Uncommon Descent Serving The Intelligent Design Community

Is the CSI concept well-founded mathematically, and can it be applied to the real world, giving real and useful numbers?

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Those who have been following the recently heated up exchanges on the theory of intelligent design and the key design inference on tested, empirically reliable signs, through the ID explanatory filter, will know that a key move in recent months was the meteoric rise of the mysterious internet persona MathGrrl (who is evidently NOT the Calculus Prof who has long used the same handle).

MG as the handle is abbreviated, is well known for “her” confident-manner assertion — now commonly stated as if it were established fact in the Darwin Zealot fever swamps that are backing the current cyberbullying tactics that have tried to hold my family hostage —  that:

without a rigorous mathematical definition and examples of how to calculate [CSI], the metric is literally meaningless. Without such a definition and examples, it isn’t possible even in principle to associate the term with a real world referent.

As the strike-through emphasises, every one of these claims has long been exploded.

You doubt me?

Well, let us cut down the clip from the CSI Newsflash thread of April 18, 2011, which was again further discussed in a footnote thread of 10th May (H’mm, anniversary of the German Attack in France in 1940), which was again clipped yesterday at fair length.

( BREAK IN TRANSMISSION: BTW, antidotes to the intoxicating Darwin Zealot fever swamp “MG dunit” talking points were collected here — Graham, why did you ask the question but never stopped by to discuss the answer? And the “rigour” question was answered step by step at length here.  In a nutshell, as the real MathGrrl will doubtless be able to tell you, the Calculus itself, historically, was founded on sound mathematical intuitive insights on limits and infinitesimals, leading to the warrant of astonishing insights and empirically warranted success, for 200 years. And when Math was finally advanced enough to provide an axiomatic basis — at the cost of the sanity of a mathematician or two [doff caps for a minute in memory of Cantor] — it became plain that such a basis was so difficult that it could not have been developed in C17. Had there been an undue insistence on absolute rigour as opposed to reasonable warrant, the great breakthroughs of physics and other fields that crucially depended on the power of Calculus, would not have happened.  For real world work, what we need is reasonable warrant and empirical validation of models and metrics, so that we know them to be sufficiently reliable to be used.  The design inference is backed up by the infinite monkeys analysis tracing to statistical thermodynamics, and is strongly empirically validated on billions of test cases, the whole Internet and the collection of libraries across the world being just a sample of the point that the only credibly known source for functionally specific complex information and associated organisation [FSCO/I]  is design.  )

After all, a bit of  careful citation always helps:

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>>1 –> 10^120 ~ 2^398

I = – log(p) . . .  eqn n2
3 –> So, we can re-present the Chi-metric:
[where, from Dembski, Specification 2005,  χ = – log2[10^120 ·ϕS(T)·P(T|H)]  . . . eqn n1]
Chi = – log2(2^398 * D2 * p)  . . .  eqn n3
Chi = Ip – (398 + K2) . . .  eqn n4
4 –> That is, the Dembski CSI Chi-metric is a measure of Information for samples from a target zone T on the presumption of a chance-dominated process, beyond a threshold of at least 398 bits, covering 10^120 possibilities.
5 –> Where also, K2 is a further increment to the threshold that naturally peaks at about 100 further bits . . . .
6 –> So, the idea of the Dembski metric in the end — debates about peculiarities in derivation notwithstanding — is that if the Hartley-Shannon- derived information measure for items from a hot or target zone in a field of possibilities is beyond 398 – 500 or so bits, it is so deeply isolated that a chance dominated process is maximally unlikely to find it, but of course intelligent agents routinely produce information beyond such a threshold.

