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ID Foundations, 11: Borel’s Infinite Monkeys analysis and the significance of the log reduced Chi metric, Chi_500 = I*S – 500

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 (Series)

Emile Borel, 1932

Emile Borel (1871 – 1956) was a distinguished French Mathematician who — a son of a Minister — came from France’s Protestant minority, and he was a founder of measure theory in mathematics. He was also a significant contributor to modern probability theory,  and so Knobloch observed of his approach, that:

>>Borel published more than fifty papers between 1905 and 1950 on the calculus of probability. They were mainly motivated or influenced by Poincaré, Bertrand, Reichenbach, and Keynes. However, he took for the most part an opposed view because of his realistic attitude toward mathematics. He stressed the important and practical value of probability theory. He emphasized the applications to the different sociological, biological, physical, and mathematical sciences. He preferred to elucidate these applications instead of looking for an axiomatization of probability theory. Its essential peculiarities were for him unpredictability, indeterminism, and discontinuity. Nevertheless, he was interested in a clarification of the probability concept. [Emile Borel as a probabilist, in The probabilist revolution Vol 1 (Cambridge Mass., 1987), 215-233. Cited, Mac Tutor History of Mathematics Archive, Borel Biography.]>>

Among other things, he is credited as the worker who introduced a serious mathematical analysis of the so-called Infinite Monkeys theorem (just a moment).

So, it is unsurprising that Abel, in his recent universal plausibility metric paper, observed  that:

Emile Borel’s limit of cosmic probabilistic resources [c. 1913?] was only 1050 [[23] (pg. 28-30)]. Borel based this probability bound in part on the product of the number of observable stars (109) times the number of possible human observations that could be made on those stars (1020).

This of course, is now a bit expanded, since the breakthroughs in astronomy occasioned by the Mt Wilson 100-inch telescope under Hubble in the 1920’s. However,  it does underscore how centrally important the issue of available resources is, to render a given — logically and physically strictly possible but utterly improbable — potential chance- based event reasonably observable.

We may therefore now introduce Wikipedia as a hostile witness, testifying against known ideological interest, in its article on the Infinite Monkeys theorem:

In one of the forms in which probabilists now know this theorem, with its “dactylographic” [i.e., typewriting] monkeys (French: singes dactylographes; the French word singe covers both the monkeys and the apes), appeared in Émile Borel‘s 1913 article “Mécanique Statistique et Irréversibilité” (Statistical mechanics and irreversibility),[3] and in his book “Le Hasard” in 1914. His “monkeys” are not actual monkeys; rather, they are a metaphor for an imaginary way to produce a large, random sequence of letters. Borel said that if a million monkeys typed ten hours a day, it was extremely unlikely that their output would exactly equal all the books of the richest libraries of the world; and yet, in comparison, it was even more unlikely that the laws of statistical mechanics would ever be violated, even briefly.

The physicist Arthur Eddington drew on Borel’s image further in The Nature of the Physical World (1928), writing:

If I let my fingers wander idly over the keys of a typewriter it might happen that my screed made an intelligible sentence. If an army of monkeys were strumming on typewriters they might write all the books in the British Museum. The chance of their doing so is decidedly more favourable than the chance of the molecules returning to one half of the vessel.[4]

These images invite the reader to consider the incredible improbability of a large but finite number of monkeys working for a large but finite amount of time producing a significant work, and compare this with the even greater improbability of certain physical events. Any physical process that is even less likely than such monkeys’ success is effectively impossible, and it may safely be said that such a process will never happen.

Let us emphasise that last part, as it is so easy to overlook in the heat of the ongoing debates over origins and the significance of the idea that we can infer to design on noticing certain empirical signs:

These images invite the reader to consider the incredible improbability of a large but finite number of monkeys working for a large but finite amount of time producing a significant work, and compare this with the even greater improbability of certain physical events. Any physical process that is even less likely than such monkeys’ success is effectively impossible, and it may safely be said that such a process will never happen.

Why is that?

Because of the nature of sampling from a large space of possible configurations. That is, we face a needle-in-the-haystack challenge.

For, there are only so many resources available in a realistic situation, and only so many observations can therefore be actualised in the time available. As a result, if one is confined to a blind probabilistic, random search process, s/he will soon enough run into the issue that:

a: IF a narrow and atypical set of possible outcomes T, that

b: may be described by some definite specification Z (that does not boil down to listing the set T or the like), and

c: which comprise a set of possibilities E1, E2, . . . En, from

d: a much larger set of possible outcomes, W, THEN:

e: IF, further, we do see some Ei from T, THEN also

f: Ei is not plausibly a chance occurrence.

The reason for this is not hard to spot: when a sufficiently small, chance based, blind sample is taken from a set of possibilities, W — a configuration space,  the likeliest outcome is that what is typical of the bulk of the possibilities will be chosen, not what is atypical.  And, this is the foundation-stone of the statistical form of the second law of thermodynamics.

Hence, Borel’s remark as summarised by Wikipedia:

Borel said that if a million monkeys typed ten hours a day, it was extremely unlikely that their output would exactly equal all the books of the richest libraries of the world; and yet, in comparison, it was even more unlikely that the laws of statistical mechanics would ever be violated, even briefly.

In recent months, here at UD, we have described this in terms of searching for a needle in a vast haystack [corrective u/d follows]:

let us work back from how it takes ~ 10^30 Planck time states for the fastest chemical reactions, and use this as a yardstick, i.e. in 10^17 s, our solar system’s 10^57 atoms would undergo ~ 10^87 “chemical time” states, about as fast as anything involving atoms could happen. That is 1 in 10^63 of 10^150. So, let’s do an illustrative haystack calculation:

 Let us take a straw as weighing about a gram and having comparable density to water, so that a haystack weighing 10^63 g [= 10^57 tonnes] would take up as many cubic metres. The stack, assuming a cubical shape, would be 10^19 m across. Now, 1 light year = 9.46 * 10^15 m, or about 1/1,000 of that distance across. If we were to superpose such a notional 1,000 light years on the side haystack on the zone of space centred on the sun, and leave in all stars, planets, comets, rocks, etc, and take a random sample equal in size to one straw, by absolutely overwhelming odds, we would get straw, not star or planet etc. That is, such a sample would be overwhelmingly likely to reflect the bulk of the distribution, not special, isolated zones in it.

With this in mind, we may now look at the Dembski Chi metric, and reduce it to a simpler, more practically applicable form:

m: In 2005, Dembski provided a fairly complex formula, that we can quote and simplify:

χ = – log2[10^120 ·ϕS(T)·P(T|H)]. χ is “chi” and ϕ is “phi”

n:  To simplify and build a more “practical” mathematical model, we note that information theory researchers Shannon and Hartley showed us how to measure information by changing probability into a log measure that allows pieces of information to add up naturally: Ip = – log p, in bits if the base is 2. (That is where the now familiar unit, the bit, comes from.)

o: So, since 10^120 ~ 2^398, we may do some algebra as log(p*q*r) = log(p) + log(q ) + log(r) and log(1/p) = – log (p):

Chi = – log2(2^398 * D2 * p), in bits

Chi = Ip – (398 + K2), where log2 (D2 ) = K2

p: But since 398 + K2 tends to at most 500 bits on the gamut of our solar system [our practical universe, for chemical interactions! (if you want , 1,000 bits would be a limit for the observable cosmos)] and

q: as we can define a dummy variable for specificity, S, where S = 1 or 0 according as the observed configuration, E, is on objective analysis specific to a narrow and independently describable zone of interest, T:

Chi_500 =  Ip*S – 500, in bits beyond a “complex enough” threshold

(If S = 0, Chi = – 500, and, if Ip is less than 500 bits, Chi will be negative even if S is positive. E.g.: A string of 501 coins tossed at random will have S = 0, but if the coins are arranged to spell out a message in English using the ASCII code [[notice independent specification of a narrow zone of possible configurations, T], Chi will — unsurprisingly — be positive.)

r: So, we have some reason to suggest that if something, E, is based on specific information describable in a way that does not just quote E and requires at least 500 specific bits to store the specific information, then the most reasonable explanation for the cause of E is that it was intelligently designed. (For instance, no-one would dream of asserting seriously that the English text of this post is a matter of chance occurrence giving rise to a lucky configuration, a point that was well-understood by that Bible-thumping redneck fundy — NOT! — Cicero in 50 BC.)

s: The metric may be directly applied to biological cases:

t: Using Durston’s Fits values — functionally specific bits — from his Table 1, to quantify I, so also  accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:

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

u: And, this raises the controversial question that biological examples such as DNA — which in a living cell is much more complex than 500 bits — may be designed to carry out particular functions in the cell and the wider organism.

v: Therefore, we have at least one possible general empirical sign of intelligent design, namely: functionally specific, complex organisation and associated information [[FSCO/I] .

