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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
I don't know, Joe. Have you reason, and data or evidence, that cause you to believe that the processes of duplication and modification were anything but stochastic?Bydand
January 30, 2012
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For clarity GAs are a good model for intelligent design evolution and even front-loaded evolution. But they mean nothing to stochastic evolution.Joe
January 30, 2012
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OK, so for clarity, that means that GA's are a good model for evolution? - (leaving aside for just one second the question of whether or not there is/was an intelligent designer - I mean the actual operation of a GA once in place)Bydand
January 30, 2012
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Yes, it depends on the characteristics used. No, not all sets of items possess characteristics that can be used to place them in a rigorously nested, deep, hierarchy. Living things do, as noted by Linnaeus.
Linneaus did not posit his nested hierarchy on descent with modification and he used it as evidence for a common design. Evos hijacked his idea, changed archetype with common ancestor, and called it their own.
Your second sentence is just wrong. Check out any paper on cladistics. In fact there are even online programs where you can run the algorithms yourself.
As for cladistics, again clades are constructed based on shared similarities, meaning they are constructed based on the rules of a nested hierarchy. The from that ancestral relationships are assumed. Also a clade is only a nested hierarchy in that all descendents of a common ancestor will consist of and contain all of its defining characteristics but it isn't a nested hierarchy in that the common ancestor does not consist of nor contain its decendents. But we know characteristics can be lost so there is no reason to assume all descendents will have them.Joe
January 30, 2012
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No. NS is a necessity process, that intervenes on and is modulated by random processes.
But this is where I think you are going wrong! As I have said, I think it is spurious to make the distinction between "random" processes and "necessity" processes. If you are defining "random" as "a system whose behaviour can best be described by some probability distribution", then both the process by which a DNA sequence in an offspring is different from those in a parent, and the process by which the possessors of one sequence tend to leave more offspring then another, are "systems whose behaviour can best be described by some probability distribution". On the other hand, if by "necssity" process, you mean one driven by, say, physical/chemical laws, then both processes are also "necessity" processes. A DNA sequence, when it duplicates itself, is exposed to chemical forces that determine just how it recombines itself into a new slighlty different sequence. Similarly, when a light moth on a dark tree is eaten by an owl, that is because of the physical processes that mean that more light is reflected from its wings than from the bark, triggering contrast neurons in the owls visual cortex. Both parts of the system are both "random" and "necessity" processes; indeed the probability distribution function that describes the behaviour of the "random" has the form it has because of various "necessity" laws. There are good physical/chemical reasons why some mutations are more likely than others, just as there are highly stochastic processes that govern whether or not a light moth happens to catch the eye of a passing owl. What IS different the two is that variance producing mechanisms have a less systematic relationship with function than "NS". Variants will tend to be, if not orthogonal to function, no more likely to be more useful than the parent sequence than less, unless the population is extremely badly adapted to start with, and may be more likely to be less than more, if the population is already well adapted. On the other hand, NS, by definition, is the process by which sequences that tend to promote better replication are themselves more often replicated - indeed that's all it means. So NS is a bias in favour of better function, whereas RV is not. In fact you could simply describe evolution as the bias by which RVs that promote better replication are filtered out from those that don't.
I have tried to make that clear in my modleing. NS is a necessity process because we can define a cause effect relationship between the variation and its consequences on reproduction. For instance, I have modeled the effect of the selection of a possible intermediate, but to do that I had to make specific assumptions on how the intermediate affected reproduction, and on how it was selected (for instance, assuming that the local function of the intermediates directly improved reproductive success, and that it could be otpimally selected. Then, once evaluated the necessity consequences of such a selected intermediate, I computed the difference in the global random system in the two different cases, with and without the contribution of the selectable intermediate. So, you see, a necessity model is always different from a random model, even if we include it in a more general model that is mainly random. The necessity model defines explicitly logic relations of cause and effect, and reasons according to those definitions. The consequences of those relations are evaluated deterministically, even if they can be modulated by other random variables.
