Home » Intelligent Design » ID Foundations, Irreducible Complexity, Origin Of Life, Tree of life » Andre asks an excellent question regarding DNA as a part of an in-cell irreducibly complex communication system

Andre asks an excellent question regarding DNA as a part of an in-cell irreducibly complex communication system

Newbie commenter Andre, in an exchange with Mr Matzke, asks some interesting questions concerning DNA.

First, let us remind ourselves of what we are discussing, courtesy NIH:

Fig I.0: DNA as a stored code exhibiting functionally specific complex digital information (HT: NIH)

Fig I.0: DNA as a stored code exhibiting functionally specific complex digital information (HT: NIH)

Next, Andre’s comment:

DNA has the following;

1. Functional Information
2. Encoder
3. Error correction
[4]. Decoder

. . . can you please show me in a step by step fashion how such a system could randomly without any intelligence, and totally unguided build itself?

Where did the functional information come from? What was first the encoder? The decoder? Error correction? Functional information?

This is an irreducibly complex system any part removed and the system fails to function. Can you prove otherwise . . . ?

It would be interesting to see the answer to this and other similar OOL-oriented questions.

(OOL is now squarely on the table as a pivotal issue in origins science. The matter here is very simple. First, as we are at origins of life, the favourite resort, to the astonishing claimed powers of “natural selection” is off the table. Why? Because there is no code based genetic reproduction to have differential reproductive success that rewards superior genetic varieties.  Second, this is the root of the Darwinist tree of life, and no roots, no trunk, no shoots and no branches. That is, the whole  iconic analogy of macroevolutionary development of the body plans of life to a growing tree is on the table.)

Let us remind ourselves of the claimed tree architecture, paying particular attention to the root:

The Smithsonian's tree of life model, note the root in OOL

The Smithsonian’s tree of life model, note the root in OOL

Because the issue Andre raises puts irreducible complexity squarely on the table, it is worth first showing the irreducibly complex logical structure of a communication system:

comms_system

The general structure of a communication system; irreducible complexity emerges as each main component is necessary for function, and the parts must be properly arranged, interfaced and coupled together. If any part is removed, function fails.

Let me add the example Andre gives, the Glolab RF IC ED4GP encoder/decoder, in encoder mode, tied to a transmitting antenna of a specified length (1/4 wave resonant, I assume with end correction optimised):

Andre_Radio_TX

A Radio transmitter (Andre’s example from comment no 1)

Now, the matching decoder IC set up (and notice, this chip has BOTH functions, so it’s “just exaptation” . . . yeah, and you better have a big parts bin to replace the ones you let the smoke out of!):

ED4GPdecoder

The decoder half, with the same ED4GP in receive mode.

(The onlooker might want to have some fun identifying the blocks in the general diagram and how they correspond to the actual chip ckt. Then ask yourselves if the ICs were designed by monkeys banging away at keyboards with an electronic cad/cam system running!!!!)

Then also, to point out the relevance of Menuge’s criteria C1 – 5 on the favourite dismissive tactic, exaptation of pre-existing entities to serve a new jury rigged by chance structure and purpose, let us clip:

For a working [bacterial] flagellum [--> as a concrete example] to be built by exaptation, the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

Let us see how well suggested answers address the concerns about irreducible complexity, the root of the tree of life and the issues in C1 – 5. While doing so, let us always bear in mind the need for observational warrant for claimed explanations.

That will tell us a lot about the true balance on the merits. END

_________

PS: Today marks seven months that the UD ~ 6,000 word (feature article length) Pro-Darwinism essay challenge has gone unanswered. The first, pivotal aspect of that challenge is to provide an observationally warranted, blind watchmaker account, in summary, for OOL. It is explicitly pointed out that this is the root of the tree of life and so must rightly be answered, if the evolutionary materialist picture is to be regarded as reasonable or credible. Dismissals and distractors aplenty but no direct take-up on a decisive free shot at goal.

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20 Responses to Andre asks an excellent question regarding DNA as a part of an in-cell irreducibly complex communication system

  1. KF Thank you!

    I need to add that the question itself is simple, but taking a look at an actual encoding and decoding flow chart highlights the issue much better. This is a simple radio encoder, decoder flow chart.

    http://www.glolab.com/encdec/images/ED4GPenc.jpg

    Can such a system even work during a supposed step by step type process (I’m building the radio a piece at a time here)? My knowledge and experience on these types of systems tells me that it is not possible at all.

    If this system can not work at all based on what I do know then it is with very good reason that any other Encoder – decoder type system biological or not will also not be functional unless all its parts are in place.

    Lastly we know that DNA is an encoder – decoder type system.

  2. The answer is “It just happened, it just happened to work and it was kept. And once it was on the scene then it could be evolved.”

  3. Andre,

    I add your IC RF encoder/decoder to the OP, as a good illustration of what is needed. (H’mm, let me also add the decoder ckt.)

    I shudder to think about a designer who would try to get that to work by letting parts just happen to get hooked up by accident — imagine a breadboard with wiring by accident!

