponge ( the sponge seeming to have all the same protein components found in C. elegans, while C. elegans has roughly the SAME number of genes (coding DNA) as that of humans), seems to point rather strongly and clearly in the direction of what has been called “front-loading” here at UD for quite some time, having itself been borrowed from some of the first IDists.

    Likewise, Mattick is basically saying that those changes in the genome that bring about significant phenotypic alterations are now being found in the “non-coding” regions which he seems quite comfortable in characterizing as “functional”.

    Well, what do you know. When I was arguing with the Darwinists five years ago, this was exactly my position (as that of most IDists): that proteins were simply the ‘building blocks’, and that what was really important was the non-coding DNA where, surely, ‘routines’ and ‘subroutines’ were to be found (i.e., regulatory networks).

    What Mattick is really telling us is that the Darwinists, as they were surveying the architectural plans of life, concerned themselves only with the “materials list”, and not the DESIGNS themselves!!! And now they’re proven wrong. Oh, well. Just invent some new “just-so” story and move on.

  5. BTW, is the cultural reference the same as kissing the gunner’s daughter?

  6. In biology, the claim “structure x has no function” can only topple in one direction, namely, towards the discovery of functions. “No function” represents a brick wall of infinite extent, from which one can only fall backwards, into the waiting arms of a function one didn’t see, or overlooked.

    Let’s see if we can fix Paul’s statement:

    In biology, the claim “structure x cannot have arisen by natural mechanisms” can only topple in one direction, namely, towards the discovery of said mechanisms. “No natural mechanisms” represents a brick wall of infinite extent, from which one can only fall backwards, into the waiting arms of a mechanism one didn’t see, or overlooked.

    Yeah, that’s better.

  7. When I was arguing with the Darwinists five years ago, this was exactly my position (as that of most IDists): that proteins were simply the ‘building blocks’, and that what was really important was the non-coding DNA where, surely, ‘routines’ and ‘subroutines’ were to be found (i.e., regulatory networks).

    E3 Ub ligases are building blocks in what way?

    I recommend that you start studying the garbage disposal. It’s more important than any design proponent dare imagine.

  8. It must be some other culture than mine, for I’ve neve heard of either “kissing the wall” or “kissing the gunner’s daughter.”

  9. Perhaps Mr Nelson has invented a new (and useful) cultural reference or adage.

  10. Ilion:

    When boys on Royal Navy ships in the days of sail were to be chastised for serious offenses, they were draped and strapped over the breech end of a cannon, to receive the ordered strokes of the “cat” on the bare breech. Then, the “cat” — or often the junior version with only five tails not the full nine cords — was taken out of its red bag. (One of the contexts for “letting the cat out of the bag.”)

    GEM of TKI

  11. 11
    San Antonio Rose

    It would seem more a reference to the Wailing Wall and the act of kissing it. That would make sense w/r/t the need of Darwinists to genuflect to the theory of evolution and how it is a brick wall preventing real scientific discovery.

  12. SAR:

    I hear you, but the controlling issue seems to be what is likely to happen once the cat is out of the bag.

    Like, just about now, as increasingly “junk” ain’t junk no more.

    Of course another connexion is that proteins are the bricks.

    Bricks have to be correctly placed to build a wall, as an up close view is telling you; even as the less than happy prospect in that red bag being ceremoniously brought out concentrates your attention wonderfully.

    G

  13. 13
    San Antonio Rose

    I was only commenting on what Paul might have meant by kissing the wall, especially since he didn’t make any mentions of cats or bags. But thank for responding to a newbie like me.

  14. SAR:

    It is always good to have a new commenter at UD.

    I suspect PN is using a multiple allusion technique common enough in literature.

    “Kissing the Gunner’s Daughter” is of course euphemistic to the uninitiated, and the part about letting the cat out of the bag is not usually said explicitly.

    And proteins are molecular bricks, so the point is well taken that he focus on coding for proteins is looking at brick recipes while ignoring the wall plans to use them. All that stuff about inhibitor segments, addressing sub-strings [both snipped off at the right time] etc . . .

    What he does specifically mention is falling back from the wall into the waiting arms of a function. [Unwelcome arms in this case, for a Darwinist.]