Well, if that is what you have done, then you have made a major error (and it's the same one made by Dembski, or one of them) which is that you haven't drawn your "cause-and-effect" NS relations from a probability distribution. In fact, even at it's simplest, when you have a single sequence with a specified selection coefficient (as in highly simplistic evolutionary models), what I do, at any rate, is express that as a probability of survival given the sequence, not as: all critters with this sequence survive, all the rest die. But that's ignoring other huge sources of variance that contributes to the total pdf.
Calling all of that “stochastic” will not help, if you don’t analyze correctly the causal relations.
Indeed. But at least it allows us to pinpoint the some of those you have failed to model stochastically :)Elizabeth Liddle
January 30, 2012
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The real problem with the concept of ID is that while the effects of stochastic change are selectable, they are not predictable.Petrushka
January 30, 2012
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Eigenstate, I think you are conflating rules with laws. They are fundamentally different concepts. There's been a lot of confusion in scientific literature between the two. Citing those sources does not help solve the problem. The only way out is stop being sloppy with the definitions. Rules are imposed on top of physicality by intelligent agents. They are not changing this reality. Again, e.g. the rules of chess or badminton do not lead to any change in the physical conditions of an actual chess or badminton tournament. It is so simple, that I am sometimes puzzled as to why people do not understand such trivia. Your attempts to label this reasoning 'anthropomorphism' do not remove the problem. cheers.Eugene S
January 30, 2012
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Humans violate many rules, that other types of designers may not want to violate. And the modalities of design implementation are obviously different.
Well, since you don't have any actual sightings of the designer of life at work, you can assign any capabilities and motives you can imagine, can't you?
The similarity between human design and biological design is the design itself:
But the design itself looks exactly like descent with modification. Try introducing your immaterial cause hypothesis at a criminal trial. What's the point of hypothesizing an immaterial cause when you have an observable physical cause? The fact that the detailed history of life has been mostly erased does not support support science fiction scenarios. I know you are enamored of your virgin birth protein domains, but they really don't present a problem if you look at the math behind them.Petrushka
January 30, 2012
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Elizabeth: No. NS is a necessity process, that intervenes on and is modulated by random processes. I have tried to make that clear in my modleing. NS is a necessity process because we can define a cause effect relationship between the variation and its consequences on reproduction. For instance, I have modeled the effect of the selection of a possible intermediate, but to do that I had to make specific assumptions on how the intermediate affected reproduction, and on how it was selected (for instance, assuming that the local function of the intermediates directly improved reproductive success, and that it could be otpimally selected. Then, once evaluated the necessity consequences of such a selected intermediate, I computed the difference in the global random system in the two different cases, with and without the contribution of the selectable intermediate. So, you see, a necessity model is always different from a random model, even if we include it in a more general model that is mainly random. The necessity model defines explicitly logic relations of cause and effect, and reasons according to those definitions. The consequences of those relations are evaluated deterministically, even if they can be modulated by other random variables. Calling all of that "stochastic" will not help, if you don't analyze correctly the causal relations.gpuccio
January 30, 2012
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OK, just checking! That's fine. In which case, would you also agree that Natural Selection is a random process? (I'd use "stochastic" in both cases, for greater precision in English - it has fewer alternative meanings)Elizabeth Liddle
January 30, 2012
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Elizabeth: Not again, please. I mean what I have always meant, as you should know, always the same thing: a system whose behaviour can best be described by some probabilty distribution, and not by a necessity model.gpuccio
January 30, 2012
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Petrushka: Humans violate many rules, that other types of designers may not want to violate. And the modalities of design implementation are obviously different. Biological design is not implemented in artificail labs, like humans do, but directly in lioving things and in the living environment, and probably through a direct interaction between consciousness and matter. That creates different possibilities, and different constraints. The similarity between human design and biological design is the design itself: the input of information into matter from conscious intelligent representations. But the modalities of implementation of that information are obviously different.gpuccio
January 30, 2012
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Excuse me, in english, I believe, “random variation” means just what it means: variation caused by random events.