    KF

  4. The good news is you don’t have to shudder about the thought, it is logically impossible for any encoder – decoder system to build itself even if the designer put all the parts neatly next to each other they still can not assemble themselves.

  5. Andre

    Just add a tornado in the electronic parts junkyard!

    Hey, presto!!!!!

    (See the search space challenge issue, TSZ objectors et al?)

    So now, put in the capacity to self assemble and self replicate. Does that increase or decrease the likelihood that we should infer design as best cause?

    Here — as clipped in IOSE for discussion to frame the OOL issue — is Paley on that topic in the Ch II of his Nat Theol that I don’t usually see addressed when folks are ever so quick to dismiss the watch example from Ch I as irrelevant to self-replicating or reproducing systems:
    ____________

    >> Suppose, in the next place, that the person who found the watch should after some time discover that, in addition to all the properties which he had hitherto observed in it, it possessed the unexpected property of producing in the course of its movement another watch like itself — the thing is conceivable; that it contained within it a mechanism, a system of parts — a mold, for instance, or a complex adjustment of lathes, baffles, and other tools — evidently and separately calculated for this purpose . . . .

    The first effect would be to increase his admiration of the contrivance, and his conviction of the consummate skill of the contriver. Whether he regarded the object of the contrivance, the distinct apparatus, the intricate, yet in many parts intelligible mechanism by which it was carried on, he would perceive in this new observation nothing but an additional reason for doing what he had already done — for referring the construction of the watch to design and to supreme art . . . . He would reflect, that though the watch before him were, in some sense, the maker of the watch, which, was fabricated in the course of its movements, yet it was in a very different sense from that in which a carpenter, for instance, is the maker of a chair — the author of its contrivance, the cause of the relation of its parts to their use. >>
    ____________

    Design inferences, anyone?

    Off to a specialist surgeons’ clinic.

    KF

  6. I recommend all materialists insert fingers into their ears, shut their eyes tight and chant the following: Deep Time. Blind Chance. Lots of chemicals bumping around in their underpants. This begets that, over time it collects, an irreducibly complex system it erects. Praise Darwin.

  7. Don’t raise your hopes too much, folks. Remember, these people are so irrational that they’ve been happily making their living from quantum mechanics for the better part of a century, confident that… ‘One day.. my son…’; even though it is founded in paradoxes and praeternatural, literally imponderable mysteries, which can and do only deepen and proliferate.

    Their irrationality needs to be explicitly reiterated, in the same way they have had the brass neck to invoke Reason, constantly, as the ‘special charism’ of their Covenant of the Double Helix; not unlike the nun in the clerical joke, who claimed ‘humility’ was the special charism of her Order.

  8. OT: Mr. Matzke, the box you refuse to come out of is shrinking again!

    Dover Revisited: With Beta-Globin Pseudogene Now Found to Be Functional, an Icon of the “Junk DNA” Argument Bites the Dust
    http://www.evolutionnews.org/2.....71421.html

  9. BA

    I read that article, what now for Ken Miller and co?

  10. H’mm:

    we know that the beta-globin pseudogene doesn’t create a complete RNA transcript for a beta-globin protein. But that doesn’t mean it can’t play roles in gene expression. That’s exactly what the investigators think this protein does, and thus they write: “the strong functional constraints underlying the decreased contemporary diversity at these two regions were not driven by protein function but instead are likely due to a regulatory role in ontogenic switches of gene expression.”

    Interestingly, they found that regions adjoining the genes exhibit high levels of variation, suggesting that the pseudogene is under “purifying selection” — i.e., it performs a function and thus natural selection selects against mutations that would change the sequence of the pseudogene:

    Taken together, the results obtained for the ?-globin cluster cannot be reconciled with other explanatory hypotheses rather than purifying selection: the low values of nucleotide diversity are confined to HBD and HBBP1 and do not extend into the flanking regions which display contrastingly high levels of variation; the haplotype structure of HBD and HBBP1 are similar across worldwide populations

    So what is the function? They write: “These recent findings suggest that HBD and HBBP1 might be involved in chromatin looping in the human ?-globin cluster, a crucial mechanism for temporal coordination of gene expression.” Specifically, they think HBD and HBBP1 play a crucial role in regulating gene expression during development: “we propose that the complex patterns of diversity observed in this genomic region arose from distinct functional constraints related with the intricate process of chromatin and protein interactions coordinating the differential expression of genes at the ?-globin cluster during development.”

    And this was “Junk dna” Exhibit A at Dover.

    Oopsie.

    KF

  11. Chirp, chirp, chirp . . .

  12. Wait a minute. Re: the beta-globin psuedogene news at ENV, Ken Miller says

    There’s no escaping the implication of these matching mistakes, and there’s no point in arguing that six identical mistakes could have turned up independently in three unrelated species.

    Isn’t that what convergent evolution says can happen? So which is it?

  13. Very good Rex!

    Lol!

  14. Mr Matzke

    Anything? Do you have the evidence or data on how this irreducible complex system evolved step by step?

    Matter (which is what you are) has had 13.8 billion years to answer the question? I give it you would love to plead for another 13.8 billion years before you’ll know?