7 –> In addition, the only observed cause of information beyond such a threshold is the now proverbial intelligent semiotic agents.
8 –> Even at 398 bits that makes sense as the total number of Planck-time quantum states for the atoms of the solar system [most of which are in the Sun] since its formation does not exceed ~ 10^102, as Abel showed in his 2009 Universal Plausibility Metric paper. The search resources in our solar system just are not there.
9 –> So, we now clearly have a simple but fairly sound context to understand the Dembski result, conceptually and mathematically [cf. more details here]; tracing back to Orgel and onward to Shannon and Hartley . . . .
As in (using Chi_500 for VJT’s CSI_lite [UPDATE, July 3: and S for a dummy variable that is 1/0 accordingly as the information in I is empirically or otherwise shown to be specific, i.e. from a narrow target zone T, strongly UNREPRESENTATIVE of the bulk of the distribution of possible configurations, W]):
Chi_500 = Ip*S – 500,  bits beyond the [solar system resources] threshold  . . . eqn n5
Chi_1000 = Ip*S – 1000, bits beyond the observable cosmos, 125 byte/ 143 ASCII character threshold . . . eqn n6
Chi_1024 = Ip*S – 1024, bits beyond a 2^10, 128 byte/147 ASCII character version of the threshold in n6, with a config space of 1.80*10^308 possibilities, not 1.07*10^301 . . . eqn n6a
[UPDATE, July 3: So, if we have a string of 1,000 fair coins, and toss at random, we will by overwhelming probability expect to get a near 50-50 distribution typical of the bulk of the 2^1,000 possibilities W. On the Chi-500 metric, I would be high, 1,000 bits, but S would be 0, so the value for Chi_500 would be – 500, i.e. well within the possibilities of chance.  However, if we came to the same string later and saw that the coins somehow now had the bit pattern of the ASCII codes for the first 143 or so characters of this post, we would have excellent reason to infer that an intelligent designer, using choice contingency, had intelligently reconfigured the coins. that is because, using the same I = 1,000 capacity value, S is now 1, and so Chi_500 = 500 bits beyond the solar system threshold. If the 10^57 or so atoms of our solar system, for its lifespan, were to be converted into coins and tables etc, and tossed at an impossibly fast rate, it would be impossible to sample enough of the possibilities space W to have confidence that something from so unrepresentative a zone T,  could reasonably be explained on chance. So, as long as an intelligent agent capable of choice is possible, choice — i.e. design — would be the rational, best explanation on the sign observed, functionally specific, complex information.]
10 –> Similarly, the work of Durston and colleagues, published in 2007, fits this same general framework . . . .
We use the formula log (20) – H(Xf) to calculate the functional information at a site specified by the variable Xf such that Xf corresponds to the aligned amino acids of each sequence with the same molecular function f. The measured FSC for the whole protein is then calculated as the summation of that for all aligned sites. The number of Fits quantifies the degree of algorithmic challenge, in terms of probability [info and probability are closely related], in achieving needed metabolic function. For example, if we find that the Ribosomal S12 protein family has a Fit value of 379, we can use the equations presented thus far to predict that there are about 10^49 different 121-residue sequences that could fall into the Ribsomal S12 family of proteins, resulting in an evolutionary search target of approximately 10^-106 percent of 121-residue sequence space. In general, the higher the Fit value, the more functional information is required to encode the particular function in order to find it in sequence space . . . .
11 –> So, Durston et al are targetting the same goal, but have chosen a different path from the start-point of the Shannon-Hartley log probability metric for information. That is, they use Shannon’s H, the average information per symbol, and address shifts in it from a ground to a functional state on investigation of protein family amino acid sequences. They also do not identify an explicit threshold for degree of complexity. [Added, Apr 18, from comment 11 below:] However, their information values can be integrated with the reduced Chi metric:
Using Durston’s Fits from his Table 1, in the Dembski style metric of bits beyond the threshold, and simply setting the threshold at 500 bits:
RecA: 242 AA, 832 fits, Chi: 332 bits beyond
SecY: 342 AA, 688 fits, Chi: 188 bits beyond
Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond  . . . results n7
The two metrics are clearly consistent . . .  (Think about the cumulative fits metric for the proteins for a cell . . . )
In short one may use the Durston metric as a good measure of the target zone’s actual encoded information content, which Table 1 also conveniently reduces to bits per symbol so we can see how the redundancy affects the information used across the domains of life to achieve a given protein’s function; not just the raw capacity in storage unit bits [= no.  of  AA’s * 4.32 bits/AA on 20 possibilities, as the chain is not particularly constrained.]>>

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So, there we have it folks:

I: Dembski’s CSI metric is closely related to standard and widely used work in Information theory, starting with I = – log p

II: It is reducible on taking the appropriate logs, to an information beyond a threshold value

III: The threshold is reasonably set by referring to the accessible search resources of a relevant system, i.e. our solar system or the observed cosmos as a whole.

IV: Where, once an observed configuration — event E, per NFL — that bears or implies information is from a separately and “simply” describable narrow zone T that is strongly unrepresentative — that’s key — of the space of possible configurations, W, then

V: since the search applied is of a very small fraction of W, it is unreasonable to expect that chance can reasonably account for E in T, instead of the far more typical possibilities in W of in aggregate, overwhelming statistical weight.

(For instance the 10^57 or so atoms of our solar system will go through about 10^102 Planck-time Quantum states in the time since its founding on the usual timeline. 10^150 possibilities [500 bits worth of possibilities] is 48 orders of magnitude beyond that reach, where it takes 10^30 P-time states to execute the fastest chemical reactions.  1,000 bits worth of possibilities is 150 orders of magnitude beyond the 10^150 P-time Q-states of the about 10^80 atoms of our observed cosmos. When you are looking for needles in haystacks, you don’t expect to find them on relatively tiny and superficial searches.)

VI: Where also, in empirical investigations we observe that an aspect of an object, system, process or phenomenon that is controlled by mechanical necessity will show itself in low contingency. A dropped, heavy object falls reliably at g. We can make up a set of differential equations and model how events will play out on a given starting condition, i.e we identify an empirically reliable natural law.

VII: By contrast, highly contingent outcomes — those that vary significantly on similar initial conditions, reliably trace to chance factors and/or choice, e.g we may drop a fair die and it will tumble to a value essentially by chance. (This is in part an ostensive definition, by key example and family resemblance.)  Or, I may choose to compose a text string, writing it this way or the next. Or as the 1,000 coins in a string example above shows, coins may be strung by chance or by choice.

VIII: Choice and chance can be reliably empirically distinguished, as we routinely do in day to day life, decision-making, the court room, and fields of science like forensics.  FSCO/I is one of the key signs for that and the Dembski-style CSI metric helps us quantify that, as was shown.

IX:  Shown, based on a reasonable reduction from standard approaches, and shown by application to real world cases, including biologically relevant ones.

We can safely bet, though, that you would not have known that this was done months ago — over and over again — in response to MG’s challenge, if you were going by the intoxicant fulminations billowing up from the fever swamps of the Darwin zealots.

Let that be a guide to evaluating their credibility — and, since this was repeatedly drawn to their attention and just as repeatedly brushed aside in the haste to go on beating the even more intoxicating talking point drums,  sadly, this also raises serious questions on the motives and attitudes of the chief ones responsible for those drumbeat talking points and for the fever swamps that give off the poisonous, burning strawman rhetorical fumes that make the talking points seem stronger than they are.  (If that is offensive to you, try to understand: this is coming from a man whose argument as summarised above has repeatedly been replied to by drumbeat dismissals without serious consideration, led on to the most outrageous abuses by the more extreme Darwin zealots (who were too often tolerated by host sites advocating alleged “uncensored commenting,” until it was too late), culminating now in a patent threat to his family by obviously unhinged bigots.)

