RNA-binding proteins: modular design for efficient function

_{Mark

May 26, 2007

Intelligent Design}

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Many RNA-binding proteins have modular structures and are composed of multiple repeats of just a few basic domains that are arranged in various ways to satisfy their diverse functional requirements. Recent studies have investigated how different modules cooperate in regulating the RNA-binding specificity and the biological activity of these proteins. They have also investigated how multiple modules cooperate with enzymatic domains to regulate the catalytic activity of enzymes that act on RNA. These studies have shown how, for many RNA-binding proteins, multiple modules define the fundamental structural unit that is responsible for biological function.

Bradley M. Lunde, Claire Moore & Gabriele VaraniÃ‚Â

Nature Reviews Molecular Cell Biology 8, 479-490 (June 2007) | doi:10.1038/nrm2178

http://www.nature.com/nrm/journal/v8/n6/abs/nrm2178.html

This paper is yet another of the many examples of howÃ‚Â intelligently designed biological systems appear to be. We are continually told to keep in mind that they are only apparently designed. When will it become acceptable to attribute realÃ‚Â design where it is clearly seen?

Comments

magnan, "These attributes presumably can potentially be defined in terms of complex specified information. So in this sense human consciousness is not wholly Ã¢â‚¬Å“otherÃ¢â‚¬Â than CSI. It is the essense or core of consciousness that is Ã¢â‚¬Å“otherÃ¢â‚¬Â." Right. I think algorithmic modes and productions of *mind* may (and often are) quantifiable in terms of CSI. But what I had in mind was something like aurel tone, color, smell, emotion, etc. How might you describe, say, the conscious qualia of blue in CSI terms (or any mathematical or logical terms)? I would have to say it's not even in the same universe. :)mike1962_{May 29, 2007
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Gentlemen I think in part you need to revisit the cosmological argument, and to assess the issue of the infinite regress. (Cf my always linked . . .] In particular, look a the observation that what begins to exist has a cause, thence address cases of FSCI [functionality helps to clarify the specification issue], in life at cellular level, in the origin of the cosmos etc. You will see that his leads to the further implication that a cosmos that arguably is contingent -- JGy's "knobs" -- as observed requires a causal explanation itself, much less life as we observe it within that cosmos. Thereafter, the issue arises that a complex of contingent beings in a cosmos that is contingent cries out for a necessary being as its explanation -- the principle of sufficient reason is easier to dismiss than to address. In that context, a necessary, eternal being is at least as plausible as a quasi-infinite wider material cosmos as a whole which is unobserved. [At minimum, there are millions who testify to knowing such an infinite-personal, necessary being.] Then, discuss the alternatives under the issue of comparative difficulties -- some above are acting as though the difficulties they perceive in someone else's argument constitute reason to reject out of hand. (Down that road lurks the fallacy of selective hyperskepticism.] At the level you are now entering, ALL major options have serious difficulties, so one is wisest to assess relative status on factual adequacy, coherence and explanatory power. For, you are now in the realms of metaphysics. Have fun . . . GEM of TKI PS: A statement of the specification in a case of CSI may itself be CSI -- i.e. it exceeds 500 or so bits of binary information, reflecting over 10^150 possible states in the configuration space. That such a statement is a product of a mind is utterly unsurprising -- have you ever seen a design spec or description that wrote itself out of lucky noise? Or, the syntax of the required language, or any associated algorithms etc? So, let us observe that we are here marking the difference between an artifact of mind -- a specification that identifies a target for a complex entity, with that most familiar of all experiences we have, mind itself. The two do not even have the same properties, e.g. statements are not conscious entities! [In short the attempted infinite regress, fails. Nor is Dawkins' attempt to say God must be complex in the same sense as a cell made of component parts is, anything but a crude projection unto another worldview of concepts from his own, i.e he begs the question of what Mind is like.]kairosfocus_{May 29, 2007
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Mung:
Do specifications themselves contain CSI? What specifies the specification?
Great question - I think. This reminds me of another concept. Consider the "knobs" and parameters that the universe is tuned by... why not more or less knobs? What factor(s) would possibly determine those variables as real variables? This is one of the primary reasons why I think the anthropic fine tuning argument is more powerful than most people think. JGyJGuy_{May 28, 2007
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Atom, I simply choose not to converse with you. Because I choose not to converse with you, you may assume you win, if you like. Have a great day! Mung: specifications do not contain CSI. CSI is a property of phenomena or events, and is called CSI to differentiate it from information simpliciter. Specifications are simply agorithmically compressible patterns.jaredl_{May 28, 2007
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Do specifications themselves contain CSI? What specifies the specification? IOW, how is the specification of the specification independent of the specification?Mung_{May 28, 2007