But, but, but . . . isn’t “natural selection” precisely NOT a chance based process, so doesn’t the ability to reproduce in environments and adapt to new niches then dominate the population make nonsense of such a calculation?

NO.

Why is that?

Because of the actual claimed source of variation (which is often masked by the emphasis on “selection”) and the scope of innovations required to originate functionally effective body plans, as opposed to varying same — starting with the very first one, i.e. Origin of Life, OOL.

But that’s Hoyle’s fallacy!

Advice: when you go up against a Nobel-equivalent prize-holder, whose field requires expertise in mathematics and thermodynamics, one would be well advised to examine carefully the underpinnings of what is being said, not just the rhetorical flourish about tornadoes in junkyards in Seattle assembling 747 Jumbo Jets.

More specifically, the key concept of Darwinian evolution [we need not detain ourselves too much on debates over mutations as the way variations manifest themselves], is that:

CHANCE VARIATION (CV) + NATURAL “SELECTION” (NS) –> DESCENT WITH (UNLIMITED) MODIFICATION (DWM), i.e. “EVOLUTION.”

CV + NS –> DWM, aka Evolution

If we look at NS, this boils down to differential reproductive success in environments leading to elimination of the relatively unfit.

That is, NS is a culling-out process, a subtract-er of information, not the claimed source of information.

That leaves only CV, i.e. blind chance, manifested in various ways. (And of course, in anticipation of some of the usual side-tracks, we must note that the Darwinian view, as modified though the genetic mutations concept and population genetics to describe how population fractions shift, is the dominant view in the field.)

There are of course some empirical cases in point, but in all these cases, what is observed is fairly minor variations within a given body plan, not the relevant issue: the spontaneous emergence of such a complex, functionally specific and tightly integrated body plan, which must be viable from the zygote on up.

To cover that gap, we have a well-known metaphorical image — an analogy, the Darwinian Tree of Life. This boils down to implying that there is a vast contiguous continent of functionally possible variations of life forms, so that we may see a smooth incremental development across that vast fitness landscape, once we had an original life form capable of self-replication.

What is the evidence for that?

Actually, nil.

The fossil record, the only direct empirical evidence of the remote past, is notoriously that of sudden appearances of novel forms, stasis (with some variability within the form obviously), and disappearance and/or continuation into the modern world.

If by contrast the tree of life framework were the observed reality, we would see a fossil record DOMINATED by transitional forms, not the few strained examples that are so often triumphalistically presented in textbooks and museums.

Similarly, it is notorious that fairly minor variations in the embryological development process are easily fatal. No surprise, if we have a highly complex, deeply interwoven interactive system, chance disturbances are overwhelmingly going to be disruptive.

Likewise, complex, functionally specific hardware is not designed and developed by small, chance based functional increments to an existing simple form.

Hoyle’s challenge of overwhelming improbability does not begin with the assembly of a Jumbo jet by chance, it begins with the assembly of say an indicating instrument on its cockpit instrument panel.

The D’Arsonval galvanometer movement commonly used in indicating instruments; an adaptation of a motor, that runs against a spiral spring (to give proportionality of deflection to input current across the magnetic field) which has an attached needle moving across a scale. Such an instrument, historically, was often adapted for measuring all sorts of quantities on a panel.

(Indeed, it would be utterly unlikely for a large box of mixed nuts and bolts, to by chance shaking, bring together matching nut and bolt and screw them together tightly; the first step to assembling the instrument by chance.)

Further to this, It would be bad enough to try to get together the text strings for a Hello World program (let’s leave off the implementing machinery and software that make it work) by chance. To then incrementally create an operating system from it, each small step along the way being functional, would be a bizarrely operationally impossible super-task.

So, the real challenge is that those who have put forth the tree of life, continent of function type approach, have got to show, empirically that their step by step path up the slopes of Mt Improbable, are empirically observable, at least in reasonable model cases. And, they need to show that in effect chance variations on a Hello World will lead, within reasonable plausibility, to such a stepwise development that transforms the Hello World into something fundamentally different.

In short, we have excellent reason to infer that — absent empirical demonstration otherwise — complex specifically functional integrated complex organisation arises in clusters that are atypical of the general run of the vastly larger set of physically possible configurations of components. And, the strongest pointer that this is plainly  so for life forms as well, is the detailed, complex, step by step information controlled nature of the processes in the cell that use information stored in DNA to make proteins.  Let’s call Wiki as a hostile witness again, courtesy two key diagrams:

I: Overview:

The step-by-step process of protein synthesis, controlled by the digital (= discrete state) information stored in DNA

II: Focusing on the Ribosome in action for protein synthesis:

The Ribosome, assembling a protein step by step based on the instructions in the mRNA “control tape” (the AA chain is then folded and put to work)

Clay animation video [added Dec 4]:

[youtube OEJ0GWAoSYY]

More detailed animation [added Dec 4]:

[vimeo 31830891]

This sort of elaborate, tightly controlled, instruction based step by step process is itself a strong sign that this sort of outcome is unlikely by chance variations.

(And, attempts to deny the obvious, that we are looking at digital information at work in algorithmic, step by step processes, is itself a sign that there is a controlling a priori at work that must lock out the very evidence before our eyes to succeed. The above is not intended to persuade such, they are plainly not open to evidence, so we can only note how their position reduces to patent absurdity in the face of evidence and move on.)

But, isn’t the insertion of a dummy variable S into the Chi_500 metric little more than question-begging?

Again, NO.

Let us consider a simple form of the per-aspect explanatory filter approach:

The per aspect design inference explanatory filter

 

You will observe two key decision nodes,  where the first default is that the aspect of the object, phenomenon or process being studied, is rooted in a natural, lawlike regularity that under similar conditions will produce similar outcomes, i.e there is a reliable law of nature at work, leading to low contingency of outcomes.  A dropped, heavy object near earth’s surface will reliably fall at g initial acceleration, 9.8 m/s2.  That lawlike behaviour with low contingency can be empirically investigated and would eliminate design as a reasonable explanation.

Second, we see some situations where there is a high degree of contingency of possible outcomes under initial circumstances.  This is the more interesting case, and in our experience has two candidate mechanisms: chance, or choice. The default for S under these circumstances, is 0. That is, the presumption is that chance is an adequate explanation, unless there is a good — empirical and/or analytical — reason to think otherwise.  In short, on investigation of the dynamics of volcanoes and our experience with them, rooted in direct observations, the complexity of a Mt Pinatubo is explained partly on natural laws and chance variations, there is no need to infer to choice to explain its structure.

But, if the observed configurations of highly contingent elements were from a narrow and atypical zone T not credibly reachable based on the search resources available, then we would be objectively warranted to infer to choice. For instance, a chance based text string of length equal to this post, would  overwhelmingly be gibberish, so we are entitled to note the functional specificity at work in the post, and assign S = 1 here.

So, the dummy variable S is not a matter of question-begging, never mind the usual dismissive talking points.

I is of course an information measure based on standard approaches, through the sort of probabilistic calculations Hartley and Shannon used, or by a direct observation of the state-structure of a system [e.g. on/off switches naturally encode one bit each].

And, where an entity is not a direct information storing object, we may reduce it to a mesh of nodes and arcs, then investigate how much variation can be allowed and still retain adequate function, i.e. a key and lock can be reduced to a bit measure of implied information, and a sculpture like at Mt Rushmore can similarly be analysed, given the specificity of portraiture.

The 500 is a threshold, related to the limits of the search resources of our solar system, and if we want more, we can easily move up to the 1,000 bit threshold for our observed cosmos.

