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ID Foundations, 8: Switcheroo — the error of asserting without adequate observational evidence that the design of life (from OOL on) is achievable by small, chance- driven, success- reinforced increments of complexity leading to the iconic tree of life

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Algorithmic hill-climbing first requires a hill . .

[UD ID Founds Series, cf. Bartlett on IC]

Ever since Dawkins’ Mt Improbable analogy, a common argument of design objectors has been that such complex designs as we see in life forms can “easily” be achieved incrementally, by steps within plausible reach of chance processes, that are then stamped in by success, i.e. by hill-climbing. Success, measured by reproductive advantage and what used to be called “survival of the fittest.”

[Added, Oct 15, given a distractive strawmannisation problem in the thread of discussion:  NB: The wide context in view, plainly,  is the Dawkins Mt Improbable type hill climbing, which is broader than but related to particular algorithms that bear that label.]

Weasel’s “cumulative selection” algorithm (c. 1986/7) was the classic — and deeply flawed, even outright misleading — illustration of Dawkinsian evolutionary hill-climbing.

To stir fresh thought and break out of the all too common stale and predictable exchanges over such algorithms, let’s put on the table a key remark by Stanley and Lehman, in promoting their particular spin on evolutionary algorithms, Novelty Search:

. . . evolutionary search is usually driven by measuring how close the current candidate solution is to the objective. [ –> Metrics include ratio, interval, ordinal and nominal scales; this being at least ordinal] That measure then determines whether the candidate is rewarded (i.e. whether it will have offspring) or discarded. [ –> i.e. if further moderate variation does not improve, you have now reached the local peak after hill-climbing . . . ] In contrast, novelty search [which they propose] never measures progress at all. Rather, it simply rewards those individuals that are different.

Instead of aiming for the objective, novelty search looks for novelty; surprisingly, sometimes not looking for the goal in this way leads to finding the goal [–> notice, an admission of goal- directedness . . . ] more quickly and consistently. While it may sound strange, in some problems ignoring the goal outperforms looking for it. The reason for this phenomenon is that sometimes the intermediate steps to the goal do not resemble the goal itself. John Stuart Mill termed this source of confusion the “like-causes-like” fallacy. In such situations, rewarding resemblance to the goal does not respect the intermediate steps that lead to the goal, often causing search to fail . . . .

Although it is effective for solving some deceptive problems, novelty search is not just another approach to solving problems. A more general inspiration for novelty search is to create a better abstraction of how natural evolution discovers complexity. An ambitious goal of such research is to find an algorithm that can create an “explosion” of interesting complexity reminiscent of that found in natural evolution.

While we often assume that complexity growth in natural evolution is mostly a consequence of selection pressure from adaptive competition (i.e. the pressure for an organism to be better than its peers), biologists have shown that sometimes selection pressure can in fact inhibit innovation in evolution. Perhaps complexity in nature is not the result of optimizing fitness, but instead a byproduct of evolution’s drive to discover novel ways of life.

While their own spin is not without its particular problems in promoting their own school of thought — there is an unquestioned matter of factness about evolution doing this that is but little warranted by actual observed empirical facts at body-plan origins level, and it is by no means a given that “evolution” will reward mere novelty —  some pretty serious admissions against interest are made.

Now, since this “mysteriously” seems to be controversial in the comment thread below, courtesy Wikipedia, let us add [Sat, Oct 15] a look at a “typical” topology of a fitness landscape, noticing how there is an uphill slope all around it, i.e. we are looking at islands of function that lead uphill to local maxima by hill-climbing in the broad, Dawkinsian, cumulative steps up Mt Improbable sense:

A “typical” fitness landscape, with local maxima, saddle and uphill trends

Now, too, right from the opening remarks in the clip, Stanley and Lehman acknowledge how targetted searches dominate the evolutionary algorithm field, a point often hotly denied by advocates of GA’s as good models of how evolution is said to have happened:

. . . evolutionary search is usually driven by measuring how close the current candidate solution is to the objective. [ –> i.e. if further moderate variation does not improve, you have now reached the local peak after hill-climbing . . . ] That measure  [ –> Metrics include ratio, interval, ordinal and nominal scales; this being at least ordinal] then determines whether the candidate is rewarded (i.e. whether it will have offspring) or discarded . . . .  in some problems ignoring the goal outperforms looking for it. The reason for this phenomenon is that sometimes the intermediate steps to the goal do not resemble the goal itself. John Stuart Mill termed this source of confusion the “like-causes-like” fallacy. In such situations, rewarding resemblance to the goal does not respect the intermediate steps that lead to the goal, often causing search to fail

We should also explicitly note what should be obvious, but is obviously not to many:  nice, trend-based uphill climbing in a situation where the authors of a program have loaded in a function with trends and peaks, is built-in goal-seeking behaviour (as the first illustration above shows).

