Two Lego block piles — what’s the difference, why?

_{kairosfocus

October 21, 2014

Design inference, ID Foundations, specified complexity}

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Lego Pile A:

Lego “Pile” B:

What’s the difference, and why is it there?

What does this tell us about functionally specific, complex organisation and associated information (FSCO/I), why?

So, bearing in mind this needle in haystack search challenge:

. . . also, the design inference process flowchart:

. . . and the use of coded paper tapes in older computers and Numerically Controlled machines:

Punched paper Tape, as used in older computers and numerically controlled machine tools (Courtesy Wiki & Siemens)

. . . what can and should we infer concerning the FSCO/I involved in the protein synthesis process (including the coded mRNA tape)?

What, then, does this tell us about the causal factors credibly involved in the origin of cell based life crucially dependent on protein synthesis for it to carry out its functions? Why? END

PS: As a supplement (post meeting), I would like us to reflect on the configuration of two dirt piles,

CASE C: About six miles south of where I type:

Soufriere Hills Volcano dome, Montserrat, at night

CASE D: On some beach or other:

Let’s pose the first two questions again:

What’s the difference, and why is it there?

What does this tell us about functionally specific, complex organisation and associated information (FSCO/I), why?

Comments

"We are I think now talking about “specification”?" Yes. And that is not something that is amenable to numerical calculation. It is a recognition of function or purpose or intentionality. So the demand that CSI must be calculated is a category mistake. Kind of like demanding: "Which is more blue? The number 7 or the number 9?"Eric Anderson_{November 6, 2014
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No worries Eric ;) We are I think now talking about "specification"?rich_{October 24, 2014
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rich @73: Fair enough -- LOL at myself! I shouldn't have referenced "more" with a percentage. Sometimes we comment too quickly. :) A has no FSCO/I. B does. That's the difference. Now that we're past the nitpick, do you want to address the substance of my comment?Eric Anderson_{October 24, 2014
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MrCollins at #54: You say: "So, I understand that it does resemble a castle and that we’re comparing it to something that we do know. I guess what I’m trying to understand is that the purpose of all of this is to decide on the ability of something to be different in such a way that it must not be natural. It makes sense in my head that in order to help prove ID of some type you have to show that something is not naturally occuring." Indeed, the concept of "natural" has nothing to do with the reasoning here. I will try to be more clear. Let's go back to the beach. We have a sand structure, Let's say that it is not a castle, but a sand "sculpture" resembling a mountain which can be seen in the far distance. Let's say that the sculpture is detailed enough, so that it really represents the form of the mountain with a high degree of precision, so that we can assume that its specified complexity as "a configuration of sand which resembles the form of that mountain" is high enough to reject the explanation that the sand assumed that configuration by random events (like the wind or other forces acting in the system). Now, to detect design, we need two conditions satisfied: a) We reject a random explanation, as said, because the configuration is part of a specified set which is too small to be attainable by random variation. b) We know if no credible necessity mechanism which can generate the configuration we observe. In this case, we can safely conclude that no credible mechanism can make the sand assume the form of the mountain. So, we reject a random explanation, and we have no necessity explanation. But we have a good alternative explanation: design. Indeed, there is only one way that the sand could assume that configuration: if some conscious intelligent agent was there, looked at the mountain in the distance, and intentionally worked on the sand to give it the form of the mountain. That's what intelligent agents do all the time: it's called drawing, or sculpting, or modeling. It's intelligent design. So, we infer design. As you can see, the concept of "natural" has no role in the reasoning. The problem is that we have to offer some credible explanation for what we observe. The mountain is a perfectly natural object. But a reproduction of the mountain, a detailed reproduction, made of sand, and without any direct necessity connection to the mountain itself, can be explained only by design. Because only design generates that kind of configurations of matter: configuration which are at the same time specified and complex.gpuccio_{October 23, 2014
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PPS: Let's observe the abstract:
Because of the molecular complexity of the ribosome and protein synthesis, it is a challenge to imagine how translation could have evolved from a primitive RNA World. [--> which world is already strictly speculative and chemically grossly implausible] Two specific suggestions are made here to help to address this, involving separate evolution of the peptidyl transferase and decoding functions. First, it is proposed that translation originally arose not to synthesize functional proteins, but to provide simple (perhaps random) peptides that bound to RNA, increasing its available structure space, and therefore its functional capabilities. Second, it is proposed that the decoding site of the ribosome evolved from a mechanism for duplication of RNA. This process involved homodimeric "duplicator RNAs," resembling the anticodon arms of tRNAs, which directed ligation of trinucleotides in response to an RNA template.