On needle in a haystack grounds, or monkeys strumming at the keyboards grounds, if we are dealing with functionally specific, complex information beyond these thresholds, the best explanation for seeing such is design.

And, that is abundantly verified by the contents of say the Library of Congress (26 million works) or the Internet, or the product across time of the Computer programming industry.

But, what about Genetic Algorithms etc, don’t they prove that such FSCI can come about by cumulative progress based on trial and error rewarded by success?

Not really.

As a rule, such are about generalised hill-climbing within islands of function characterised by intelligently designed fitness functions with well-behaved trends and controlled variation within equally intelligently designed search algorithms. They start within a target Zone T, by design, and proceed to adapt incrementally based on built in designed algorithms.

If such a GA were to emerge from a Hello World by incremental chance variations that worked as programs in their own right every step of the way, that would be a different story, but for excellent reason we can safely include GAs in the set of cases where FSCI comes about by choice, not chance.

So, we can see what the Chi_500 expression means, and how it is a reasonable and empirically supported tool for measuring complex specified information, especially where the specification is functionally based.

And, we can see the basis for what it is doing, and why one is justified to use it, despite many commonly encountered objections. END

________

F/N, Jan 22: In response to a renewed controversy tangential to another blog thread, I have redirected discussion here. As a point of reference for background information, I append a clip from the thread:

. . . [If you wish to find] basic background on info theory and similar background from serious sources, then go to the linked thread . . . And BTW, Shannon’s original 1948 paper is still a good early stop-off on this. I just did a web search and see it is surprisingly hard to get a good simple free online 101 on info theory for the non mathematically sophisticated; to my astonishment the section A of my always linked note clipped from above is by comparison a fairly useful first intro. I like this intro at the next level here, this is similar, this is nice and short while introducing notation, this is a short book in effect, this is a longer one, and I suggest the Marks lecture on evo informatics here as a useful contextualisation. Qualitative outline here. I note as well Perry Marshall’s related exchange here, to save going over long since adequately answered talking points, such as asserting that DNA in the context of genes is not coded information expressed in a string of 4-state per position G/C/A/T monomers. The one good thing is, I found the Jaynes 1957 paper online, now added to my vault, no cloud without a silver lining.

If you are genuinely puzzled on practical heuristics, I suggest a look at the geoglyphs example already linked. This genetic discussion may help on the basic ideas, but of course the issues Durston et al raised in 2007 are not delved on.

(I must note that an industry-full of complex praxis is going to be hard to reduce to an in a nutshell. However, we are quite familiar with information at work, and how we routinely measure it as in say the familiar: “this Word file is 235 k bytes.” That such a file is exceedingly functionally specific can be seen by the experiment of opening one up in an inspection package that will access raw text symbols for the file. A lot of it will look like repetitive nonsense, but if you clip off such, sometimes just one header character, the file will be corrupted and will not open as a Word file. When we have a great many parts that must be right and in the right pattern for something to work in a given context like this, we are dealing with functionally specific, complex organisation and associated information, FSCO/I for short.

The point of the main post above is that once we have this, and are past 500 bits or 1000 bits, it is not credible that such can arise by blind chance and mechanical necessity. But of course, intelligence routinely produces such, like comments in this thread. Objectors can answer all of this quite simply, by producing a case where such chance and necessity — without intelligent action by the back door — produces such FSCO/I. If they could do this, the heart would be cut out of design theory. But, year after year, thread after thread, here and elsewhere, this simple challenge is not being met. Borel, as discussed above, points out the basic reason why.