The trouble, gpuccio, is that in English, "random" can mean a great number of different things. What do you mean by it, in this context?Elizabeth Liddle
January 30, 2012
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Just about anything can be put into a nested hierarchy- it all depends on the criteria used. Descent with modification does not lead to a nested hierarchy based on characteristics as one would expect a blending of characteristics with dwm and nestred hierarchies do not allow for that.
Yes, it depends on the characteristics used. No, not all sets of items possess characteristics that can be used to place them in a rigorously nested, deep, hierarchy. Living things do, as noted by Linnaeus. Designed things don't. Features of designed things, not surprisingly, are constantly being transferred by designers from one design lineage to another. Which is why even cheap makes of car now have features developed in expensive lineages. Your second sentence is just wrong. Check out any paper on cladistics. In fact there are even online programs where you can run the algorithms yourself.Elizabeth Liddle
January 30, 2012
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eigenstate: I don't know if you are really interested in a serious discussion (champignon evidently is not). If you are, I invite you too to read my posts here: https://uncommondescent.com/intelligent-design/evolutionist-youre-misrepresenting-natural-selection/ (post 34 and following) and comment on them, instead of just saying things that have no meaning. You say: Once you understand this, that gpuccio isn’t even addressing evolutionary processes at all, that his metric neither addresses nor even attempts to consider evolutionary processes, but only looks at what he call “RV”, dFSCI can be apprehended for what it is and where it fits in the discussion (if anywhere). ‘RV’ was a stumbling point for me, because that expands to “Randome Variation” in my mind, where variation implies *iteration* as in evolutionary processes of inheritance with variation across reproductions. For gpuccio (and I understand English may not be his first/primary language, and I certainly couldn’t converse in his native language at this level if the tables were turned!), “RV” is really “Random Combination” or “Random Shuffling”. That is both wrong and unfair. I have addressed evolutionary processes in great detail. Read and comment, if you like. And yes, english is not my primary language at all, but I don't believe there is any mystery or misunderstanding in the way I use RV. It measn random variation, exactly as you thought. But I really don't u8nderstand what you mean when you say, in what I hope is your prmary language, that: "variation implies *iteration* as in evolutionary processes of inheritance with variation across reproductions.". Excuse me, in english, I believe, "random variation" means just what it means: variation caused by random events. In biology, the meaning of random variation is very clear: any variation in gene sequence that is cause by ranodm events. I prefer the term to "random mutation" because RM could be identified only with single nucleotide mutations, while RV clearly ecompasses all the random mechanisms of sequence variation, including indels, chromosome rearrangeements, shuffling, and anything else. The only mechanism not included in RV is NS. As you can verify if you read my posts, I have modeled both RV (Using the concept of dFSCI and NS. Whatever you folks may like to repeat, dFSCI is very useful in modeling the neo darwinian algorithm. So, if you want to discuss, then please address my real points. Otherwise, go on with your unilateral expressions. You are in good company.gpuccio
January 30, 2012
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champignon: I have abswered your "arguments". You go on repeating the same things, without adding anything, and wothout addressing any of my points. I have invited you to comment about my detailed modeling of RV and NS. You haven't. I have nothing more to say to you. I wish you good luck.gpuccio
January 30, 2012
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At the risk of being repetitive - then again, what is not getting repeated? For the sake of argument I'm setting aside the numerous contradictions in such hierarchies. Let's just say that all living things fit neatly into nested hierarchies. It's absurd to cite the hierarchies as evidence while ignoring that pretty much every single life form that makes them up defies explanation by any of the mechanisms cited as the reasons why they are arrangeable in hierarchies. Put another way, darwinian mechanisms predict a hierarchy. They do not predict avian lungs, bats, insect metamorphosis, human intelligence, or really anything else placed in those hierarchies. So merely pointing out that there are nested hierarchies is cherry-picking for confirming evidence. Everything that tells you what you want to hear is confirmation. The contradictory evidence is just a temporary uncertainty, a gap. You've already decided what must fill it, so the contradictions can be safely ignored, and you can assume that whatever fills them will meet your expectations.ScottAndrews2