And, now also you know the most likely why of TWT’s attempt to hold my family hostage by making the mafioso style threat: we know you, we know where you are and we know those you care about. END

Comments
Serious: The above was an answer to essentially a mathematical challenge, and is couched in those terms in light of the issues then under contention. It was necessary to connect CSI to the standard results of info theory, and to show how a metric could be deduced and applied in direct response to Patrick May's sock-puppet persona, Mathgrrl. Notice the core challenge he raised:
a rigorous mathematical definition and examples of how to calculate [CSI]
That is what you see above. If you want a somewhat simpler look at the issue, try here. Sorry, the math is necessary when something mathematical has to be shown. And this math is much simpler than the alternative formulations on statistical and classical thermodynamics. Yes the multiverse does imply that the fine tuning point is made, but it is the credibility of CSI as a mathematical quantity that can be used in actual biological contexts which was on the table here. KFkairosfocus
January 3, 2013
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I think 3 points must be made. First, these arguments must be reduced and simplified as the points are lost. There is no point in arguing with someone whose point has a ton of convoluted garbage on top of it. The 2nd is Cosmology has already moved to Multiverse --which is essentially conceding design to any unbiased thinker. The probabilities in Cosmology are actually tiny in comparison to abiogenesis. The 3 point is most biologist consider multiverse to be metaphysical nonsense. So we have a conundrum here. Cosmologists and Theoretical physicists accept must lower odds. Essentially, the universe we live in is impossible if there is only one. Yet biologists will not accept what is obvious to everyone else --indicating a pathological bias. So you are trying to reason with people who have crippled their intellect. So arguments must contain grander premises and not allow this piling on of techno babble garbage that these crippled minds can hide underneathserious123
January 3, 2013
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Elizabeth, are crystals self-replicators?Mung
July 24, 2011
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Elizabeth, do you consider crystals to be self-replicators?Mung
July 22, 2011
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"And if every Planck Time Quantum state in this cosmos spawned another universe of same size with the same number of PTQS’s, we go to 10^150 squared or 10^300." Brilliant! Now we're making headway. In such a situation, ten-million, trillion, trillion, trillion universes would be spawned every second, which would be 10^43 UPS (universes per second) and 10^123 atoms (that's a trillion, trillion, trillion, trillion, trillion, trillion, trillion... never mind) per second. It would take a full 15 billion years of 10^43 UPS to approach your 10^300. (I thought your 1000 bits was too generous. Actually, I think 500 bits is also. Then again, that's the point, isn't it.) And we still fall well-short of imagining 10^520, which is the search space of a single solitary protein with a paltry 400 aminos.material.infantacy
July 22, 2011
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Yup. And if every Planck Time Quantum state in this cosmos spawned another universe of same size with the same number of PTQS's, we go to 10^150 squared or 10^300. Hence my resort of going to 1,000 bits not 500. if you cannot sample as much as 1 in 10^150th of a space of possibilities, such a relatively tiny sample can only reasonably hope to capture typical configs. So, if we are looking at events E from UNrepresentative narrow zones T in a possibilities space W, where E is functionally specific, complex and informational, we have good reason to accept that it is only intelligence that is credibly able to land us in T. A blind sample, we have no good reason to hope will land us in such a narrow and UNrepresentative T. But then if you are wedded to a different view, this can be hard to see indeed. Gkairosfocus
July 22, 2011
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"Tell me, did you actually count off 520 zeros?" Yes. It is my way. Speaking of HP calculators, these numbers choke my old 49g. Properties of logarithms to the rescue. Considering ten raised to the power of five-hundred and twenty (10^520). Just how large is this number: If every atom in the universe were another identical universe, we'd only have 10^160 atoms.material.infantacy
July 22, 2011
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MI: Tell me, did you actually count off 520 zeros? Shakkin me haid . . . And you are right, I ent goin to count off 60,000+ zeros! Thank God for old Mr Smith and the Cambridge Elementary mathematical tables. Not to mention a good old circular slide rule! Then there was that fondly remembered HP 21 . . . GEM of TKIkairosfocus
July 22, 2011
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KF, "Sometimes, I think part of the problem lies in a power of the very exponential notation used." I agree. Seeing something like 10^520 hardly does justice the depth of this number. But then again, neither does seeing this: 10000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000. (I dare you to try that with your numbers.) xpmaterial.infantacy
July 22, 2011
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Chris:
Morning Lizzie, We certainly do have different mental images here! I think that’s because I’m talking about self-replication and you’re talking about something else (I’m trying to think of a technical term for disassembling and reassembling lego blocks… but can’t)!
Well, I'm talking about what I mean by self-replication - when something does something that results in two copies of the original.
Crucially, the ability of the first self-replicating molecule to self-replicate (a small part of which may involve splitting down the middle) comes from its molecular shape and content so, that will include its sequence.
Not necessarily, although possibly.
The process of self-replication does not and cannot rely upon random free-floating monomers being in the right place at the right time: self-replication needs to be far more self-contained than that or else the parent would almost certainly lose the daughter (and itself!) in the very process of reproduction. Besides, if self-replication was merely the “ability to split down the middle, and for both halves to then attract to each now-unmated unit” then surely the most likely outcome would be for the two halves of the peptide chain to merely come back together again.
Possibly. Certainly in the absence stuff to make a copy out of, a thing won't copy. That's why photocopiers need paper and toner, and people need food :) But yes, you need at least two conditions for self-replication to occur: a mechanism, and resources. You can't spin straw into gold.