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Also, your "axiom" is not true, even physically. There are programs which consist entirely of an initial state and transformation rules. (cf A new Kind Of Science by Stephen Wolfram) For example, I can create an "inputless" random number generator from a one-dimensional cellular automaton using rule 30. (rule 00011110). This automaton does not need any input, yet produces an arbitrary length of output. You may now object, "Well the initial state works as the input." In that case, then all you need is an initial state: the unitary agent conciousness is an initial state, a "thing" to begin with. Furthermore, the transformation rules can be the very act of agency by the agent. Again, there is no real difficulty present. Sorry.Atom_{May 28, 2007
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jaredl: "From this, I assume, as an axiom, what I call a Ã¢â‚¬Å“processorÃ¢â‚¬Â model of intelligence;..." This is the usual deterministic mechanical model of consciousness. How do you regard the wonderful examples of musical and literary creativity that I cited? I suppose you may regard such things rather coolly and cerebrally as the output of vastly complex algorithms embedded in the neural nets of the composer's and playwright's brains. jaredl: "...intelligence, like the processor of a computer, requires input in order to create output." Obviously some precursor input is needed, as I pointed out. Anyway, needed input may be very little. A computer program can produce output almost entirely from execution of simple or complex mathematical algorithms, which are themselves entirely a part of the software itself. An example would be an algorithmic digital random number generator. However, it requires a lot of faith in materialism to ascribe artistic, musical and literary creativity (among many other human qualities, products and experiences) to execution of internal algorithms and logic processing.magnan_{May 28, 2007
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mike1962: "It likewise makes no sense to speak of how much CSI an instance of human consciousness has. It seems to be wholy Ã¢â‚¬Å“other.Ã¢â‚¬Â" Attributes of conscious personality include past aquired skills, memories and ways of thinking and reacting. These attributes presumably can potentially be defined in terms of complex specified information. So in this sense human consciousness is not wholly "other" than CSI. It is the essense or core of consciousness that is "other". Mike1962: "Human consciousness is a screaming clue to me that something Ã¢â‚¬Å“otherÃ¢â‚¬Â than meterial reality exists (and I am it.) Amazing to me that some canÃ¢â‚¬â„¢t see this." I agree - it is incredible.magnan_{May 28, 2007
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Mung, "makes no sense to speak of Ã¢â‚¬Å“how much CSIÃ¢â‚¬Â God has." Indeed. It likewise makes no sense to speak of how much CSI an instance of human consciousness has. It seems to be wholy "other." Human consciousness is a screaming clue to me that something "other" than meterial reality exists (and I am it.) Amazing to me that some can't see this.mike1962_{May 27, 2007
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In plain english, nobodyÃ¢â‚¬â„¢s original; all patterns concocted by intelligences are cobbled together by integrating pieces of patterns observed elsewhere.
Perhaps not wholly original, but at least original in part (or else no new information could ever be produced, since all "information" would be redundant, and therefore not new information.); and once you admit that some new CSI can be generated ex nihilo, you've conceded my point. Furthermore... If there exist what are called Necessary Truths, then you have a set of objects to begin contemplating and combining to produce new CSI. So there'd be no problem. Take your new processor axiom for example. Either all of it's "parts" always existed (Necessary Truths) or they are "cobbled together" "pre-existing truths" (note, the "cobbling" demonstrates new choices being made, thus new bits of information being generated), or they came into existence from nothing (new agent created CSI.) In the first case, we already have our explanation of where that CSI came from: we have a set of Necessary truths (which do not need any further explanation, being Necessary) and an agent to process them (assuming intelligences exist). If the second case, we already have shown new bits of information being generated, which could be functional, and therefore "specified" by their function. Furthermore,we must ask: where did the pre-existing portions come from? The problem then repeats, one step back. (Which could lead to an infinite regress, if this is the only possible explanation. Lucky for us, it is not.) In the last case, you'd concede my point. Only the second case presents a difficulty, and so it is a false paradox. AtomAtom_{May 27, 2007
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Let me recap - all observed intelligences utilize observations of existing states of reality in order to combine elements of these observations into complex specified information. In plain english, nobody's original; all patterns concocted by intelligences are cobbled together by integrating pieces of patterns observed elsewhere. From this, I assume, as an axiom, what I call a "processor" model of intelligence; intelligence, like the processor of a computer, requires input in order to create output. So where could the patterns which the God of classical theism utilized to pattern this world after have come from? This question admits of no answer.jaredl_{May 27, 2007