In short, long on speculation concerning the remote past, rather short on demonstrating the feasibiloity of the RNA world in realistic environments. Then, on that shaky foundation, an inverted pyramid of involved speculations with scant empirical warrant on the proposed -- note that word! -- evolutionary path. Here is Shapiro's rebuke in Sci Am to all such RNA World speculations:
RNA's building blocks, nucleotides contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern . . . . [[S]ome writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case. A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . . To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . .
Orgel, had put his own rebuke to metabolism first speculations:
If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . . It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield . . . . Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [[for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [[8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [[6]? . . . Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . . The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.
Mutual ruin in short. Neither is good enough, absent the sort of ideological a prioris that led to refusal to see the obvious in the OP, and is now well off base on speculative tangents. KFkairosfocus_{October 23, 2014
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PS: You may also find is wise to ponder here, DDD #16, on the tactic of willfully distorting the design inference -- often as part of a process of red herrings led away to strawmen soaked in ad hominems and set alight to cloud, confuse, poison and polarise the atmosphere of discussion.kairosfocus_{October 23, 2014
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Rich: "Hardly conclusive (more like conjecture!) but at least something amenable to further exploration?" Except when you quoted the Abstract, you deliberately left out the first sentence which was extremely important. Why ? "Because of the molecular complexity of the ribosome and protein synthesis, it is a challenge to imagine how translation could have evolved from a primitive RNA World." No problem, I believe I understand the why now. Besides, RNA World works only in cartoons published on YouTube anyways. Often times quote mining can become so creative.DavidD_{October 23, 2014
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Rich, 60:
On FSCO/I. You keep bringing it up but not actually doing any math.
False. Joe is correct that the Math was done. Not just general Math on specified complexity, but on the underlying statistical thermodynamics [since 1984 on by Thaxton et al], as well as -- in response to the P May Sockpuppet Mathgrrl [who on the amnesty can pop back up . . . ] -- three years ago. Not to mention the work by Durston et al using the Shannon H metric. I suggest, you read the summary here in context before making such an assertion without merit again. (And BTW, kindly cf the linked briefing note throuhgh my handle, which starts all the way back at info theory 101.) KFkairosfocus_{October 23, 2014
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rich: "Personally I don’t know. Was that article I linked to any help?" No. By the way, you have answered everybody except me! (post #45). I feel neglected. :)gpuccio_{October 23, 2014
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rich:
Hardly conclusive (more like conjecture!) but at least something amenable to further exploration?
Maybe- we shall see. My bet is further exploration will show the conjecture to be pure fantasy based on a world-view.Joe_{October 23, 2014
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rich:
I found this, not my area of expertise though: http://www.ncbi.nlm.nih.gov/pubmed/20610545 Thanks all.
Speculation based on a world-view is not science, rich. And that article is pure speculation- untestable, untested and purely based on a world-view. But you, having no science background, wouldn't understand that.Joe_{October 23, 2014
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rich:
1) On FSCO/I. You keep bringing it up but not actually doing any math. An uncharitable interpretation would be you want the trappings of a mathematical analysis but can’t do one. So just stop.Say “It seems improbable to me” because that’s the actual argument you’re making.
LoL! The math has been done. And wrt biology is has been done in peer-review. As for probabilities it is up to YOUR position to supply them as your position is the one that relies on chance. BTW humans are intelligent agencies.Joe_{October 23, 2014
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Yes, as I said I am familiar with the content of the paper, and its introduction. On the whole, the paper is an affinity piece. Of course, there is nothing particularly wrong with that; it goes are far as it can go, but the factual resources simply don't exist to close the loop. Instead, it takes a very informative tour through the individual mechanics of genetic translation, rather like a computer scientist explaining PNP objects. Unfortunately, the fundamental aspects of a translation system, including the organization of translation, are left to the wayside.Upright BiPed_{October 22, 2014