So, the self-replicating molecule would (and we’re dramatically oversimplifying here) need to start off with something like: AC CA CA DB DB BD CA CA AC AC DB BD And then, after a self-contained and straightforward process of self-replication, we end up with two: AC AC CA CA CA CA DB DB DB DB BD BD CA CA CA CA AC AC AC AC DB DB BD BD
Yes. The first splits vertically, like this: A C C A C A D B D B B D C A C A A C A C D B B D Then spare monomers attach to the links of each single chain, resulting in two identical chains, like this: AC CA CA AC CA AC DB BD DB BD BD DB CA AC CA AC AC CA AC CA DB BD BD DB Flip the second one over and you have: AC AC CA CA CA CA DB DB DB DB BD BD CA CA CA CA AC AC AC AC DB DB BD BD
Given that such a self-replicating molecule must have existed if life just made itself, then I can see no scope for copying error that will not impair or destroy the ability to self-replicate.
Why not? Consider: AC CA CA DB splits to form A C C A C A D B Then the first acquires a B on the end (a passing monomer): A C C D B The second loses a C from one end (bumps into a rock): A A B Each then joins up with free matching monomers giving: AC CA CA DB BD and AC AC BD Which, if we flip the second over are: AC CA CA CA CA DB DB BC both being mutant daughters of the original AC CA CA DB And both being just as capable of reproducing themselves as their parent.
There is only perfect and eternal cloning. And, this heredity is a much more important feature of life than copying errors. So, tell me Lizzie, how can we realistically move beyond this first self-replicating molecule?
But there isn't only "perfect and eternal cloning". There can be lots of imperfect clones. And if some of them turn out to be better than others, more clones of the good cloners will exist.Elizabeth Liddle
July 22, 2011
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I need to learn how to use tags properly (actually, this might work)! Here's a good old fashioned link to the Joe Francis article: http://www.4truth.net/fourtruthpbscience.aspx?pageid=8589952959Chris Doyle
July 22, 2011
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"So why isn't every can of soup you open teeming with novel life forms as a new start world of life?" A very good question, kairosfocus. We've provided a number of major obstacles on this thread - not one of which has been dealt with by our opponents yet. If the arguement is not already settled in our favour, then I think this article by Joe Francis surely finishes the job off: Oxygen, Water and Light, Oh My! The Toxicity of Life's Basic Necessities (hopefully that's a link)Chris Doyle
July 22, 2011
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GP: Not only must these paths exist, but they would have to be accessible so that within a few 100 mn yrs of the end of the late bombardment era on the usual timeline, life emerges on earth. This means they search for such has to be MUCH simpler than a search for a 1000 bit dFSCI object. More like that for a 20 - 30 bit object. So, using the usual RNA world type model, we are looking at 10 - 20 monomer RNAs that self replicate and template "proteins" at that length that have significant replication- rewardable function etc. There is of course a lot of speculation on this sort of thing, too much of it presented as though it were proved fact. As for the onward imagined process by which such would now create a code for DNA [a near optimal code!], regulatory networks, and the complex machinery of life to implement algorithms expressed in the DNA etc etc, of this we find nowhere the faintest empirical trace in the body of observations. And, we are looking at the issue of 100+ k bits worth of control, data and algorithmic code writing themselves out of lucky noise here on our one little planet or in our solar system. [Has anyone worked out how long drift at any reasonable speed for organic molecules that are fairly fragile -- a supernova would rip 'em up -- takes to bridge interstellar space!] Berlinski's recent rebuke to such unbridled speculation is well worth clipping:
At the conclusion of a long essay, it is customary to summarize what has been learned. In the present case, I suspect it would be more prudent to recall how much has been assumed: First, that the pre-biotic atmosphere was chemically reductive; second, that nature found a way to synthesize cytosine; third, that nature also found a way to synthesize ribose; fourth, that nature found the means to assemble nucleotides into polynucleotides; fifth, that nature discovered a self-replicating molecule; and sixth, that having done all that, nature promoted a self-replicating molecule into a full system of coded chemistry. These assumptions are not only vexing but progressively so, ending in a serious impediment to thought. That, indeed, may be why a number of biologists have lately reported a weakening of their commitment to the RNA world altogether, and a desire to look elsewhere for an explanation of the emergence of life on earth. "It's part of a quiet paradigm revolution going on in biology," the biophysicist Harold Morowitz put it in an interview in New Scientist, "in which the radical randomness of Darwinism is being replaced by a much more scientific law-regulated emergence of life." Morowitz is not a man inclined to wait for the details to accumulate before reorganizing the vista of modern biology. In a series of articles, he has argued for a global vision based on the biochemistry of living systems rather than on their molecular biology or on Darwinian adaptations. His vision treats the living system as more fundamental than its particular species, claiming to represent the "universal and deterministic features of any system of chemical interactions based on a water-covered but rocky planet such as ours." This view of things - metabolism first, as it is often called - is not only intriguing in itself but is enhanced by a firm commitment to chemistry and to "the model for what science should be." It has been argued with great vigor by Morowitz and others. It represents an alternative to the RNA world. It is a work in progress, and it may well be right. Nonetheless, it suffers from one outstanding defect. There is as yet no evidence that it is true . . .
And a look at the video here will help. Folks, we can put this in terms of a pointed question: your friendly local soup can has in it much more than the sort of thing that is being imagined for OOL. So why isn't every can of soup you open teeming with novel life forms as a new start world of life? GEM of TKIkairosfocus
July 22, 2011
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Indium: By the way, I still cannot access your links. Could you please post the complete URL?gpuccio
July 22, 2011
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Indium: Therefore, the ratio of the target/total search space is irrelevant as long as there is a somehow viable evolutionary pathway. That's the point you have wrong. As long as we know, those pathway don't exist. We have never seen them, and there is absolutely no logical reason, except for the blind faith of darwinists, for them to exist. All that we know about complex information, both in human artifacts and computer programming and biology, tells us that those path do not exist. These are the facts. So, unless and until someone shows those paths to exist, my argument is completely relevant. Remember again, science is about known facts, not fairy tales or dogmatic hopes and beliefs.gpuccio