January 30, 2012
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Just about anything can be put into a nested hierarchy- it all depends on the criteria used. Descent with modification does not lead to a nested hierarchy based on characteristics as one would expect a blending of characteristics with dwm and nestred hierarchies do not allow for that.Joe
January 30, 2012
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Comparative genomics as well as comparative anatomy can be used as evidence for a common design, which is something we observe and have experience with. What we need is some way to take fish, for example, perform some targeted mutagenesis on fish embryos, and get them to start developing tetrapod characteristics until they eventually become tetrapods- studying the mutation- phenotypic effect relationship(s) along the way. And if we cannot perform such a test then what good is the claim of universal common descent seeing it would not have any practical application at all? Might as well be philosophy...Joe
January 30, 2012
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We also have direct evidence that designers do not create nested hierarchies. ID advocates love to cite humans as creators of dFSCI, but they are reluctant to acknowledge that humans routinely violate the rules of descent with modification. Not just in the creation of mechanical devices. When humans engage in genetic engineering they tend to copy entire genes across phyla, even across kingdoms. We have evidence of horizontal gene transfer in nature, but we do not have evidence of the kind of manipulations done by human agriculture and by people engaged in medical research. We have, for example, evidence that viruses can insert genes into the human genome, but we see no natural occurrence of human genes, like insulin, inserted into bacteria. This "backwards" transfer would cause one to suspect design. Particularly if it violated Darwin's rule of thumb, that evolution would be violated by a characteristic in one species that only benefits another species. Moving right along, there are potential kinds of forensic evidence that would support design. Our successors or descendants will be able to look at the evidence and see where we have tampered with genomes in our engineering efforts.Petrushka
January 30, 2012
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It all about gaps, isn't it? Darwin asserted common descent and predicted gap fillers before there were any hominid fossils, before there were any whale fossils, before there were any fossils blending the characteristics of birds and reptiles. He even asserted that evolution could occur at different rates at different times and places, anticipating punk eek. (The evidence for smooth evolution is much better at the molecular level than at the level of bone length. Small changes in regulatory sequences can make dramatic differences in the size and shape of animals, as can be seen in dogs.) Now we can do comparative genomics as well as comparative anatomy, and we can create and test gap fillers at the molecular level. You cannot "prove" history. You can only say, as police detectives do, that this hypothesis requires that certain things had to have been possible. Each time you find one of those required things, you support the hypothesis. Jury trials do not provide logical proof that a particular hypothesis is correct. They just look at evidence and decide if a conclusion is sufficiently warranted to deprive a person of life or freedom. Juries routinely do this with far less evidence than we have for evolution. Evidence gets erased over time. You will never find the videotape of evolution. You will never find a fossil for every species that ever lived. We can't even find fossil evidence for passenger pigeons.Petrushka
January 30, 2012
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Petrushka, One has only to search this very page to find your references to Thornton 'doing research' on the subject. To paraphrase gpuccio, that's great that he's doing research. What has he found? I understand that when your conclusion is assumed, any research in the area looks like progress. If Thornton had found evidence that distinct proteins or any other such functionality were connectable by an evolutionary search, that would not be "interesting." It would be the one of the most significant discoveries in biology, ever. The hardest part would be announcing it without anyone noticing that the ship had already sailed decades ago without anyone bothering to wait for such evidence. How do you "prove" what everyone says they already know?ScottAndrews2
January 30, 2012
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That's why direct evidence of connectability is so interesting. Such as Thornton's.Petrushka
January 30, 2012
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Champignon,
If the functional space is connected and all life is related by descent, then we should see a single nested hierarchy.