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Perhaps I misunderstand this discussion, but it seems to me that it is obvious that all existing CSI cannot have totally originated from absolutely nothing. That would indeed be magic, but it seems a trivial point. What is important is that based on fundamental probability considerations the CSI in organisms must mostly have originated from intelligence (aside from the intelligence behind the origin of the universe itself and the physical laws). This intelligence must necessarily incorporate vast amounts of preexisting CSI. This intelligence must also have the capacity to create additional CSI. Examples of human music, art and literature surely demonstrate this creation of new CSI (much of which is "subjective" but nevertheless real) from a necessary background and initial condition of preexisting CSI. It seems to me that it is obvious that Mozart's piano sonatas and symphonies and Shakespeare's plays incorporate CSI that did not exist prior to their creation. The particular CSI of these works did not already exist somehow within their creators. What is an absolute necessity in this is a focused aware intelligence with "free will" that is not totally deterministic. In other words, not a "zombie". Such an "intelligence" could not really create anything. Small amounts of CSI can originate from RM&NS processes, but since these processes do not incorporate creative intelligence, this CSI must be in truth entirely preexisting, presumably in the complex specified information inherent in the mathematics of natural laws. An alternate interpretation would be that the RM and NS processes themselves were directly injected with CSI by the designing intelligence, whatever it is. Getting back to the intelligent agent(s) behind evolution, the CSI forming them must logically in itself have had an origin. It appears to me that human reason and logic can't really push any further in this analysis, except to speculate that this origin must be in areas only accessible if at all in religion and metaphysics.magnan_{May 27, 2007
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It is not a brush-off. It is a simple concept. For agents to have agency, they need to be capable of making choices. If these choices are strictly the result of deterministic interactions of background knowledge and external input, then agents are automata, nothing more than information processors. This is somewhat less than what we usually mean by "agent". Now, when an agent makes a choice, it is between at least two outcomes. This choice represents a new bit of information generated by the agent. These bits can result in CSI, depending on which choices are made. For example, I may make a series of choices that spells out, using ASCII coded letters, Shakespeare's plays; or I may simple randomly choose which bits to output, resulting in no CSI (the output would not match a specification.) But make no mistake, this ability to choose is essential to our definition of an agent, which is necessary for our definition of an intelligent agent. Without this ability, we are simply discussing a form of secondary, deterministic, machine intelligence, regardless of what the underlying implementation is.Atom_{May 27, 2007
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In other words, Great_Ape's point needs more than a brush-off; and, moreover, has no answer from within classical theism. That was the beauty of conversing with an intelligent classical theist, such as Dr. Welles; he did not insult my intelligence by the quick brush-off, saw the thrust of the question clearly, which I knew because he restated it, and simply declined to speculate on an answer. Would that more here were so honest. Great_ape, there need not be prior CSI, but there does need to be something, and you have hit upon another of what I consider to be the prima facie problems ID actually poses to the theology of most of its creators. We all understand this, at least intuitively - you don't get something from nothing, even information.jaredl_{May 27, 2007
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Here's the cite:
In this case the specification itself acts as a logical bridge between chance elimination and design inference. HereÃ¢â‚¬â„¢s the rationale: If we can spot an independently given pattern (i.e., specification) in some observed outcome and if possible outcomes matching that pattern are, taken jointly, highly improbable (in other words, the observed outcome exhibits specified complexity), then itÃ¢â‚¬â„¢s more plausible that some end-directed agent or process produced the outcome by purposefully conforming it to the pattern than that it simply by chance ended up conforming to the pattern. Accordingly, even though specified complexity establishes design by means of an eliminative argument, it is not fair to say that it establishes design by means of a purely eliminative argument. The independently given pattern, or specification, contributes positively to our understanding of the design inherent in things that exhibit specified complexity. Design by Elimination vs. Design by Comparison (Chapter 33 from The Design Revolution) By William A. Dembski
Dembski nowhere claims that the patterns can be originated ex nihilo, and indeed, as I mention above, to claim such is to make a counter-inductive claim. Now, counter-inductive claims are fine, I suppose, when you have a doctrinal allegiance to a proposition, say, creatio ex nihilo, of which I think this particular claim is a variant of. However, I fail to see the difference between claiming intelligences can create CSI ex nihilo and another idea Dembski pans, that of the origins of everything coming from set-theoretic operations on the empty set. Dembski there defending the idea that getting something for nothin is a claim to magic, and rightly derides it - but isn't that the whole idea of creatio ex nihilo, and information ex nihilo?jaredl_{May 27, 2007