July 22, 2011
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MI: Understood. I just wanted to underscore the force of the point. Sometimes, I think part of the problem lies in a power of the very exponential notation used. Its compression. Odds of 1 in 10^60 or a ratio like that are comparable to a grain of sand to the mass of the atomic matter in our observed universe. Or try one atom to our solar system. A genome of 100,000 -- too small, actually -- corresponds to a space of configs of order 9.98*10^60,205. That is a staggering number. Maybe if we had to write out pages and pages of zeroes it would help us see the unimaginable scale of such a number. The resources of the observed universe could not begin to even pretend to sample it. And the space we are dealing with for all genomes runs out to about 700 BILLION bases, so far. 3.75 * 10^ 421,441, 993,929 possibilities swamps the number of individual organisms that has ever existed. Sampling theory tells us loud and clear that when we take a tiny nick out of a huge population, the most we can hope for is that we have something reasonably typical. Even at the 1,000 bits end, our cosmos cannot begin to explore a tiny fraction of the possibilities. So, the notion that a chance based random walk can land us on the shores of ANY island of function that is even reasonably isolated, is nonsense. We are looking at a very different set of options for evo mat at this point:
1: functional states DOMINATE the space, which is patently not so. 2: Function begins so early, at such a simple level of complexity, and leads through a smoothly branched tree pattern to all major forms, that the first forms are easy to get to and lead on to the others. 80+ years of OOL studies give the lie to this. 3: Life is literally programmed into the laws of physics, so once a suitable environment forms, it is inevitable. (This would mean that every can of soup in the supermarket would be brimming over with spontaneously formed life.) 4: Our understanding of thermodynamics [e.g the implications of diffusion], information theory, chemistry and physics is totally inept. 5: The apparent design is not just apparent. And, actually, 3 would be the same as this.
Perhaps someone can suggest another, but so far it looks like the signs are speaking loud and clear. GEM of TKIkairosfocus
July 22, 2011
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Hi KF, Thanks for taking the time to answer my questions. They were partially of a rhetorical nature, however the answers are still interesting. 1) Has anyone an idea of how many likely functional targets exist in a space of, say, 20^400? (This represents a protein chain of 400 aminos.) I take it from your reply that it's veritably irrelevant, since the search space is so large and the search resources so small. My point was that we would need a huge number of targets, > 10^370, in order for the feasibility of even this one protein to be found by a blind process. (20^400 is around 10^520.) I realize this is a drastic understatement of the problem, since it is compounded with folding contingencies, and again with every disparate protein in a cell, and again with every contingent arrangement of proteins into functional parts (organelles in the single-celled case). The magnitude of the problem is staggering. It would literally take a multiverse probablistic resources just for a single 400 length chain to be found by a random search.
Actually that falls apart on closer inspection: not least, this quietly slips across the border into metaphysical, philosophical speculation. The empirical, observed evidence for a quasi-infinite, eternal multiverse is NIL.
World views (beliefs) seem to be given top billing as a fact of human nature. There is nothing we observe or reasone that cannot be sacrificed to protect our world view. The only hope we have is to believe that truth exists. This is a spiritual matter, of course. I've seen reason itself denied (in the name of reason, go figure) more than once on this blog by those opposed to the possibility of design in nature.
For the 128 ascii characters to be used to make sentences in English, some highly restrictive rules have to be used to select sequences in strings, and this locks out the vast majority of sequences.
Yes, even this paragraph is beyond the search capabilities of the entire universe, multiplied many times. This is the observed reality that must be rejected if one is to maintain a world view that doesn't include a creator.
The gap here is that the problem is to get to the shorelines of those incredibly isolated islands of function, not to move around within such an island. (This has been underscored many, many times, but is routinely ignored or brushed aside. But it is the decisive issue
I think that movement on these islands would be limited. Even if we stipulate to some mysterious process finding the island, I don't believe it's been shown (by anyone, ever) that we can jump to a neighboring function, unless it's within rowing distance. In other words, for a given protein, it's limited to rather minor variations (a few aminos), rather than bridging larger differences in protein structure (and therefore function). If these bridges exist, we should know already. 2) Is there any known probability distribution that would allow bridges between functional targets given a reasonable target estimate? I'm assuming the answer here is plainly no. Any uniform or non-uniform distribution of targets across the search space will yeild practically the same results for most proteins, since the search space is so large and the functional permutations likely vanishingly small by comparison. m.i.material.infantacy
July 21, 2011
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MI: Actually, all that is needed for the considerations above to become extremely relevant, is for:
1: the appropriate config space to be extremely large relative to the available search resources so as to reduce a search process on the relevant scale to be not significantly different from zero in a needle in a haystack search [500 bits -- solar system swamped, 1000 bits -- observed cosmos swamped] 2: we have credible reason to hold that the objects in view are functionally specific, and complex so that they are deeply isolated in the space of possibilities for something of that bit depth of complexity