Chas was clear that the evidence for evolution (descent) is not evidence of any particular mechanism at work. You appear to be saying the opposite. A nested hierarchy can be used as evidence of descent. (I'm not addressing at this point how well this particular hierarchy does so.) It is not evidence that the various items in the hierarchy are connectable by any particular mechanism such as variation and selection or gene duplication with variation. The capacity of those mechanisms to connect items in the hierarchy (or whether they are so connectable - same question, different words) requires its own evidence. You cannot smuggle it in with nested hierarchies. Determining that B descended from A does not indicate how or why the variations between A and B came about. It does not follow that any given mechanism must have been the cause. You're trying to sneak in a conclusion where it isn't warranted or even supported while ignoring evidence to the contrary.ScottAndrews2
January 30, 2012
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Btdand: blockquote>I also fail to see why, once there is a system of replication with variation, some random event process such as gene duplication followed by mutation can’t result in a new function – thereby incrementing the repertoire of functions in that genome. I believe such things have been documented. How was it determined that a gene arose via stochastic processes, was duplicated and modified via stochastic processes? You need that first.Joe
January 30, 2012
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Yes, biological evolution by design.Joe
January 30, 2012
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So GA's are easily implemented; can be used to vary, search, select, and improve; and they are not explicitly required to produce useful results. A bit like biological evolution, then?Bydand
January 30, 2012
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kairosfocus attempts to defend gpuccio:
Again, it has long since been pointed out that the differential reproductive success leading to culling out of less successful variants SUBTRACTS information in the Darwinian algorithm, it does not ADD it... What adds information, if any, is the chance variation.
Which is quite sufficient. Suppose a particular allele has become fixed in a population. There is a random gene duplication followed by random variation of one of the copies. The variation confers a selective advantage and becomes fixed by selection. You now have a net increase in the information contained in the genome (which is why Upright Biped and nullasalus were afraid of answering Nick Matzke's question about gene duplication in another thread). Variation plus selection together have increased the information content of the genome. Since gpuccio freely acknowledges that this happens, I'm not sure why you are arguing otherwise in his defense.
Of course there is a long debate on how we can assume a continent of function across the domain of the tree of life, but in fact there is little or no actual empirical support for that. The debate boils down to the advocates of darwinian macro evo want there to be such, assume life forms MUST have arisen by that sort of thing and demand the default.
Evolutionary biologists don't claim "continents" of function. They just claim that the functional space is connected. The evidence for that is massive:
1. If the functional space is connected and all life is related by descent, then we should see a single nested hierarchy. 2. Analysis of the evidence confirms this to an astounding degree of accuracy: the monophyly of life has been confirmed to better than one part in 10 to the 2680th power; the nested hierarchy of the 30 major taxa has been confirmed to better than 1 in a trillion trillion trillion trillion. 3. Design does not predict a nested hierarchy.
To argue that for disconnected "functional islands", you would have to argue that
1. The islands are far enough apart that evolution can't jump the gaps, but close enough together that a nested hierarchy is still produced. 2. The designer avoids the trillions of ways of designing life that would not produce a nested hierarchy, and insists on designing in a way that produces a nested hierarchy and is therefore indistinguishable from evolution.
If you want to make those ridiculous claims, be my guest.
He is then entirely in order to draw the inductive inference that such dFSCI is an empirically reliable sign of design as cause.
dFSCI would support such a conclusion only if you could show that dFSCI cannot be produced by evolution. Even gpuccio acknowledges that dFSCI does not take evolution into account:
As repeatedly said, I use dFSCI only to model the probabilitites of getting a result in a purely random way, and for nothing else. All the rest is considered in its own context, and separately.
champignon
January 30, 2012
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Hi eigenstate, I wrote: "Petrushka, have you ever tried to convert your genetic algorithm into another type of algorithm/heuristic?" You responded,
Some types of GAs produce algorithms and finite automata directly; that is what the “animals” are, in some GA implementations. Tierra, for example, works at the instruction level for a virtual machine. That means that what gets created are “programs”, discrete configurations of instructions that consume memory resources and CPU cycles. In those kinds of implementations, such GAs are a kind of “mother of all algorithm generator”.
(I'll assume that you didn't intend to answer my question, but just used it as a springboard for providing your own thoughts on the efficacy of GAs.) Let's be clear that GAs usually make use of heuristic variations that are rewarded by a fitness assessment, in accordance with desired outcomes. This is intelligent variation merged with intelligent selection. Genetic algorithms map inputs to outputs by way of intelligent selection and variation acting upon probabilistic necessity. They are a special case if iterative improvement, and are desirable for their simplicity. But citing a genetic algorithm as a demonstration of what "evolution" can accomplish is begging the question.