Comments
eigenstate: I disagree with you (and with Elizabeth). I am sure I will not convince you, but I have the duty to answer you anyway. First of all, however, you must be consistent with what you say, and admit, if you want, when you have said a wrong thing. So, I am afraid I have to start with one thing where you are obviously wrong, and you have not admitted it. The lottery example. I wrote: "Let’s go to your examples of the lottery and the deck of cards. The example of the lottery is simply stupid (please, don’t take offense). The reason is the following: in a lottery, a certain number of tickets is printed, let’s say 10000, and one of them is extracted. The “probability” of a ticket winning the lottery is 1: it is a necessity relationship. But a protein og, say, 120 AAs, has a search space of 20^120 sequences. To think that all the “tickets” have been printed would be the same as saying that those 20^120 sequences have been really generated, and one of them is selected (wins the lottery). But, as that number is by far greater than the number of atoms in the universe (and of many other things), that means that we have a scenario where 10000 tickets are printed, each with a rnadom numbet between 1 and 20^120, and one random number between 1 and 20^120 is extracted. How probable is then that someone “wins the lottery”?" It seems clear, isn't it? The lottery example is wrong and stupid. To this, exactly to this, you answer: No one I’ve ever read on this supposes that all the possible permutations have been generated, nor that they need be generated for the theory to hold. Note the phase space for for the double deck of 104 cards – there are 10^166 possible sequences there, more combinations than you amino acid sequences. Now, that's obviously not fair. You are evading my comment. You are not discussing at all the lottery example, and shifting to the deck of cards. But my comment on the deck of cards were not those you quoted. So, please, answer my comment on the lottery example, ot just admit that uou were wring in making that argument. That would be the only fair behaviour possible. Now, let's go on, in order.
It’s the “conscious observer to recognize it and define it” part that is the big problem, here. The reaction acceleration is not a problem — I have no issues with identifying such a reaction as an objectively observable physical process. But the metric fails to be an objective metric if it depends on “conscious recognition”. If you think about why “conscious recognition” is required here by you, it should be evident that such “non-algorithmic steps” are needed because it defies objective formalization. Or to put a more fine point on it, it enables us to put our own subjective spin on it, and not just as a qualitative assessment around the edges, but as a central predicate for the numbers you may apply. That;’s why I say this is question-begging in its essence; unless one BEGINS with prior recognition (“conscious observer” recognizing function), the metric doesn’t get off the ground. If you BEGIN with such conscious recognition, the game’s over, and FSCI, or whatever acronym you want to use to apply to this idea, won’t tell you anything you haven’t already previously concluded about the designedness (or not) of any given phenomenon.
I would say this is your main argument. Probably the only argument. And it is completely wrong. First of all, you (and Elizabeth) are still not understanding my definition of dFSCI and my procedure. You still equivocate its nature, its purpose, and its power. dFSCI is an empirical concept. The resoning goes this way, in order a) We look at things that we know are designed (directly, because we have evidence of the desogn process). And we look for sone formal property that can help us infer design when we have not that direct evidence. b) We define dFSCI as such a property. c) We verify that on all sets of objects of which we know if they were designed or not (human artifacts, or certainly non designed objects) the evaluation of dFSCI give no false positive, although it gives a lot of false negatives. d) Having verified the empirical utility of dFSCI, we apply it to object whose origin is controversial (biological information). The point is, it is not important how we define dFSCI: the important thing is that it works. There are conceptual reasons why we define dFSCI as we do, but in the end they would beof no value it dFSCI did not work. It does work, and we can verify that on all the onbjects for which we have a reasonable certainty that they were designed or not. So, again, it is an empirical procedure. And it works. You say: The reaction acceleration is not a problem — I have no issues with identifying such a reaction as an objectively observable physical process. But the metric fails to be an objective metric if it depends on “conscious recognition”. I am happy that the reaction acceleration is not a problem for you. So, we need conscious recognition to find something that is an objective physical process. Why? It is very simple. All science is based on consscious recognition of objective physical processes. Who do you think recognized gravity, and found the laws that explained what he had recognized? An algorithmic process? Have you ever heard of Newton? Who recognized relativity? Have you problems with the theory because a conscious being was the originator of it? Would you refuse to do experiments about gravity because the definition of gravity required a conscious observer to be given? This kind of reasoning is absolute nonsense, and it is really sad for me that intelligent persons like you and Elizabet go on defending nonsense. However, sad or not sad, I go on. The role of the conscious observer is very simple: there is a protein that has an objective function, but that function can only be described by a cosncious observer. Why? Because only conscious observers recognize and define function. An algorithm can perfectly recognize some specific function, aftfer a conscious observer has programmed, dorectly or indirectly, the properties of that particular function in the algorithm. But not before. You yourself say: "If you think about why “conscious recognition” is required here by you, it should be evident that such “non-algorithmic steps” are needed because it defies objective formalization." That's it. That's exactly my point. "Function", as you say, "defies objective formalization". It's perfectly true. Function is related to the conscious experience of puprose, and all conscious experience in essence "defy objective formalization". That's exactly the point I have discussed many times with Elizabeth, and that she vehemently denies. And so? What shall we do? We build our science suppressing the concept of function, because it "defies objective formalization"? We build our science suppressing the concept of "meanign", because it "defies objective formalization"? We build our sceince suppressing the concept of "objective formalization", because it "defies objective formalization"? How do you define "formalization" without the concepts of meaning, of cause and effect, and many others, that require a cosncious being to be understood? Absolute nonsense! if the function is objectivelt definable, as you admit, and objectively measurable, as you admit, that's it. The fact that it has been recognized and defined by a conscious observer has no importance, because it works, and the property that depends on that function, its inherent complexity, is there for us to measure, and that measure is an empirical marker of design. Would you say that I cannot diagnose a leukemia by looking at a bone marrow smear and seeing that it is made of blasts, just because I am a conscious being, and I am not giving an algorithmic formalization of what a blast is? If my diagnoses are always right, that just means that I know how to recognize a blast. Or to put a more fine point on it, it enables us to put our own subjective spin on it, and not just as a qualitative assessment around the edges, but as a central predicate for the numbers you may apply. That's not true. Once we define a function, the definition is objective, and the measurement of dFSCI is objective. Of what "subjective spin" are you speaking? The choice of the function to define? But, as I have alredy dais, we can define any function we want: the meausrement of dFSCI will be for that function, and the methodological use of that measurement will be only in relation to that function, as I have shown commenting your deck of card example. That;’s why I say this is question-begging in its essence; unless one BEGINS with prior recognition (“conscious observer” recognizing function), the metric doesn’t get off the ground. Again nonsense. The metric is a metric applied to a function. Why should it "get off the ground", if we don't say in advance to which function we are applying it? I think you are really violating the essential fundaments of reasoning here. If you BEGIN with such conscious recognition, the game’s over, and FSCI, or whatever acronym you want to use to apply to this idea, won’t tell you anything you haven’t already previously concluded about the designedness (or not) of any given phenomenon. Again, completely wrong. You are equating "recognizing a function" with "affirming that that function is designed". That's completely wrong, and if you don't understand that, you will never understand dfSCI or ID. Let's try this way. A random mutation in a protein (certainly a random event) can confer a new function. It is rare, it is usually true only in very special circumstances, but it is true. Let's take the classicla example of S hemoglibin and malaria resistance. The idea is, although S hemoglobin is a disease, it gives some protection form malaria. We can certainly define that as a function, recognizing it, even if we are conscious observers! So, we have a function that has been generated by a random system (random single point mutations), and than partially selected through NS. OK? As you can see, I am recognizing a function, defining it, and still in no way I am assuming that it is designed. The point is: is that function complex? And the answer is: no, its complexity is just 4.3 bits. So, while I have recognized and defined a function, I have no reason to infer design from it. Therefore, all your reasoning about "question-begging" is nonsense: it is wrong, makes wrong interpretations of what I have very clearly stated, and means nothing. Well, I will go on in next post.gpuccio
January 22, 2012
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And just to get things back on track: I too am interested in seeing a clear operational definition for either gpuccio's or kairosfocus's metric, i.e. one that does not rely for one of its terms on some subjective evaluation of designed-lookingness. There may well have been one posted, but I haven't seen it. All the ones I have seen have white spaces in them, as it were. We are all programmers here, I think (in some sense or other). So we know that if you are going to code somethign you need an actual parameter or variable to put into our functions, not a string :) I think we can all agree that "Looks designed" is a string.Elizabeth Liddle
January 22, 2012
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oops, messed out the tags, though. Original is here.Elizabeth Liddle
January 22, 2012
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Eigenstate wrote:
@gpuccio, That’s the basic point. You are wrong here. Defining explicitly a function that can be objectively neasured does generate a functional subset in the set of possible outcomes. As the function objectively exists, you cannot say that we have invented if “post hoc”. I will refer to the function of an enzyme that amazingly accelerates a biochemical reaction, that otherwise could never happen or would be extremely slow. That function is objective. We need a conscious observer to recognize it and define it (because the concept itself of function is a cosncious concept). So, I am not saying that there is not a subjective aspect in the function. There is, always. What I am saying is that the function, once recognized and defined consciously, can be objectively observed and measured ny any conscious observer, for instance in a lab. It’s the “conscious observer to recognize it and define it” part that is the big problem, here. The reaction acceleration is not a problem — I have no issues with identifying such a reaction as an objectively observable physical process. But the metric fails to be an objective metric if it depends on “conscious recognition”. If you think about why “conscious recognition” is required here by you, it should be evident that such “non-algorithmic steps” are needed because it defies objective formalization. Or to put a more fine point on it, it enables us to put our own subjective spin on it, and not just as a qualitative assessment around the edges, but as a central predicate for the numbers you may apply. That;’s why I say this is question-begging in its essence; unless one BEGINS with prior recognition (“conscious observer” recognizing function), the metric doesn’t get off the ground. If you BEGIN with such conscious recognition, the game’s over, and FSCI, or whatever acronym you want to use to apply to this idea, won’t tell you anything you haven’t already previously concluded about the designedness (or not) of any given phenomenon. So, I can compute the probability of such a sequence, with such a property, emerging in a purely random system. There is no such thing as a “purely random system”. “System” implies structure, constraint, rule, and process. But that’s not just being pedantic on casual speaking on your part, it’s the core problem here. The AA sequence is not thought to be emergent in a random way. There’s a fundamental difference between one-time “tornado in a junkyard” sampling of a large symbol set from a huge phase space, and the progressive sampling of that same large symbol set as the result of a cumulative iteration that incorporates positive and negative feedback loops in its iteration. So the probability of the sequence is NOT a matter of 1 shot out of n where n is vast. If, in my card deck example, we keep after each shuffle, the highest two cards we find out of the 104 (per poker rules, say), and set them aside as “fixed” and continue to shuffle the remaining cards, and repeat, we very quickly arrive at very powerful and rare (versus the 104 card phase space) deck after just a few iterations. That’s brutally quick as an “iterative cycle”, but it should convey the point, and the problem with “tornado in a junkyard” type probability assignments. Let’s go to your examples of the lottery and the deck of cards. The example of the lottery is simply stupid (please, don’t take offense). The reason is the following: in a lottery, a certain number of tickets is printed, let’s say 10000, and one of them is extracted. The “probability” of a ticket winning the lottery is 1: it is a necessity relationship. But a protein og, say, 120 AAs, has a search space of 20^120 sequences. To think that all the “tickets” have been printed would be the same as saying that those 20^120 sequences have been really generated, and one of them is selected (wins the lottery). But, as that number is by far greater than the number of atoms in the universe (and of many other things), that means that we have a scenario where 10000 tickets are printed, each with a rnadom numbet between 1 and 20^120, and one random number between 1 and 20^120 is extracted. How probable is then that someone “wins the lottery”? No one I’ve ever read on this supposes that all the possible permutations have been generated, nor that they need be generated for the theory to hold. Note the phase space for for the double deck of 104 cards – there are 10^166 possible sequences there, more combinations than you amino acid sequences. The question is not a math question, wondering how likely 1 chance in 20^120 is, that’s evident in the expression of the question. The question is the “recipe” for coming to an AA sequence that achieves something we deem “functional”. If you have a a cumulative filter at work – environmental conditions which narrow the practical combinations in favorable ways, stereochemical affinities that “unflatten” the phase space so that some permutations are orders of magnitude more likely to occur, including permutations that contribute to the functional configuration we are looking at, then the “1 in 20^120? concern just doesn’t apply. It’s not an actual dynamic in the physical environment if that’s the case. Or, cumulative iterative processes with feedback loops completely change probability calculations. That is why scientists laugh at the absurd suggestion that these processes are like expecting a tornado in a junkyard to produce a 747. Your “100000 in 20^120? depends on this same kind of simplistic view of the physical dynamic. So, I will simply state that your sequence has no dFSCI, because it is not functionally specified, and that therefore we cannot infer design for it. You say: Is it SPECIFIC? Yes, it is a single, discrete configuration out of a phase space of 104! = 10^166 available configurations. This configuration is as constricted as the choices get. Well, specific does not mean functionally specified. Each sequence is specific. If used as a pre-specification, each sequence is a good specification. But that has nothing to do with functional specification, that can be used “post hoc”. This is, again, where the question-begging obtains. If you are going to assert that it is only “functionally specified” if it’s the product of intelligent choices or a will toward some conscious goal, then (d)FSCI *is* a ruse as a metric, not a metric toward investigating design, but a means of attaching post-hoc numbers to a pre-determined design verdict. Which just demands a formalism around “functionally specific”? That seems to be the key to what you are saying. Can you point me to some symbolic calculus that will provide some objective measurement of a candidate phenomenon’s “functional specifity”? If you cannot, and I think you cannot, else you’d have provided that in lieu of the requirement of a conscious observer who “recognizes” functional specificity, then I think my case is made that you are simply begging the question of design in all of this, and (d)FSCI is irrelevant to the question, and only a means for discussing what you’ve already determined to be designed by other (intuitive) means. That is not a functional specification. Or, if it is, is a very wide one. I will be more clear. According to my definition od dFSCI, the first step is that a conscious observer must recognize and define a function in the digital sequence, and specify a way to objectively measure it. Any function will do, because dFSCI will be measured for thet function. IOWs, dFSCI is the complexity necessary to implement the function, not the complexity of the object. That is a very important point. This renders dFSCI completely impotent on the question of design, then! That requirement — that a “conscious observer must recognize and define a function in the digital sequence” — you’ve already past the point where dFSCI is possibly useful for investigation. Never mind that the requirement is a non-starter from a methodological standpoint – “recognize” and “defined” and “function” are not objectively defined here (consider what you’d have to do to define “function” in formal terms that could be algorithmically evaluated!), even if that were not a problem, it’s too late. dFSCI, per what you are saying here, cannot be anything more than a semi-technical framework for discussing already-determined design decisions. And even then, you have a “Sophie’s Choice” so to speak in terms of how you define “function”. Either you make it general and consistent, in which case it doesn’t rule out natural, impersonal design processes (i.e. mechanisms materialist theories support), or you define ‘functional’ in a subjective and self-serving way, gerrymandering the term in such a way as to admit those patterns that you suppose (for other reasons) are intelligently design, and to exclude those (for other reasons) which you suppose are not. So, trying to interpret your thought, I could define the following fucntions for your sequence: a) Any sequence of that length that can be statistically analyzed b) (I don’t know, you say: I don’t understand well your second point) c) Any sequence of that length that can be good for encrypting data. While I wait for a clarification about b) (or for other possible definitions of function for your sequence), I will notice that both a) and c) have practically no dFSCI, because any sequence would satisfy a) (the functional space is the same as the search space, and the probability is 1), ans all random sequences, for all I know of crypting data, would satisfy c) at least as well as your sequence (the functional space is almost as big as the search space, the probability is almost one). I hope that is clear. I think you are close to getting my point. A random sequence is highly function, just as a random sequence. It’s as information rich as a sequence can be, by definition of “random” and “information”, which means, for any function which requires information density — encryption security, say — any random string of significant length is highly functional, optimally functional. If my goal is to secure access to my account and my password is limited to 32 characters, a random string I generate for the full 32 characters is the most the most efficient design possible. Sometimes the the design goal IS random or stochastic input. Not just for unguessability but for creativity. I feed randomized data sets into my genetic algorithms and neural networks because that is the best intelligent design for the system — that is what yields the optimal creativity and diversity in navigating a search landscape. Anything I would provide as “hand made coaching” is sub-optimal as an input for such a system; if I’m going to “hand craft” inputs, I’m better off matching that with hand-crafted processes that share some knowledge of the non-random aspects of that input. When you say “That is not a functional specification. Or, if it is, is a very wide one.” I think that signals the core problem. It’s only a “wide” specification as a matter of special pleading. It’s not “wide” in an algorithmic, objective way. If you think it is, I’d be interested to see the algorithm that supports that conclusion. Which is just to say you are, in my view, smuggling external (and spurious) design criteria into your view of “function” here. This explains why you do not offer an algorithm for determining function — not measuring it but IDENTIFYING it. If you were to try to do so, to add some rigor to the concept, I believe you would have to confront the arbitrary measures you deploy and require for (d)FSCI. If I’m wrong, providing that algorithm would be a big breakthrough for ID, and science in general.
And I think he nails it, gpuccio. I await your response (and/or kf's) with interest :DElizabeth Liddle
January 22, 2012
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KF:
Pardon, but why do you find it so hard to see that the claimed “source” of novel bio-info, “natural selection,” is an obvious misnomer?
I don't think that selection is the "source" of the information, I think selection is what transfers information from the fitness function to the genome. As Dembski puts it in LIFE'S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information:
His [Kenneth Miller's] claim that the information comes from the selective process is then correct but, in context, misleading. Miller suggests that [Schneider’s simulation] ev, and evolution in general, outputs more information than it inputs. In fact, selective processes input as much information from the start as they output at the end. In Schneider’s ev, for instance, the selective process inputted prior information in the form of a precisely specified error-counting function that served as a fitness measure.[reference 45] Thus, instead of producing information in the sense of generating it from scratch, evolutionary processes produce it in the much weaker sense of merely shuffling around preexisting information.
While this is only true for some measures of information (gripe: people in these discussions often seem to assume there's one true definition of information; they are utterly wrong), I think it's the most useful way to view what's going on here. (BTW, while I basically agree with the Dembski in the section quoted above, I disagree with his assumption that "active information" in the fitness function must itself come from intelligent sources.) Note that, while you and Dembski are both working toward the same conclusion, your arguments for that conclusion clearly conflict with each other: KF: Selection cannot add information to the gene pool. Dembski: Selection can add information to the gene pool, but only the information it gets from the fitness function. KF:
And, pardon, that is why your incremental variation on a file example also fails. The selector is looking at variations that come from something else, and it is that something else that faces the config space challenge.
No, it clearly doesn't face the config space challenge. After an hour (assuming a 64-character alphabet), you'll have an average of 56.25 characters (=337.5 bits) of fully prespecified information. After two hours, 112.5 characters (=675 bits). After an 8-hour shift, 450 characters (=2,700 bits). After a full 40-hours work week, 2,250 characters (=13,500 bits). That's a huge config space, but a reasonable period of time (long enough to go out of your mind with boredom, but still...). KF:
Again, variation within islands of function do not explain arrival at such islands. Where, once we face complex, integrated function, the credible default is that we are looking at islands of function based on complex integration of matched parts.
I think this may hint at the root of our disagreement here: you seem to be thinking that selection only takes place within well-defined "islands of function". In the first place, this is a result of an assumption about the shape of the fitness function, not (as you have stated it) an intrinsic limitation of selection. If this assumption is wrong, and the fitness function isn't just flat outside the islands, then this certainly will affect the probability of reaching an island. Second, even if the fitness function is completely flat outside of these islands of function, selection may still affect the probabilities if the islands tend to clump together -- in archipelagos of function, if I may extend the metaphor. I would argue that the existence of gene families (where the family members have different functions) at least suggests that this is the case. Islands in archipelagos are much more likely to be found than isolated islands because: 1: The probability of stumbling across some island increases proportional to the number of islands in the archipelago (and note that an archipelago may contain far more islands than we know about). 2: Once one of the islands is found, selection for it means that it tends to act as a starting point for mutational excursions, increasing the chance that more islands in the group will be found. Gauger and Axe's The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway is the obvious reference here; I don't want to get distracted by discussing its merits and limitations (not my field of expertise), but just note that their estimate of the time required to evolve a new family member is far far far less than it would've been (using similar assumptions) to evolve a new enzyme from scratch. Again, the point is that you cannot legitimately dismiss the effect of selection. Worse, in order to properly take selection into account, you need to know a lot more than we actually do about the large-scale shape of the fitness function. KF:
You will notice, for instance, that you have implicitly assumed that tiny initial steps will provide relevant function. But in fact, you need to account for a metabolic, self-replicating entity that uses coded representations to carry out both processes, as the OP documents, and as the successor post further discusses here. Without that metabolic-self-replicating entity, you do not have minimal relevant function.
There are a number of different "problems" to be solved, with different constraints; I think it's best to be as clear as possible about what we're discussing at any given point. Here are some that come to mind (in roughly decreasing order of "difficulty"): 1: The origin of the first self-replicating organism. 2: The origin of completely new genes (i.e. finding the first island in an archipelago). 3: The origin of gene variants with new functions (i.e. new islands in a "discovered" archipelago). 4: Optimizing an existing function of a gene. You seem to agree that RM+NS can achieve #4. I don't claim I can prove that RM+NS can achieve #2 and #3, but I don't see a solid argument that can't (and if you want to make that argument, you must take NS into account). RM+NS clearly cannot achieve #1 because they only take place after replication get going; but I don't see solid argument that other natural (unintelligent) processes cannot achieve this. ________________ GD, kindly see the OP. If you want more on origin of life cf here, and more on origin of body plans, cf here. The islands of function issue is discussed here, kindly note that incremental changes within the sea of non-function cannot have a differential reproductive success, as 0 - 0 = 0, so we are back to blind chance variation in a vast config space. (That is, once we splash into non-function, there is no fitness gradient to guide variation, Darwinian style evo may explain niches based on adaptation of a body plan, but it does not explain origin of body plans, starting with the first ones, moving on to the Cambrian revolution, and in a world where the fossil record is dominated by "sudden" appearance, stasis and disappearance.) KF, Jan 22. Gordon Davisson
December 1, 2011
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KF, Excellent. I am famous at last :)Eugene S
December 1, 2011
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ES: I see you caught me before I caught myself! I have now put up the post here at UD, thanks very much. KF PS: Pardon some oddities of format, Blogger and WordPress do not work together very well. I actually ended up doing something so rough and ready as inserting breaks to get some of the worst parts!kairosfocus
December 1, 2011
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The above links to the Russian text. The English version is here. Cheers. ThanksEugene S
December 1, 2011
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My pleasure.Eugene S
December 1, 2011
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ES: Excellent! Folks, here [oops, here] is Dr ES's pro-con summary on ID, in English and Russian. (He was kind enough to do an English version.) GEM of TKIkairosfocus
December 1, 2011
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KF, I have done what you requested. Please see my blog (the most recent post). Thanks for expressing your interest in my thoughts and as I said in the comments on my blog, I think this OP of yours is really great.Eugene S
December 1, 2011
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GD: Pardon, but why do you find it so hard to see that the claimed "source" of novel bio-info, "natural selection," is an obvious misnomer? The source of the info has to be the variation, the culler-out, quite plainly subtracts from what has to already be there, variation:
Chance Variation --> Varieties; differential success --> subtraction of "less fit" varieties; surviving varieties --> establishment of new sub populations in niches
And so, the underlying issue is that you have to search a space to first get to complex integrated function -- which points to islands of function -- and then you have to face the implications of large config spaces and limited resources, such that 500 - 1,000 bits swamps the capacity of our solar system or observed cosmos. And, pardon, that is why your incremental variation on a file example also fails. The selector is looking at variations that come from something else, and it is that something else that faces the config space challenge. Again, variation within islands of function do not explain arrival at such islands. Where, once we face complex, integrated function, the credible default is that we are looking at islands of function based on complex integration of matched parts. You will notice, for instance, that you have implicitly assumed that tiny initial steps will provide relevant function. But in fact, you need to account for a metabolic, self-replicating entity that uses coded representations to carry out both processes, as the OP documents, and as the successor post further discusses here. Without that metabolic-self-replicating entity, you do not have minimal relevant function. And the evidence of living organisms, the only observational anchor point we have, points to 100,000+ bits as the minimum for that. This takes us well beyond the observed cosmos search threshold. Not to mention, that we empirically and analytically know just one competent cause of such symbolically coded complex algorithmic functionality: intelligent design. So, we are well warranted to infer that the origin of such entities is designed. And, when we see the further jump in specifically functional complexity to account for major body plans, 10 - 100+ millions of bits, we are looking at the same as the best empirically warranted explanation for the novel body plans that must unfold from the Zygote or equivalent. Within body plans yes, incremental variations (usually quite limited) do crate varieties that fit niches, we see that with dogs and red deer or cichlids, or people etc. But we must not fall into a category confusion between adaptations of a body plan and the origin of same, starting with the first one, OOL. Nor should we allow our attention to be misdirected, nor should we permit censorship under teh ideological domination of a priori materialism to distort our ability to see what is going on. GEM of TKIkairosfocus
December 1, 2011
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I'm not saying "don’t look at the wizard behind the curtain, please"; I'm saying "look closely at what the wizard is doing -- he's adding information by selecting among random variants". While selection is in some senses a purely eliminative process, that doesn't mean it's eliminative in all senses. Let me give you an even simpler scenario to (hopefully) make this point clear. Consider a computer program I call the worlds worst word processor (WWWP): * it starts with an empty file * once a second, it adds a random character (letter, digit, etc) to the end of the file * at any time, the user may press the Delete key, which removes the last letter from the file * the user cannot do anything else Since the user cannot add anything to the file, only delete, it seems obvious that the user cannot add information to the file. But in fact the user can add whatever information they want: the user decides what they want to write, and anytime the program adds a character that doesn't match what they want, just press delete. When the program happens to add the "right" character, they don't press delete and the character remains in the file. Obviously, it takes a while to write anything, but not on the scale of the history of the universe. Say you have a 64-character alphabet; that means that on average it'll progress a little slower than one ("right") character per minute. A 100-character message would take almost 2 hours. But that 100-character message contains 600 bits of information, completely specified in advance by the user; that's well past all the usual probability bounds. The point here is that you cannot legitimately dismiss the effect of selection. As someone recently said, it is utterly revealing, to see how consistently hard it is for this to be seen and acknowledged. (BTW, I don't want to distract from this point, but I can't resist making the paradoxical nature of WWWP even more explicit by asking exactly when the amount of information in the file increases: When the random generator adds a character? When the generator happens to add a "right" character? When the user deletes a "wrong" character? When the user doesn't delete a "right" character (even though this is not an action but an inaction, and it doesn't change the file's contents in any way)? The answer will depend on exactly how you define and measure information, but for any sane definition at least one of these steps must add information, even though it may seem intuitively obvious that none of them do.)Gordon Davisson