The first criterion is fairly obvious. If you can only do a relatively tiny sample the only things you will credibly pick up by a random walk and trial and error search process -- and something dominated by molecular noise or the like will be like that -- will be something typical of the broad bulk of the distribution. This is not far from the statistical basis for the second law of thermodynamics. It is the second criterion that seems difficult to accept. But the principle can be seen from the text in this thread. For the 128 ascii characters to be used to make sentences in English, some highly restrictive rules have to be used to select sequences in strings, and this locks out the vast majority of sequences. Similarly, when we look at proteins, at length DM seems to have had to acknowledge that the vast majority of AA sequences -- we need not pause to look at issues on chirality, peptide vs non peptide bonds and interference by cross reactions etc -- will be unlikely to fold and function properly in the context of a living cell. (Indeed the whole class of prion diseases is one where propagating misfolds play havoc with properly sequenced proteins. Thence, mad cow disease etc.) Similar constraints affect DNA and RNA chains. So, the blind evolutionary argument [which is not the same as all evolutionary arguments] is in effect asserting that chance sequences can find function. For small changes in things that already work, such may work, but when you are looking at coming up with novel body plans the problems literally exponentiate. Every additional bit of info doubles the space of possible configs. So, once we reach the sort of thresholds above, we run into the problem that the search resources that are relevant -- and for practical purposes our solar system is our chemically available "universe" -- soon become utterly inadequate. Indeed this is a part motivation for the sudden popularity of quasi-infinite multiverse models or rather speculations. Proponents of such, basically hope that the quasi infinite scope they propose will swamp all search space challenges, so that we "should" not be surprised if we see ourselves as the lucky winners. Actually that falls apart on closer inspection: not least, this quietly slips across the border into metaphysical, philosophical speculation. The empirical, observed evidence for a quasi-infinite, eternal multiverse is NIL. And once we are in the province of phil -- despite intemperate objections -- other non-scientific, historical and current evidence becomes very relevant such as the literally millions over the centuries who claim to have met and come to know God in positively life transforming ways. Once the door to phil is open, thank you we can go through it and address the full panoply of comparative difficulties across live option worldviews. But the focus is on scientific matters here. For that, we have empirical evidence of but one observed cosmos, with a credible beginning, and with evidence of locally highly sensitive fine-tuning that puts it at an operating point fitted for C-chemistry, cell based life. We also observe that that life is based on digital code bearing molecular technologies and algorithms. The only empirically credible explanation for such is intelligence, and we have excellent analytical grounds for backing that up. Now that does not tell us whodunit, where, when or how, but it strongly suggests on empirical evidence that twerdun is the best explanation. And through that door lie many interesting scientific and even technological possibilities. GEM of TKI PS: Indium in 142 does not seem to recognise a key begged question:
There are huge amounts of possible sequences which most likely don´t make any sense and don´t even result in folded proteins. Evolution does not waste its resources to search these spaces, by definition it only looks in the vicinity of existing genomes. Therefore, the ratio of the target/total search space is irrelevant as long as there is a somehow viable evolutionary pathway.
1 --> The gap here is that the problem is to get to the shorelines of those incredibly isolated islands of function, not to move around within such an island. (This has been underscored many, many times, but is routinely ignored or brushed aside. But it is the decisive issue.) 2 --> Such starts with OOL and goes on to origin of body plans. (Cf here on whales and here on OO life.) 3 --> If you don't have an existing functional genome for a body plan, you don't have a start point for searching for improved performance in its near vicinity. 4 --> So, let us un-beg that question: on empirical evidence, how can chance variations in still warm ponds or unicellular organisms filtered through trial and error and relative success. originate cell based life and originate embryologically feasible body plans? 5 --> Specifically, how do we account for the origin of the cell and the origin of the whale, on OBSERVED evidence that answers to the functional info origination challenge, within the relevant scopes of resources? Beyond just so stories. 6 --> Where was the work done, by whom, when, and where is it published in the serious literature?kairosfocus
July 21, 2011
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Indium tells me that:
Evolution is not random.
According to the theory the processes are blind and undirected/ unguided- ie accumulations of genetic accidents. And you still cannot provide any evidence for that mechanism constructing new, useful and functional multi-part systems. So the bottom line remains-> every time we have observed CSI and knew the cause it has always been via agency involvement- always. Therefor it is safe to infer a designing agency was involved when we observe CSI and do not know the cause.Joseph
July 21, 2011
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Mung @ 142: "And that makes your argument a non sequitur, which means you should reformulate it or discard it." Also, if one cares to notice it, one can see that Indium's particular argument you quote and critique is denying that Darwinism is true, is denying that "evolution" has the power to move off those "incredibly tiny" "islands of fitness." Or, to look at it in a slightly different direction, he is denying that "evolution" has the power to create new "islands of fitness."Ilion
July 21, 2011
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"There are huge amounts of possible sequences which most likely don´t make any sense and don´t even result in folded proteins."
Has anyone an idea of how many likely functional targets exist in a space of, say, 20^400? It seems that if finding any functional target in the first place is to be considered plausible then somebody should have an idea. That's not to say we can start with the proposition that *evolution* is true and then reason backwards that there are at least 20^400 / 10^150 functional targets in that sequence space (~10^520 / 10^150 = 10^370) although I can see where that would be tempting for some. I'd wager it's the other way around, that in a 20^400 space there are fewer than 10^150 functional permutations, leaving an effective search space of 10^370 (inhibitively large). Islands of function in a sea of configurations doesn't do this problem justice. We'd be better off thinking of this as atoms of function in a multiverse of configurations.
"Evolution does not waste its ressources to search these spaces, by definition it only looks in the vicinity of existing genomes."
I'm not sure what "by definition" means here. Rather, if variations are confined around existing function, it would suggest a mechanism for a non-random search.
"Therefore, the ratio of the target/total search space is irrelevant as long as there is a somehow viable evolutionary pathway."