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In other words, intelligence can create CSI ex nihilo. Actually, that's not clear from Dembski's work either, neither is it an inductive claim. Dembski stated somewhere (and, given enough time, I will track down this cite) that his argument's foundation is that an intelligence purposefully conforms an outcome to a specification utilizing background knowledge. What he leaves untouched is precisely what you wish to claim, Atom, and your claim doesn't hold true in our experience. I brought this up in a recent DI conference in DC with Dr. Welles, who saw my point and did not answer it. Intelligences, in our universal experience utilize background knowledge from which they construct specifications to which they conform events. The claim that CSI can be concocted ex nihilo is an extraordinary claim - meaning it is counter-inductive - and must be justified with reference to extraordinary evidence. I'm not holding my breath.jaredl_{May 27, 2007
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And, under the logic of the design inference, its very existence (now logically premised) warrants another such inference to a still higher level CSI. Unless, of course, you posit a metaphysical Ã¢â‚¬Å“first cause CSIÃ¢â‚¬Â that requires no further explanation.
Hey great_ape, The design inference doesn't say you need a "higher level of CSI source", only that intelligence is THE source of CSI. In other words, intelligence can create CSI ex nihilo. If you are left with only chance and necessity, it only shuffles CSI around; intelligence creates it. Thus, you'd need to examine the source intelligence to see if it is: 1) Complex, 2) Contingent and 3) Specified before you demand "What imparted that CSI to the designer(s)?"Atom_{May 27, 2007
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great_ape: Just to be sure for the record, I am not opposed to all metaphysical argumentation. I think there are useful logical arguments to be made that essentially disregard the physical realm. However, my argument only addresses the argument (that the designer requires a designer), beause it assumes that beyond our space time domain that "things" and/or "events" - and it's already a significant assumpton that even two concepts apply as valid - operate the same as we recognize in our domain of existence. So, that argument is actually an uninformed metaphysical argument. Also, as I undertand ID, ID does not assume upon itself any onus to identify a designer. Neither to identify the location or environment of any such designer. ID by itself relates whether a particular feaure of (or within) the universe is designed. However, other fields of study, theology or simply individuals posting to blogs on an individual basis, might utilize ID to idenitfy the source of the design. For example, I think the ultimate designer is the God of the Bible (eternal and not bound to space or matter). And if anti IDist argue that that ultimate Designer requires a designer, then they are actually treading into the metaphysical grounds, beyond our space+time domain, where ID in actuality can not thrust into - for lack of knowledge. Using ID, however, we can, I think, at the least make a reasonable guess that their is an ultimate designer to cause our universe outside of our space time domain, but that is the extent, as I see it, that ID can be utilized in "locating" or identifying the Designer. I think it's helpful to see that this is not an issue for ID, b/c ID does not elope into the realm of metaphysical. It can, I think, at the least, end at the beginning of the metaphysical.JGuy_{May 27, 2007
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ie. My post argued against using metaphysical arguments for OR against a requirement of designer (outside of our space-time domain) requiring a designer. --Jguy You are correct; my bad. I was overly eager to embark on a lecture discouraging metaphysical conjectures in arguments and, in doing so, neglected this last point of yours. I do not, however, think that this reluctance to address metaphysical questions fully protects ID from the "who designed the designer? issue," as I think, under ID, CSI always requires a source with equal or greater CSI. (Thus the motivation behind the original inference) So once the design inference is made (from organic life, for instance), a higher level CSI becomes an established premise. And, under the logic of the design inference, its very existence (now logically premised) warrants another such inference to a still higher level CSI. Unless, of course, you posit a metaphysical "first cause CSI" that requires no further explanation. Basically, you accept some higher level CSI as a metaphysical given. But if you're willing to take CSI as a metaphysical given at some upper level, then why not just accept it as a metaphysical given at the level of organic life as we know it? For it seems you are now rather arbitrarily choosing where CSI without an intelligent forbearer is intellectually tolerable and warrants no further inference of design... Anyhow, I realize this is all old territory rehashed, but I remain rather fond of the essence of the argument no matter how many times I hear it dismissed as childish.great_ape_{May 26, 2007
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jaredl:
Pardon me, but I donÃ¢â‚¬â„¢t think modern physics, qua physics, can, in fact, affirm an absolute beginning to matter and space.
No one on this site that I have seen seems to be making such an affirmation. Rather we are mentioning possibilities such as the multiverse and the big crunch conjectures. However Stephen Hawking, reguarded as the greatest mind of physics alive today, is of the mind that there is an absolutte beginning to matter, space and time. Obviously that position is a reasonable conclusion based upon the current understanding of physics.bFast_{May 26, 2007