November 30, 2011
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GD: Let us begin with a clip from Wiki on GA's, per the principle of testimony against known interest:
In a genetic algorithm, a population of strings (called chromosomes or the genotype of the genome), which encode candidate solutions (called individuals, creatures, or phenotypes) to an optimization problem, evolves toward better solutions. Traditionally, solutions are represented in binary as strings of 0s and 1s, but other encodings are also possible. [--> the strings map to degrees of performance within a zone of function] The evolution usually starts from a population of randomly generated individuals and happens in generations. In each generation, the fitness of every individual in the population is evaluated [--> per algorithmic procedures] , multiple individuals are stochastically selected from the current population (based on their fitness), and modified (recombined and possibly randomly mutated) to form a new population. The new population is then used in the next iteration of the algorithm. Commonly, the algorithm terminates when either a maximum number of generations has been produced, or a satisfactory fitness level has been reached for the population.
GA's, in short, work based on strictly limited variations WITHIN an island of function -- how else will they be able to see that the "genome" string of a particular case corresponds to a certain degree of function in a zone of functionality? Certainly, the GA and fitness function and string plus the various tuned parameters and subroutines to manipulate it do not write themselves somehow out of lucky noise then proceed to effect a wonderful uphill process to peaks of functionality. As in, don't look at the wizard behind the curtain, please. Sorry. That is, GA's are based on intelligently designed software that acts in a zone of function to find PEAKS of function, or on the dual to that, minima of cost, where the cost is some undesirable aspect of performance. In short, GA's begin within target zones in a much wider config space for bit strings of length equal to that of he overall program, so they are able to make incremental uphill progress based on built in intelligently designed procedures and an equally intelligently designed fitness function, so called -- a map of how to move uphill. In that environment, one may indeed examine a narrow ring of randomly sampled neighbouring points, and generally speaking, trust the uphill trend, culling out what points downhill. Notice, again, the selection process ELIMINATES variation per algorithmic constraint, it does not add it, that is, again, selection is NOT the source of novel information or variety. It is utterly revealing, to see how consistently hard it is for this to be seen and acknowledged. GEM of TKI PS: More details here.kairosfocus
November 29, 2011
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If we look at NS, this boils down to differential reproductive success in environments leading to elimination of the relatively unfit. That is, NS is a culling-out process, a subtract-er of information, not the claimed source of information. That leaves only CV, i.e. blind chance, manifested in various ways.
If this were true, genetic algorithms could not possibly work. The standard ID explanation for the success of GAs is that information must be "smuggled in" via the fitness function. But the only way that information could move from the fitness function to the genome is by selection. If your reasoning were right, this could not happen; it does happen, therefore there's something wrong with your reasoning. (BTW, later in the essay, you said that GAs "start within a target Zone T, by design, and proceed to adapt incrementally based on built in designed algorithms." First, they generally don't start in the target zone (the entire point of a GA is to solve some problem; if you have to start with an existing solution, the GA is rather pointless). Second, at least in a pure GA, the "built in designed algorithms" are designed to simulate random variation and [artificial] selection.)Gordon Davisson
November 28, 2011
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The above word chemistry exercise shows the limited range of possibilities one can achieve with only simple successive modifications. And, as Kairos points out, this is with very short strings. There's another way to look at this. It involves foresight. An organism that appears accidentally has no particular reason to continue to reproduce for indefinite number of generations. Similarly, a designer with limited foresight might choose to create a life form that could replicate for multiple generations providing utility for the lifespan of the designer. The vast separation between proteins ensures that successive slight variations will not succeed in climbing the so-called Mt. Improbable. A designer who desires the design to endure for ages could choose these vast separations to enforce stasis. To me, this latter pattern fits the life we see better than the model of accidental emergence. The evidence is in the design for endurance.dgw
November 27, 2011
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Kairos, Thanks for your good thoughts. Two things about the Dawkins approach to "weasel" differ from the random typing of letters and searching to see what matches Shakespeare. Dawkins does an incremental search for closeness to his end excerpt. He knows what the specific goal is at the end. On the other hand, random typing of letters is followed by a final search for a phrase from Shakespeare. Also, intermediate results in Dawkins search are not necessarily valid words. They would be rejected by error correction. Your point about how short the strings are in the word chemistry example I pose is a good one. The one-letter distance between word changes significantly constrains the words that can be formed. It's also interesting to observe that complex words do not morph into other complex words without going through a simple intermediates. One can construct ever more complex sets of rules to build new word sets (and permit greater Hamming distances). However, at some point, the complexity of the rules will exceed the complexity of the words. One can attempt the same exercise with sentences or paragraphs. It turns out it is fairly straightforward to negate a sentence by word insertion, but changing its meaning becomes very difficult with only simple moves. Paragraphs are particularly problematic because of the built in redundancy. It's possible to insert a sentence with general background, but changing the meaning of the paragraph incrementally requires careful surgery, and as one might expect, deletions are easier than insertions. Adding information in context is harder work than removing content while preserving a grammatically correct sentence or phrase.dgw
November 27, 2011
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F/N: I have added, in the OP, a diagram (courtesy Wikipedia, public domain) of a D'Arsonval galvanometer movement, and a caption. I have also given additional links on the tree of life and OOL.kairosfocus
November 27, 2011
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PPS: A Jamaican peasant proverb is a suitable appendix: fire de pon mus mus tail, but him think seh a cool breeze deh deh. (Translated: the complacent mouse has a fire burning at its tail, but in its folly and delusion, it imagines that it is a cool breeze blowing on it.)kairosfocus
November 27, 2011
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PS: Solomon: The laughter of fools is as the crackling of thorns under a pot. (And, think about why thorn branches crackle under the pot, and what it means for their future . . . )kairosfocus
November 27, 2011
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DGW, First, of course, Dawkins' pre-loaded target phrase in Weasel, came from Shakespeare! In TBW, as previously linked, this is what Dawkins said:
I don't know who it was first pointed out that, given enough time, a monkey bashing away at random on a typewriter could produce all the works of Shakespeare. The operative phrase is, of course, given enough time. [NB: cf. Wikipedia on the Infinite Monkeys theorem here, to see how unfortunately misleading this example is.] Let us limit the task facing our monkey somewhat. Suppose that he has to produce, not the complete works of Shakespeare but just the short sentence 'Methinks it is like a weasel', and we shall make it relatively easy by giving him a typewriter with a restricted keyboard, one with just the 26 (capital) letters, and a space bar. How long will he take to write this one little sentence? . . . . It . . . begins by choosing a random sequence of 28 letters ... it duplicates it repeatedly, but with a certain chance of random error – 'mutation' – in the copying. The computer examines the mutant nonsense phrases, the 'progeny' of the original phrase, and chooses the one which, however slightly, most resembles the target phrase, METHINKS IT IS LIKE A WEASEL . . . . What matters is the difference between the time taken by cumulative selection, and the time which the same computer, working flat out at the same rate, would take to reach the target phrase if it were forced to use the other procedure of single-step selection: about a million million million million million years. This is more than a million million million times as long as the universe has so far existed . . . . Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective 'breeding', the mutant 'progeny' phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution. [notice the underlying attitudes and dismissiveness] In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success. [[TBW, Ch 3, as cited by Wikipedia, various emphases, highlights and parentheses added.]