A viable pathway would seem a requisite condition for accepting the validity of a variation mechanism independent of design. Also, the target/space ratio is still completely relevant, since reasonable estimates of the distance between functional intermediates would depend on knowing both the search space and the likely number of permutations that would yeild valid targets. Is there any known probability distribution that would allow bridges between functional targets given a reasonable target estimate? I'd wager again that in order for functional targets to be bridged by any Darwinian variation mechanism, all reachable functions couldn't be more than a couple aminos apart. If each permutation in the target space were a vertex in a graph, the graph's edges would be formed by any two vertices where the cost of traversal was within either the known abilities of Darwinian evolution, or within an exploration bound reasonable to the size and age of the universe (read UPB) for a random search. That's not even considering the difficulties of trait fixation and selective advantage.
"...and for many or even most cases we may never recover these pathways."
That's a little too convenient for a purported biological theory of everything.
"...at this point your CSI argument is more or less completely irrelevant."
It couldn't be more relevant, especailly given the statement that "There are huge amounts of possible sequences which most likely don´t make any sense and don´t even result in folded proteins." The very concept of CSI is present in the analysis of the search space vs the functional target space. If SS/TS > 10^150, there's not even a prayer of a blind mechanism driving novelty in biology, and that's being extremely generous. --- m.i. ---material.infantacy
July 21, 2011
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Indium:
There are huge amounts of possible sequences which most likely don´t make any sense and don´t even result in folded proteins.
That is correct. And the possible sequences are what define the size of the search space. Agreed?
Evolution does not waste its resources to search these spaces
Evolution does not know whether it is wasting resources or not. But you made the following claim: you guys often vastly overestimate the search space. How so? And you appeared to reason that this is the case because: Evolution searches in the vicinity of viable and reproducing organisms and therefore only “tests” an incredibly tiny amount of the total possible DNA sequences. So I ask again, how does the fact that evolution can only search an “incredibly tiny amount” of the search space somehow change the size of the search space? The answer is simple, it does not. Why not just say so? And that makes your argument a non sequitur, which means you should reformulate it or discard it.
Therefore, the ratio of the target/total search space is irrelevant as long as there is a somehow viable evolutionary pathway.
A completely different argument. If that is what you meant you should have said so rather than accusing us of vastly overestimating the search space. I mean you should hear yourself. First you say we often vastly overestimate the search space. Then you say it's irrelevant. So you say what's important is whether there is a pathway. Fine. How many pathways are there? Call each pathway a target. You're still faced with the same problem. You make it sound like viable pathways are no problem. And you make it seem like finding a viable pathway is similarly no problem. The only way you have to look for a viable pathway is a toss of the proverbial dice. So you're right back where we started, with no counter-argument.Mung
July 21, 2011
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Gpuccio:
Have you models for more recent protein families?
I will probably not be able to match the level of detail you are used to from your design hypothesises, but a quick search shows things like this. But maybe you can first comment on the previous paper I linked? Or you can link me to a similarly detailed design hypothesis and we might argue about that? Mung:
How does the fact that evolution can only search an “incredibly tiny amount” of the search space somehow change the size of the search space?
There are huge amounts of possible sequences which most likely don´t make any sense and don´t even result in folded proteins. Evolution does not waste its ressources to search these spaces, by definition it only looks in the vicinity of existing genomes. Therefore, the ratio of the target/total search space is irrelevant as long as there is a somehow viable evolutionary pathway. You may dispute this, and for many or even most cases we may never recover these pathways. In any case, at this point your CSI argument is more or less completely irrelevant. Joseph: Evolution is not random.Indium
July 21, 2011
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Onlookers: First, within an island of existing function, you can indeed move around by hill climbing. That is common ground that even the despised Young Earth Creationists would agree to. The issue is, to get to islands of function, and to do so from initial reasonable starting points. To give an idea of what is going on, observe above, whether there is any darwinian answer to say transforming a wolf or a cow into a whale. Plainly not. So why is there such a confident presentation of the sequences alleged to show this? (Cf Sternberg's video here, recall this is an evolutionary biologist speaking. And while you are at it, take a look at Paley's self replicating watch case in light of the key point on ADDITIONAL capacity of self-replication -- the watch story has been routinely stramannised in the common discussions by Darwinists; they only discuss Ch I, and skip over Ch II. That would cover a self replicating house too, complete with sprinkler; cf. the vNSR discussion here.) Remember, the claim is, functional small steps from one end to the other. Where are they? I mean, observationally? Who has actually OBSERVED such, where, when, published where? Without empirical facts in evidence as an answer to empirical tests are we not really talking philosophical speculation, not science? Chirp, chirp, chirp . . . Now, if we turn instead to moving from a unicellular animal to get a multicellular one, we are talking of moving the genome from about 1 million bases, lets round town to 1 mn bits. Going to about 10 - 100+ mn, on observed genome sizes. How are you going to by random variation, innovate then fix then re innonvate to get embryologically feasible body plans, 9 mn bases -- lets call them bits to allow for various issues -- worth? As a matter of fact, we do not have even a good account of the origin of the flagellum on darwinian terms, only a just so story on something that looks very much like a derivative of the flagellum, the T3SS. In short, this stuff is v long on speculation, very short on empirical data to show the alleged branching tree pattern of small incremental variations at genetic level. We do directly know that intelligences routinely generate 1 mn to 10 or 100 mn bits worth of functionally specific complex information. So the only leap there is like causes like, and the problem of making a self replicating automaton. We can analyse them, but have yet to build a kinematic self replicator. So, we