Similarly, we see how the underlying assumption of a smoothly progressive Hill- Climbing trend to the goal is highly misleading in a world where there may be irreducibly complex outcomes, where the components, separately do not move you to the target of performance, but when suitably joined together we see an emergent result not predictable from projecting trend lines. (Of course, Stanley and Lehman tiptoe quietly around explicitly naming that explosive concept. But that is exactly what is at work in the case where “intermediate steps” do not lead to a goal: it is not “steps” but components that as a core cluster must all be present and must be organised in the right pattern to work together, to have the resulting function. Even something as common as a sentence tends to exhibit this pattern, and algorithm-implementing software is a special case of that. Think about how often a single error can trigger failure.)

The incrementalist claim, then, is by no means a sure thing to be presented with the usual ever so confident, breezily assured assertions that we hear ever so often. For, the fallacy of confident manner lurks.

Secondly, let us also note how the incrementalist objection actually implies a key admission or two.

For one, we can see that apparent design is a recognised fact of the world of life, i.e. as Dawkins acknowledges in opening remarks of his The Blind Watchmaker, 1986; as, Proponentist has raised in the current Free Thinker UD thread:

Biology is the study of complicated things that give the appearance of having been designed for a purpose.

Elsewhere, in River out of Eden (1995), as Proponentist also highlights, Dawkins adds:

The illusion of purpose is so powerful that biologists themselves use the assumption of good design as a working tool.

These two remarks underscore a point objectors to design thought are often loathe to acknowledge: namely, that Design Scientist, William Dembski is fundamentally right: significant increments in functionally specific complexity beyond a threshold by blind chance and/or mechanical necessity, are so improbable as to be effectively operationally impossible on the gamut of our observed universe.

Similarly, as Proponentist goes on to ask:

How does Mr. Dawkins know that something gives the appearance of design? Can his statement be tested scientifically?

Obviously, if Mr. Dawkins is correct, then he is talking about “evidence that design can be observed in nature” . . . . You can either observe design (of some kind) or not. If you can observe it, then you already distinguish it from non-design.

This is already a key point: as a routine matter, we recognise that — on a wealth of experience and observation — complex, functionally specific arrangements of parts towards a goal, are best explained as intentionally and intelligently chosen, composed or directed. That is, as designed.

Darwin’s original sketch of his Tree of Life icon of Evolution

But, the onward Darwinist idea is that every instance of claimed design in the world of life can be reduced to a process of incremental changes that gradually accumulate from some primitive original self-replicating organism (and beyond that, original self replicating molecule or molecular cluster), through the iconic Darwinian tree of life — already, a consciously ironic switcheroo on the Biblical Tree of Life in Genesis and Revelation.

So, already, through the battling cultural icons, we know that much more than simply science is at stake here.

So also, we know to be on special guard against questionable worldview assumptions such as those promoted by Lewontin and so many others.

Now, too, Design objector Petrushka, has thrown down a rhetorical gauntlet in the current UD Freethinker thread:

One can accept the inference that a complex system didn’t arise in one step by chance without saying anything specific about its history.

The argument is about the specific history, not whether 500 or whatever bits of code arose purely by chance . . . . The word “design,” whether apparent or otherwise means nothing. It’s a smoke screen. The issue is whether known mechanisms can account for the history.

Words like “smoke screen” imply an unfortunate accusation of deception, and put a fairly stiff burden of proof on those who use them. Which — on fair comment — has not been met, and cannot be soundly met, as the accusation is simply false.

Similarly “purely by chance” is a strawman caricature.

One, that ducks the observed fact that there are exactly two observed sources of highly contingent outcomes: chance [e.g. what would happen by tossing a tray of dice] and intelligent arrangement [e.g. arranging the same tray of dice in a specific pattern]. Mechanical necessity [e.g. a dropped heavy object reliably falls at 9.8 m/s2 near earth’s surface] is not a source of high contingency. So, in the combination of blind chance and mechanical necessity, the highly contingent outcomes would be coming from the chance component.

Nevertheless, we need to show that “design” is most definitely not a meaningless or utterly confusing term, generally or in the context of the world of life.

That’s why I replied:

Design is itself a known, empirically observed, causal mechanism. Its specific methods may vary, but designs are as familiar as the composition of the above clipped sentences of ASCII text: purposeful arrangement of parts, towards a goal, and typically manifesting a coherence in light of that purpose.

The arrangement of 151 ASCII 128-state characters above as clipped [from the first part of the cite from Petrushka], is one of 1.544*10^318 possibilities for that many ASCII characters.

The Planck Time Quantum State resources of the observed universe, across its thermodynamically credible lifespan, 50 million times the time since the usual date for the big bang, could not take up as many as 1 in 10^150 of those possibilities. Translated into a one-straw sized sample, millions of cosmi comparable to the observed universe could be lurking in a haystack that big, and yet, a single cosmos full of PTQS’s sized sample would overwhelmingly be only likely to pick up a straw. (And, it takes about 10^30 PTQS’s for the fastest chemical interactions.)

It is indisputable that a coherent, contextually responsive sequence of ASCII characters in English — a definable zone of interest T, from which your case E above comes — is a tiny and unrepresentative sample of the space of possibilities for 151 ASCII characters, W.