    GEM of TKI

  15. My impression of what Paul was saying regarding “kissing the wall” was that he was using this image to express the extreme position that Darwinists have taken: viz., that there is NO function for non-coding DNA. The other ‘wall’, if this image is correct, would be that ALL non-coding DNA has function. You can’t “kiss” a wall from a distance; you have to be right next to it.

  16. Regarding “kissing the gunner’s daughter”, I have read that ship’s crew quarters were among the guns and sometimes there would be women on board and children born there. Hence “son of a gun”. Being bent over a cannon to be whipped then led to the expression “kissing the gunner’s daughter.” I believe this line was used in The Bounty.

  17. I recommend that you start studying the garbage disposal. It’s more important than any design proponent dare imagine.

    I don’t know about your garbage disposal, but mine’s designed. So yeah, maybe you have a point.

    But then again, so does Paul. If you step back from looking at some specific brick(s) in the cell, what do you find. Not just a bunch of functioning parts, but a functioning WHOLE.

    Garbage disposal, great. But who needs it?

  18. Let’s see if we can fix Paul’s statement:

    In biology, the claim “structure x cannot have arisen by natural mechanisms” can only topple in one direction, namely, towards the discovery of said mechanisms. “No natural mechanisms” represents a brick wall of infinite extent, from which one can only fall backwards, into the waiting arms of a mechanism one didn’t see, or overlooked.

    Yeah, that’s better.

    That’s not a fix to Paul’s statement. I’m not sure that it is, but it does seem to be aimed at, though poorly, the ID community.

    No ID’ist that I know would say, “structure x could not have arisen by natural mechanisms.”

    So just who are you talking about?

    I mean, just look at all the fantastic things which humans have created, just sitting there waiting for a non-intelligent-design explanation.

    Even Michael Behe, who you perhaps allude to, does not say structure x could not have arisen by natural mechanisms.

    What he said was, that certain structures could not have arisen by A PARTICULAR DARWNINIAN MECHANISM.

    Making your argument a classical straw-man.

  19. Hi Art,

    I don’t know if you’re still reading this thread, but your take on ID (in comment #6, above) misses the mark.

    Here’s why “no function” is an impassable wall, whereas the ID heuristic is not:

    1. No function. Why? Because what we’re looking at [structure x] was produced by primal chaos, and the null state for primal chaos is, well, more chaos.

    2. Function, very probably, even if we can’t see it at the moment. Why? Because what we’re looking at [structure x] was produced by primal intelligence, and the null state for primal intelligence is rationality, logic, systems within systems, subtlety, comprehensibility — in short, design, waiting to be discovered and elucidated.

    When Francis Crick thought as a de facto design theorist — e.g., in his deduction, in the mid-1950s, of the necessity for an “adaptor molecule” for information transfer between nucleic acid and protein [leading to the discovery of transfer RNA] — he did great science. By contrast, when he thought as a Darwinian or a primal chaos guy, as in his junk DNA publications of the early 1980s, he got it wrong.

  20. 1. No function. Why? Because what we’re looking at [structure x] was produced by primal chaos, and the null state for primal chaos is, well, more chaos.

    So, the null state for 6×10^23 molecules of H2 and 3×10^23 molecules of O2, after a spark, is chaos? As in uncountable combinations of H and O (H28 O238, HO7, H16O3, etc., etc.?) Paul, your statement appears to deny that chemistry exists. (You’re not alone – Sewell in another thread here does the same. I don’t know what ID proponents have against chemistry.)

    The fact is that chemistry is quite the antithesis of chaos, and to create a caricature of nature as a bunch of inert ping pong balls is to construct a poorly-conceived (silly, even) strawman.

    2. Function, very probably, even if we can’t see it at the moment. Why? Because what we’re looking at [structure x] was produced by primal intelligence, and the null state for primal intelligence is rationality, logic, systems within systems, subtlety, comprehensibility — in short, design, waiting to be discovered and elucidated.

    That’s a whole lot of unsupported assertions built into a tidy fallacy.

    BTW, just what is the function of garbage (such as the vast majority of the RNAs that Mattick was so excited about, and turn out to be very transient moieties whose sole destiny is the garbage disposal)?

  21. 21

    Arthur Hunt,

    That’s a whole lot of unsupported assertions built into a tidy fallacy.

    That’s a tidy assertion that doesn’t actually explain why it’s a fallacy.

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