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Whoops, UP > UB. Sorry.rich_{October 22, 2014
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Hey UP! From the intro: "Two specific suggestions are made here to help to address this, involving separate evolution of the peptidyl transferase and decoding functions. First, it is proposed that translation originally arose not to synthesize functional proteins, but to provide simple (perhaps random) peptides that bound to RNA, increasing its available structure space, and therefore its functional capabilities. Second, it is proposed that the decoding site of the ribosome evolved from a mechanism for duplication of RNA. This process involved homodimeric "duplicator RNAs," resembling the anticodon arms of tRNAs, which directed ligation of trinucleotides in response to an RNA template." Hardly conclusive (more like conjecture!) but at least something amenable to further exploration?rich_{October 22, 2014
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Hello rich, I'm sorry, I did not see that you cited the Noller paper (it wasn't addressed to me). I'm fairly familiar with the paper, in fact it's one of my favorites because it thoroughly lays out ribosomal activity and is so well written - perfect for a non-specialist like myself to study in detail over time. Unfortunately, it doesn't give an explanation for the rise of translation, other than to simply acknowledge that it happened (which is not particularly useful).Upright BiPed_{October 22, 2014
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Personally I don't know. Was that article I linked to any help?rich_{October 22, 2014
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Rich, you might have missed my question at 31. I'm genuinely interested. "Rich, will you please explain how RNA and recursion achieve translation. Thanks."Upright BiPed_{October 22, 2014
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Barry, as I look at a nice cup of coffee, I think "Hmmmm... that's a nice cup of coffee". Sophisticated theologians(c) will have to hep me with the religious bit ;) I've not accusing you all of being religiously motivated... just trying to start some science here. Which I think would be best for ID?rich_{October 22, 2014
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100% more (or "double", for the layman like me) than "doesn't have any" (Zero), is zero. This is why I think you guys should get into math a bit more.rich_{October 22, 2014
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rich:
But it seems you are so wed to your religious lens you must look at all things through it.
Do you seriously believe you don't look at all things through your own religious lens? Astounding, because in this very thread you've demonstrated that your metaphysical commitments make you almost literally blind to certain propositions of simple logic. Barry Arrington_{October 22, 2014
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rich @2: Your question betrays a misunderstanding of how the design inference works. In the example pictures provided in the OP, the question is not about an amount of complexity. The complexity threshold is only relevant to ascertaining whether the functional specification is likely the result of chance. It is certainly possible for a non-designed object to have more "complexity" in the sense of simple calculations a la Shannon than a designed object. That is not the issue. Thus, in answer to your question @2: the answer is that B has 100% more FSCO/I than A, because A doesn't have any. Whether B has more sheer "complexity" than A is another matter, but is not the issue.Eric Anderson_{October 22, 2014
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What exactly would you like links to, Cantor?rich_{October 22, 2014
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68 rich October 22, 2014 at 9:15 pm you are so wed to your religious lens you must look at all things through it
You really stepped into a pile there rich. I'm calling your bluff. Links please.cantor_{October 22, 2014
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Not really, Cantor. I suppose I am a materialist, provisionally. Things can change. But it seems you are so wed to your religious lens you must look at all things through it.rich_{October 22, 2014
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You seem to be embarrassed to be a materialist, ~~Peter~~ rich. You have now denied your RM+NS deity 3 times...cantor_{October 22, 2014
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Feel free to keep embarrassing yourself, Cantor: http://en.wikipedia.org/wiki/Cromwell%27s_rule Maybe Barry will make a post about you?rich_{October 22, 2014
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64 rich October 22, 2014 at 8:06 pm Actually I don’t.
Sure you do. You're a materialist. Game... Set... Match...cantor_{October 22, 2014
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Actually I don't. 0/2. Do you know the odds of you getting the next one right?rich_{October 22, 2014
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62 rich October 22, 2014 at 7:19 pm I’m not pretending to make a probabilistic argument, Cantor.
Sure you are. You think the probability is 1.cantor_{October 22, 2014
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