    Given enough time anything can happen right? Even the step by step assembly of an unguided unintelligent process can accomplish specified complexity hey Mr Matzke? All it needs is time right?

  15. WJ Murray:

    Deep Time. Blind Chance. Lots of chemicals bumping around in their underpants. This begets that, over time it collects, an irreducibly complex system it erects. Praise Darwin.

    Is this the level of discourse to which Uncommon Descent has descended?

  16. Andre writes in #14:

    Mr Matzke

    Anything? Do you have the evidence or data on how this irreducible complex system evolved step by step?

    Interesting to phrase the question this way to Nick M. In October 2006, Matzke along with Mark Pallen of the Univ. of Birmingham, had an article published in Nature entitled From The Origin of Species to the origin of bacterial flagella. (Nature Reviews Microbiology 4, 784-790 (October 2006)) The article was a review article rather than a research study attempting to refute Dr. Michael Behe’s claim of irreducible complexity with respect to this particular biological system. Behe originally made the claim in his groundbreaking book Darwin’s Black Box published in 1996, some 10 years prior to this article.

    One of the main claims that Behe made, and the one that really roiled the waters in the Darwinian camp was that there was not a single peer reviewed research study in any relevant scientific journal providing any sort of step-by-Darwian-step explanation for how Darwinian evolution accounted for the bacterial flagellum. Many Darwinists, including Matzke (as well as Ken Miller and others) wrote books and articles and made posts on the internet not only saying that Behe was dead wrong, but also providing lists of supposed studies that…oopsies…Behe somehow missed. Of course, it was rightly pointed out that all this was little more than literature bluffing, as none of the studies in these lists provided the explanation to which Behe was referring.

    So now, 10 years later in 2006 Matzke and Pallen come along with this review article. The interesting thing about this article is that, despite all the hand waving claims about all these dozens if not hundreds of peer reviewed research studies showing how evolution built a flagellum, Matzke and Pallen didn’t have a single such reference in their bibliography. Nor did they reference any such study in the article. Rather, the article went into great lengths to explain how a researcher might go about conducting a study to show how evolution could have produced the system. Well, if all those articles and studies were already there, why not just point them all out? In shorty, the entire article was a tacit admission that Behe had been right all along.

    Fast forward to now and Andre’s question directed to Matzke. We’re now some 17 years after Behe’s book came out where he made that famous claim. And, no surprise, there still is not a single peer reviewed research study that provides the Darwinian explanation for a bacterial flagellum (or any of the other irreducibly complex biological systems Behe mentioned in the book). We’re almost 7 years after the Matzke & Pallen article. So where are all these research studies? There’s been ample time for someone to do something in this regard.

    Matzke will not answer the question because there is no answer he can give…no peer reviewed research study he can reference, other than the usual literature bluffing he’s done in the past. But Nick, along with all his fellow Darwinists know in their bones that such an explanation will be forthcoming…someday…some decade…some century…some millenium.

  17. WJ Murray:

    Deep Time. Blind Chance. Lots of chemicals bumping around in their underpants. This begets that, over time it collects, an irreducibly complex system it erects. Praise Darwin.

    ———————

    ‘Is this the level of discourse to which Uncommon Descent has descended?’

    Indeed, Daniel, it is Uncommon Descent’s humiliating misfortune to have been set up precisely in order to descend to the level necessary to refute the unbelievably foolish notions of Darwinists; notions which are routinely, and more and more comprehensively, rebutted by current science – although only since what is inescapably obvious to 95% or more of mankind, eludes those ‘minds like steel traps’ of the Darwinists.

  18. DonaldM:

    Fast forward to now and Andre’s question directed to Matzke. We’re now some 17 years after Behe’s book came out where he made that famous claim. And, no surprise, there still is not a single peer reviewed research study that provides the Darwinian explanation for a bacterial flagellum (or any of the other irreducibly complex biological systems Behe mentioned in the book). We’re almost 7 years after the Matzke & Pallen article. So where are all these research studies? There’s been ample time for someone to do something in this regard.

    Doesn’t that depend on how much level of detail you’re asking for? You are right in the sense that there are no peer reviewed papers detailing a mutation-by-mutation evolutionary pathway for the origin of the bacterial flagellum. But there have been papers in the primary literature that have outlined some steps (e.g., in 1987 Cavalier-Smith published a paper that listed a few steps, and in 1989 there was a paper on the eukaryotic flagellum). Note that I do not think the bacterial flagellum evolved, but I’m just curious on how much level of detail you’re asking for.

  19. Genomicus,

    If someone is claiming that changes to a genome can produce, say, a bacterial flagellum in a population that never had one, don’t you think that they should demonstrate such a thing is possible?

    Don’t blame us because you (speaking to evolutionists) made a claim that is apparently untestable.

    Otherwise call it an idea or working hypothesis, but not a theory and definitely not settled science.

  20. If someone is claiming that changes to a genome can produce, say, a bacterial flagellum in a population that never had one, don’t you think that they should demonstrate such a thing is possible?

    Yes.

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