can easily infer to best explanation on known capacity and known lack of capacity. Design is not a gaps inference, but an inference from what has known capacity as opposed to what has known challenges to do the task. Have you ever seen complex functional digital codes, algorithms, and implementing machines originate from scratch, without intelligent input? Life forms self replicate such systems, but -- even as Paley also pointed out 200 years ago -- replication is not origination. It is origination that needs to be answered to, and complex information bearing codes are not observed to occur by lucky noise captured by success. They are designed. So much so that we are entitled to infer from these as reliable signs to their most credible cause, per inference to best explanation. This is not about geochronology or the debated interpretations of religious texts. Nope, this is on the conventional timeline and sequences of life forms, starting with the Cambrian explosion and going on to other significant body plan innovations. The fossil timeline -- since the days of Darwin -- says we have had a burst of dozens of body plans some 500 - 600 MYA. That means, dozens of times over, accounting for 10+ mn bits of fresh functionally specific info in the genome, preferably with fossil evidence to back up such a claim. Wasn't there in Darwin's day, still isn't there. And we know that the atomic resources of our observed cosmos are insufficient to search out he set of configs for just 1,000 bits of storage. We are dealing with UN-representative, highly specific, organised informational patterns. So, the needle in the haystack challenge with an effectively zero scope sample, obtains, for the resources of the observed cosmos. But, just considering this post, which is well past the search capacity of the observed cosmos, the author as an intelligent designer was able to type it up in some minutes on a computer, which weighs about 2 lbs. That should tell us the difference between random walks rewarded by successful trial and error and intelligence. So plain is the point that it is clear that the reason it is resisted is plainly as Lewontin et al pointed out so plainly: ideological captivity of science to a priori evolutionary materialism. So, let Philip Johnson have the last word for the moment:
For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]
GEM of TKIkairosfocus
July 21, 2011
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Clearly there’s more that doesn’t work in that analogy than the fact that houses don’t reproduce and sprinkler systems aren’t passed on as traits, but at least adding such would address Chris’ issue.
You're right. The analogy fails. Every analogy fails. The trouble is that we can't find anything in the same league as biology to compare to it. We could compare it to houses, satellites, supercomputers, literature, in fact the sum of all human knowledge (and let's not forget sprinkler systems.) But then we'd be oversimplifying.
Of course, I didn’t say anything about dropping in the sprinkler system fully formed
No, you didn't. You said "randomly generated," which I suppose is much more plausible. After all, that is the underlying principle currently used to explain all of life.ScottAndrews
July 21, 2011
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Hi Doveton, The thing is, the human body is vastly more sophisticated than a house and our immune system is vastly more sophisticated than a sprinkler system. If the analogy fails, it is only because it doesn't do justice to say, human physiology and biochemistry. When evolutionists try to downplay impossible probabilities and buy themselves near infinite time and resources to explore the sequence space they haven't managed to sweep under the carpet with the preceding downplaying, they are forgetting just how urgent and inexplicably interdependent these amazingly advanced functions are. Frankly, you've got more chance of success dealing with spontaneous randomly appearing sprinkler systems, than you do with dealing with real-life biology!Chris Doyle
July 21, 2011
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Blind and unguided processes for a search? Now that is funny...Joseph
July 21, 2011
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Indium:
At the same time, you guys often vastly overestimate the search space. Evolution searches in the vicinity of viable and reproducing organisms and therefore only “tests” an incredibly tiny amount of the total possible DNA sequences for example.
So you agree the size of the search space is very large and is related to the total possible DNA sequences, correct? How does the fact that evolution can only search an "incredibly tiny amount" of the search space somehow change the size of the search space?Mung
July 21, 2011
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ScottAndrews,
At first I thought you were making a very funny joke. “Randomly generated sprinkler system?”
I think people get their ideas about evolution from X-Men and Heroes. It’s this magic force that randomly drops fully-developed, useful gifts on unsuspecting individuals.
I'm just running with the inaccurate sprinkler system analogy as presented. Clearly there's more that doesn't work in that analogy than the fact that houses don't reproduce and sprinkler systems aren't passed on as traits, but at least adding such would address Chris' issue. Of course, I didn't say anything about dropping in the sprinkler system fully formed, so I'm not sure why you think I presume such represents how evolution actually works. I pointed out one aspect of actual evolution that would have to be in place to overcome Chris' problem. If you want to discuss how organisms might actually gain a sprinkler system in a biological context, that's a different discussion.Doveton
July 21, 2011
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Ilion: a) The target space designation is post hoc and arbritary. It is based on what we observe and must explain. That's what science does. b) The search space volume is vastly exaggerated. Evolution does not have to explore the full sequence space when there are intermediate bridges. Those bridges don't exist. Show them if you can. Therefore, the search space is not exaggerated at all. c) So the only question that remains is this: Can we construct such bridges or not. I say you can't. But you are free to try. After all, it's you who have faith that they exist. I don't. d) Your fancy numbers however have no meaning at all, they can tell us nothing regarding the question wether or how some sequence evolved. You will always have to look at potential precursers to do an exact calculation. This is probably why you are concentrating on RP S2: It is so old that it is quite unlikely that we will be able to build a model of it´s evolutionary history. Have you models for more recent protein families? d) I can't access the link. e) On the other hand I am happy to accept that we don´t know exactly how these extremely old parts of the genome evolved. I accept your result that they did not form randomly, so, ahem, well done! Thank you.gpuccio
July 21, 2011
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