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Multiverse is a metaphysical speculation as much as the existence a Designer outside our own space time. To have any explanatory power, multiverse theory must speculate about the existence of more other universes than there are fundamental particles in our own universe. ID, if the Designer is outside the univerese, requires only one eternal Designer. When we postulate something that is not subject to direct testing wholly from within space time, it is metaphysical proposition.idnet.com.au_{May 26, 2007
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Pardon me, but I don't think modern physics, qua physics, can, in fact, affirm an absolute beginning to matter and space.jaredl_{May 26, 2007
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great-ape: I don't think you applied my arguyment to your analogy thoroughly. ie. The analogy is not actually analogous. AS evidence, read the last sentence of my posting: "What does stand regarless is that from repeated observation that when the cause of CSI is found, it is always from an intelligent source - within our space time domain." To more correctly, respectfully, translate to your analogy..this would mean.. "What does stand regardless is that from repeated observations is that when the wife complains about the trash not being where it's suppose to be, the wife is always right - within our space time domain." ie. My post argued against using metaphysical arguments for OR against a requirement of designer (outside of our space-time domain) requiring a designer.JGuy_{May 26, 2007
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Patrick: You're correct - I believe. And actually, my actual intent was to comment about the idea that he was mocking... I didn't think he was serious :)JGuy_{May 26, 2007
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great_ape, lets begin with simple big bang cosmology. According to modern physics all of the mater and all of the energy in the universe, and even time as we understand it had a distinct beginning. I know that there are a bunch of wonderful conjectures floating around like multiverses and big crunches. These conjectures assume that there was some physical stuff that preceeded the big bang, that some sort of time preceeded the big bang. Even this view suggests that for some strange reason "stuff" always existed, and that time has an eternal past. However, Stephen Hawking has discussed his "north pole" analogy, which strongly suggests to me that he is radically unconvinced of either a multiverse or a big crunch model. So we are stuck with the need for a "first cause" or we are stuck with a scientifically unsupported conviction that "stuff" and time always existed. Alas, there has been a conjecture floating around since well before the big bang. It goes something like this, "In the beginning (time starts) God created the heavens (space) and the earth (matter). And the earth was without form and void (a singularity)." I concede that scientifically this is only conjecture, but it is every bit as valid as a conjecture as the other three currently recognized options: multiverse, big crunch or "north pole" are. This conjecture suggests that the designer invented time itself. As such the designer must not be a "time" thing. In the current state of physics, we are limited to conjecture. Lets not diss the conjecture that has been the most effectively predictive.bFast_{May 26, 2007
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However, this only is seen true in the space+time state that WE understand (not the eternal). --JGuy Unfortunately, the invocation of the eternal-unfathomable metaphysical perspective--however real such a perspective might be--lends itself to almost any conclusion whatsoever in an argument. Imagine, for example, that my wife complains about my not having taken out the trash. Well, I say, that is only true of the world as we understand it. Stepping outside of space-time, the trash is precisely where it needs to be. So, dear, you need to consider our limitations as human beings. I don't think it would work for me. But if anyone has any success with this approach, please let me know.great_ape_{May 26, 2007
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I think he's mocking that common Darwinist argument...Patrick_{May 26, 2007
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The whole premise of the idea that the designer needs a designer is based on the IDist paradigm [not false] of specified complexity itself. That is, the evolutionists try to use CSI as an indicator of intelligent cause to disprove intelligence as the cause of CSI. However, this only is seen true in the space+time state that WE understand (not the eternal). Suppose that there is an ultimate designer (I believe it is the God of the Bible), then why is it neccessary to say that this ultimate designer needs a designer (ie. using our limited knowledge which is based on the paradigm of what we observe in the universe alone)? I suggest, if the anti IDist were to adhere to the idea that a designer needs a designer.. then I think it is neccessary to use the same reasoning to say that if things arrived from chaos, then there needs to be even more chaos in the past (ad infinitum)... but more chaos would require more stuff to be chaotic. From whence does such stuff derive? So, it seems, the argumentation refutes itself by virtue of the fact it can defeat both sides of the argumentation. What does stand regarless is that from repeated observation that when the cause of CSI is found, it is always from an intelligent source - within our space time domain.JGuy_{May 26, 2007
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Come on! We know that if life is very complex this means that the designer is much more complex and thus doesn't exist :DIDist_{May 26, 2007
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