In short, Weasel is much as I summarised earlier, according to Dawkins, its author. Similarly, your chaining rules constitute intelligent constraint, implicitly moving towards a target. Where in fact the D/RNA chain uses a generic coupler along the chain, so that there is no serious sequence constraint -- that is how it can store information. Also, in the tRNA, the AA-carrier coupler is a CCA sequence that ties to the COOH end of the AA, another generic coupler. Indeed it is the loading enzyme that specifies what AA gets tied to what tRNA with what anticodon sequence, and this has been manipulated experimentally in recent days, to create novel protein chains under intelligent control. Similarly, the protein chain is based on a similar generic coupler, and so sequences of AA's are informationally constrained at the assembly point in the Ribosome, using codon- anticodon key-lock fitting and advance to the next triplet; they are not pre-programmed based on mechanical forces. It is after the AA sequence has been formed through step by step instructions that it is folded (often with help of chaperones) and may agglomerate and be subject to activation. It is that folded, agglomerated, activated form that is used in the cell, based on key-lock fitting of parts. Next, observe how short the strings you are discussing are? That defines a scope of config space that is such that the Hamming-type distance between functional sequences in the config space is low. The problem with life systems is the components are exceedingly complex -- 300 AA is a typical "average" protein length -- and so we are looking at deeply isolated isloands of funciton int eh realistically scaled spaces. In addition, starting with the prelife situation, the issue of L/R hand mixes -- thermodynamically equivalent, geometric mirror images [where geometry is important], handedness of life molecules [L proteins, R for nucleotides], and the existence of many more active cross-interfering species, in a context where the protein chains of life are energetically unfavourable [notice the ubiquity of the energy battery molecule, ATP, and the complex specificity of the ATP Synthetase "factory" molecule] all point to insuperable challenges to get to cell based life. At least, without pretty knowledgeable and skilled intelligent direction. Within such life, the focus of the OP has been on the challenge of finding functional clusters in the space of possibilities. And, for that, GP has given us a fairly sobering assessment of what we can realistically expect to see in life forms. And that is before we look at the issue of the evident use of digital (yes, discrete state MEANS digital] information to control the chemistry, as can be seen for protein synthesis. GEM of TKIkairosfocus
November 27, 2011
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Continuing this bit of whimsy. Indigo, violet, and purple appear to be too complex to be constructed using the simple rules of adhesion, substitution, and insertion we have devised for our "word chemistry". Do we need a more complicated set of rules? Are there other colors that can be reached? pink = red to fed to fen to fan to pan to pin to pink (bypassing ran) black = red to fed to fen to fan to ran. ran+k = rank, rank to rink to link. b+link = blink. blink to blank to black. brown = red to rod to row. b+row = brow, brow+n = brown. tan = red to fed to fen to fan to tan gray = red to bed to bad to bay to ray. g+ray = gray white = red to rid to bid to bin to win. win+e = wine, wine to whine by insertion, whine to white by substitution.dgw
November 26, 2011
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In the above comment, the pathway from "red" to "orange" passed an anchor word "ran". The path from "red" to "ran" followed the sequence--red to fed to fen to fan to ran. Another sequence exists: red to bed to bad to ban to ran. Continuing from above, is it possible to change colors from yellow to green? Again it turns out to be easier to start with red: red becomes reed by insertion. g+reed = greed. Greed becomes green by substitution. Next is blue: Blue's path goes from red through ran. Then, ran becomes pan by substitution, s+pan = span, span becomes spam becomes slam becomes slum becomes glum becomes glue becomes glue, all by substitution.dgw
November 26, 2011
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This is all purely whimsical, but the analogy between language and genetic code, provides for some interesting thought experiments. Can "word drift" enable an organism to change color. Let's suppose an organism finds the word "red" in it's genetic code and therefore produces a "red" body color. (This is of course fanciful.) If there were two sites with the word "red", then one could be used to encode the body color, and the other might be free to "drift". However, we constrain drifting to be within the bounds of the dictionary so that error detecting codes will not excise the changed text. (One could also look at how error correcting codes could change the errored word into a correct word, but a different one.) If "red" can drift through a sequence of valid words until it reaches "orange", then once again it could be used to encode body color. So, is there a path of valid words between red and orange that achieves the above objective? Try this: red becomes fed becomes fen becomes fan becomes ran by substitution. ran+g = rang, rang+e = range, o+range = orange. This path is reversible. Can orange become yellow in the same way? Here's a path. Is there a shorter one? It requires a new rule: Rule 3: Insertion. A letter can be inserted into a word to make a new word. bred + a inserted between e and d = bread. It turns out it is easier to go from red to yellow then from orange to yellow. The path from orange to yellow leads through "ran". Red becomes fed becomes fen becomes fan becomes ran becomes becomes rat becomes rot becomes lot by substitution; a+lot = alot. By insertion, alot + l = allot. Allot becomes allow by substitution, f+allow = fallow, fallow becomes fellow becomes yellow, by substitution. It's interesting that in conceiving of a path, it's easier to start from the destination than from the source to find a reasonable pathway.dgw
November 26, 2011
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As an aside, note that Shakespeare did not write his plays by selecting one letter at a time. He selected words from the common vocabulary (with a few neologisms) and assembled his text consistent with the rules of the grammar and meter. Of course Shakespeare knew when to break the rules for maximum effect, a computer code would follow the rules exactly.dgw
November 26, 2011
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The above "word chemistry" concept may need some refinement. Can a set of rules be devised to generate a sufficient set of valid English words to use in generating Shakespeare. Let's use the now infamous "Methinks it is like a weasel." Rule 1. Adhesion. Individual letters stick together to form words. "i" + "s" = "is." If "is" is floating in the soup, then "h" could attach to form "his", "t" could attach to form "this", etc. Words can adhere to form larger compound words: heart + felt = heartfelt Rule 2. Substitution. Individual letters can replace letters in a word. From the above, "his", can become "has", or "hip" if an "a" or a "p" is encountered. OK. Let's try (out of order). "a" Trivial Check i + t = "it" Check i + s = "is" Check Path to "like": i+s = is, h+is = his, substitute "d" for "s" to become hid, hid+e = hide, substitute "k" for d to form "hike", substitute "l" for "h" to obtain "like". How probable is this path, I wonder? (Note: Word-frequency tables using this method of generating words won't match word-frequency tables of Shakespeare.) Check. Path to "weasel": a+t = at, b+at=bat, bat+s = bats, bats becomes bass and then base by substitution, base becomes ease by substitution, ease+l = easel, w+easel = weasel. Check. (Paths are not unique. What is probability of each step? Is it easier to form a word from the bottom up or by changing existing words?) Path to "methinks": Me+thinks = Methinks. m+e = me, i+s=is, h+is = his, t+his = this. This becomes thin by substitution, thin+k = think, think+s = thinks. Check. I wonder if there any "irreducibly complex" words that cannot be formed with a simple set of rules?dgw
November 26, 2011
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Thanks kairos. My recollection of Dawkins's weasel is a bit different. In the case of Shakesepare, the "monkeys" type sequences of letters, and there is a "Shakespeare" filter at the end. It's that which survives. Dawkins, if I remember correctly searched for random letters and when the correct letter was found in the correct position, it was retained. His was a search for a weasel not a segment of Elizabethan drama. An interesting aside to this discussion is whether or not there is a better way to build up sequences of Shakespeare (or other works of great literature). One could imagine a soup of random letters. When "i" and "s" approach each other, they stick together to form an English word. Words precipitate to the bottom of the soup and can be filtered out. Then, Shakespeare might be constructed from random selections of English words rather than random collection of letters. If the rules of this "chemistry" are natural language rules (corrected for the time period), then perhaps this process might be more successful at generating Shakespeare. This thought experiment is ignoring the Bottom-up vs. top-down view of the world. Monkeys or random number generators might produce Shakespeare, but they would have know way of recognizing it.dgw
November 26, 2011
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Joe: Thanks for sharing your thoughts. I do note, I am precisely not doing probability calcs, but identifying when sample sizes are so small relative to spaces that we have no right to expect to observe unusual, atypical outcomes. This, BTW, is exactly how the very common practice of Hypothesis testing by seeing if one is in a far skirt vs a bulk of a distribution works. GEM of TKIkairosfocus
November 26, 2011
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I am with "Programming Of Life" author Dr Johnson on this one- you cannot climb Mt Improbable until you can show it exists. He said that you cannot calculate the probabilty of something you cannot show is even feasible. "They" will always laugh at posts like this because "they" say "here we are so the probabilty is moot", obviously not understanding we are trying to determine HOW we came to be here, or "you cannot calculate the probability because you do not know the formula, ie you are doing it wrong", yet they don't know the formula and and "they" don't have any idea what is right. The point being is probability calculations actually give "them" the benefit of the doubt and "they" cannot even understand that.Joe
November 26, 2011
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DGW: Interesting comment. Actually, ASCII codes are plainly in use, as we see upper and lower case letters, numerals, etc. So, we can see up to about 25 letters, or 128^25 ~ 4.8 * 10^52 possibilities is a successfully searchable config space. This is in the ballpark of Borel's earlier estimates. The threshold in view starts -- for our solar system -- at 3 * 10^150, about 72 ASCII characters. For the cosmos we observe, 1,000 bits weighs in at 3 * 10^301, or about 143 ASCII characters. The monkeys are about 1 in 10^100 of the sort of spaces that need to be searched. And REAL monkeys just made several pages of mostly S's. There is a "monkeys are writing Shakespeare" exercise out there, but on closer inspection the reason we are getting Shakespeare out is because someone first put Shakespeare in. If you doubt me, observe:
Instead of having real monkeys typing on keyboards, I have virtual, computerized monkeys that output random gibberish. This is supposed to mimic a monkey randomly mashing the keys on a keyboard. The computer program I wrote compares that monkey’s gibberish to every work of Shakespeare to see if it actually matches a small portion of what Shakespeare wrote. If it does match, the portion of gibberish that matched Shakespeare is marked with green in the images below to show it was found by a monkey. The table below shows the exact number of characters and percentage the monkeys have found in Shakespeare. The parts of Shakespeare that have not been found are colored white. This process is repeated over and over until the monkeys have created every work of Shakespeare through random gibberish.
For that, the minimum number of keystrokes to get the works is 27 plus the numbers -- light up all cases if a key is pressed. Bottomline: SISO, Shakespeare in, Shakespeare out. Just as Mr Dawkins did with the notorious Weasel. GEM of TKIkairosfocus
November 26, 2011
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