But even so, we are optimizing in those cases a design we’d never have come up with on our (human) own. The brute force got us very close to something we can make good use of, and we take that innovation and “put the frosting on”.
It's unclear what sort of "innovation" you're referring to, and whether you're crediting the GA with innovation or optimization, and whether the "frosting" is optimization or innovation. It wouldn't surprise me if you credit a GA with innovation, and human intelligence with the frosting, especially considering I take the exact opposite view. Consider a GA intended to optimize a shovel, perhaps the head or even the handle. Now it's quite possible that a shovel could be optimized by a GA, as well as by other methods. But the GA will only produce shovels, it will not innovate an excavator -- EVER -- or any other type of unexpected, configurationally unrelated device. It will output variations which are explicitly dependent on a priori established parameters. The very reason a GA works is because it can be programmed to take shortcuts corresponding to specific functional requirements, not because it magically traverses vast expanses of unexpected configuration spaces, to produce novel, never-before expected results. The output is a direct, necessity-driven result dependent upon variation parameters and initial state.
That produces a different kind of asset. It’s GA-generated, for the most part, but human tweaked to form a kind of functional hybrid.
"GA-generated" implies a novelty otherwise completely unknowable from the beginning. Computation saves us time, it doesn't do its own innovating. Algorithms and heuristics, along with the computers which run them, automating the finding of solutions in a defined space, GA or not, are examples of artifice. Computers are glorified calculators. They do exactly what they're told. Their tasks can all be carried out, step by step, directly by a human being, although it's computationally impractical to do so. We employ algorithms, "genetic" or otherwise, to automate with speed, by making use of computers, a marvel of human design, engineered for the very purpose of automating intelligent tasks at a clip. I wrote, "Do you think it’s possible to construct a heuristic that can generate comparable output with higher efficiency?" You replied,
Depends on what you mean by efficiency.
I'll take that as a "yes." I'm happy to stick with time complexity, f(x) = O(g(x)), as the fundamental measure of an algorithm's efficiency (perhaps with some consideration given to memory footprint).
There is a profound insight into the aphorism “nature is the most clever designer”. Natural process are unthinkably slow, and terrifyingly expensive in terms of resources consumed, but because they are not human, and not bound to human limitations of patience, persistent and creativity, they are demonstrably more efficient than human designs because they are immensely scalable.
This is begging the question. The question is whether natural processes, independent of the clockwork mechanics of living systems, can produce the systems under consideration. Ascribing the integrated sophistication and operation of a DNA-based self-replicator to material processes -- to "evolution" -- is begging the question, if by "evolution," we mean, "what living systems can do." There is no theory which can even hope to span the gap at this point, from physicochemical interactions in matter, to living systems. I'm reserving the right to remain unimpressed with a putative force, defined as "evolution," which presupposes the system it attempts to explain.
If you intend “shortest route in time and resources to a workable solution”, for many targets, humans are more efficient, and by many orders of magnitude. Humans a “forward looking” simulation capability that can accomplish not just a couple, but many integrated steps that are staggeringly difficult to arrive at in an incremental, stochastically-driven search.
Humans are more efficient at certain things, simply because humans can solve difficult problems, such as path finding, by way of conscious intelligence (itself a seemingly intractable phenomenon). Where these abilities are amenable to quantification or modeling, they can be converted to heuristics or algorithms, and optimized by taking advantage of sophisticated calculators (computers). GAs produce novel solutions, much the same as hammers and nails produce structures. A GA is a hammer; it can do nothing on its own, but relies on the skill of the builder.
So humans are much more efficient in one class of solution finding. And they are absolutely pathetic compared to impersonal, mindless, incremental processes that don’t care about anything at all, and thus will embarrass humans when it comes to brute force methods for solutions.
Again, this is question begging. We have no empirical indication that mindless methods can do much of anything with regard to innovating the staggering sophistication present in living systems, even in deep time. Also, computation doesn't embarrass humans -- it's an edifice of human intelligence, even if the computation includes exploring pre-defined spaces by generating pseudo-random variations of the initial product, for the purposes of optimization. Remove intelligent variation and selection from a GA, and what's left is a true brute force search, truly random and utterly inept at traversing any but trivial spaces.
For that class of solutions, humans are useless, and brute force, scalable methods (like evolution) are vastly more efficient in creating effective and durable designs.
I'm not sure which class of solutions you refer to, for which humans understand nothing of the solution space or the problem being modeled.
This is one reasons why ID strikes so many scientists as a conceit. Once you understand the tradeoffs, what impersonal, brute force search processes are really good at and what human schemes are good at, observed biology is decidedly a “brute force” product. As glorious as humans are, it’s a folly to think that kind of intelligence can compete with the mind-numbing scale of deep-time, vast resources, and stochastic drivers that just… never… stop. If there is a feedback loop in place (which there is), humans are great at local, small, and highly creative short cuts, but are wannabes at macro-design, designs that adapt, endure, thrive over eons.
Conceit is calling a computer a natural process, then proclaiming that natural processes produce computers, without an empirically verifiable proposed mechanism. If one is going to assess the provenance of living systems by material causes, one should invoke processes extrinsic to the configuration of the system, instead of appealing to the capabilities unique and specific to the system's sophisticated construction. Deep time does not rescue intractable searches through vast combinatorial spaces. A 256 bit key lies in a space of around 1.2*10^77. In 4.6 billion years of 10^20 attempts per second, only about one out of every 8*10^39 sequences will have been tested. 256 bits is about equivalent to a 54 character alphabetic string such as this one: "abcdefghijklmnopqrstuvwxyz_abcdefghijklmnopqrstuvwxyz_" The above string will simply never be found by a blind (random) search. Nor will it likely be found by searches which make use of linguistically common features of language in their variation and selection. The above can however readily be found by a heuristic that intelligently presupposes a lexicographical sorting of sequences where 'a' < 'b' < ... < 'z' < '_'. Such is the case with any search through a space of that size. A genetic algorithm, or alternate heuristic, must be able to cull the 2^256 space to a manageable size, via initial, intelligent, parametric optimization. It's the intelligence required to establish this parametric control which should impress. I presume that not many processes modeled by a GA depend inherently on the GA itself, but rather on the heuristic/algorithmic processes of targeted variation and intelligent selection, which effectively cull the search space. I think it's generally the case that a GA is replaceable by other, more efficient and direct methods of heuristic iterative improvement. This is not to say that genetic algorithms can't be used to vary, search, and select -- and thereby improve -- only that they are not explicitly required to produce results that have concrete, real-world applications. GAs are desirable because they are simple to implement. Where computation is expensive, such as in realtime, other approaches will likely be favored. Even where GAs may be uniquely helpful, they are likely non-critical. From The Algorithm Design Manual 2nd Edition, by Steven S. Skiena, Section 7.8: Other Heuristic Search Methods, page 267,
Take Home Lesson: I have never encountered any problem where genetic algorithms seemed to me the right way to attack it. Further, I have never seen any computational results reported using genetic algorithms that have favorably impressed me. Stick to simulated annealing for your heuristic search voodoo needs. (original emphasis) © Springer-Verlag London Limited 2008
Best, m.i.material.infantacy
January 29, 2012
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That humans can design, and produce objects exhibiting very high levels of dFSCI, is a fact (not a theory).
It's neither a fact nor a theory that humans can design coding sequences for proteins or for regulatory networks without using some variety of evolution. Not has it been demonstrated that humans can design a completely novel sequence without using evolution and GAs. Not only do you have no candidate for the designer of life (except in your imagination), you have no precedent for the design of a complex biological molecule that is not derived from an existing one, with variation. Once you conceded that "intelligent" selection can assist in designing molecules and sequences, you conceded that functional space can be traversed by incremental change. The "top down" portion of your scenario simply translates to copying what is already known to work. There is no theory that assists in designing new sequences from scratch.Petrushka
January 29, 2012
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