We habitually and routinely know of just one cause that can credibly account for such a purposeful arrangement of ASCII characters in a string structure that fits into T: design. The other main known causal factors at this level — chance and/or necessity, without intelligent intervention — predictably would only throw out gibberish in creating strings of that length, even if you were to convert millions of cosmi the scope of our own observed one, into monkeys and world processors, with forests, banana plantations etc to support them.

In short, there is good reason to see that design is a true causal factor. One, rooted in intelligence and purpose, that makes purposeful arrangements of parts; which are often recognisable from the resulting functional specificity in the field of possibilities, joined to the degree of complexity involved.

As a practical matter, 500 – 1,000 bits of information-carrying capacity, is a good enough threshold for the relevant degree of complexity. Or, using the simplified chi metric at the lower end of that range:

Chi_500 = I*S – 500, in bits beyond the solar system threshold.

So, when we see the manifestation of FSCO/I, we do have a known, adequate mechanism, and ONLY one known, adequate mechanism. Design.

That is why FSCO/I is so good as an empirically detectable sign of design, even when we do not otherwise know the causal history of origin.

{Added: this can be expressed through the explanatory filter, applied per aspect of a phenomenon or process, allowing individual aspects best explained by mechanical necessity, chance and intelligence to be separated out, step by step in our analysis:

The (per aspect) Design Inference Explanatory Filter}

Do you really mean to demand of us that we believe that design by an intelligence with a purpose is not a known causal mechanism? If so, what then accounts for the PC you are using? The car you may drive, or the house or apartment etc. that you may live in?

Do you see how you have reduced your view to blatant, selectively hyperskeptical absurdity?

And, of course, the set of proteins and DNA for even the simplest living systems, is well beyond the FSCI threshold. 100,000 – 1 mn+ DNA bases is well beyond 1,000 bits of information carrying capacity.

Yes, that points to design as the best explanation of living systems in light of the known cause of FSCO/I. What’s new about that or outside the range of views of qualified and even eminent scientists across time and today?

Similarly, the incrementalist mechanism of blind chance and mechanical necessity through trial and error/success thesis has some stiff challenges to meet:

. . . the usual cases of claimed observed incremental creation of novel info beyond the FSCI threshold, as a general rule boil down to:

(a) targetted movements within an island of function, where the implicit, designed in information of a so-called fitness function of a well behaved type — trends help rather than lead to traps — is allowed to emerge step by step. (Genetic Algorithms are a classic of this.)

(b) The focus is made on a small part of the process, much like how if a monkey were to indeed type out a Shakespearean sonnet by random typing, there would now be a major search challenge to identify that this has happened, i.e. to find the case in the field of failed trials.

(c) We are discussing relatively minor adaptations of known functions, well beyond the FSCI threshold — hybridisation, or breaking down based on small mutations etc. For instance, antibiotic resistance, from a Design Theory view, must be recognised in light of the prior question: how do we get to a functioning bacterium based on coded DNA? (Somehow, the circularity of evolutionary materialism leads ever so many to fail to see that ability to adapt to niches and changes may well be a part of a robust design!)

(d) We see a gross exaggeration of the degree and kind of change involved, e.g. copying of existing info is not creation of new FSCI. A small change in a regulatory component of the genome that shifts how a gene is expressed, is a small change, not a jump in FSCI. Insertion of a viral DNA segment is creation of a copy and transfer to a new context, not innovation of information. Etc.

(e) We see circularity, e.g. the viral DNA is assumed to be of chance origin.

And so forth.

In short, some big questions were silently being begged all along in the discussions and promotions of genetic algorithms as reasonable analogies for body plan level evolution, and in the assertions that blind chance variations plus culling out of the less reproductively successful can account for complex functional organisation and associated information as we see in cell based life.

Let us therefore ask a key question about the state of actual observed evidence: has the suggested gradual emergence of life from an organic chemical stew in some warm little pond or a deep-sea volcano vent or a comet core or a moon of Jupiter, etc, been empirically warranted?

Nope, as the following recent exchange between Orgel and Shapiro will directly confirm — after eighty years of serious trying to substantiate Darwin’s warm little pond suggestion, neither the metabolism first nor the Genes/RNA first approaches work or are even promising:

[Shapiro:] RNA’s building blocks, nucleotides contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern . . . .  [[S]ome writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . .To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . .Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . .
[Orgel:] If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . .It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield . . . .  Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [[for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [[8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [[6]? . . .  Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . .  The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.  [[Emphases added.]

Of course, in the three or so years since (and despite occasional declarations to the contrary; whether in this blog or elsewhere . . . ), the case has simply not got any better. [If you doubt me, simply look for the Nobel Prize that has been awarded for the resolution of the OOL challenge in the past few years. To save time, let me give the answer: there simply is none.]

Bottomline: the proposed Darwinian Tree of Life has no tap-root.

Modern presentation of the Darwinian Tree of Life — note the origin of life bubble at its root, which shows the pivotal importance of the root, the main trunk and branches

No roots, no shoots, and no branches.

[Cont’d. on  p. 2]

Comments
Dr Liddle the molecules you speak of are set up in environments that are utterly irrelevant to biology. Indeed, they are manifestations of how self-replication -- templating actually -- is produced by careful and skilled design. GEM of TKI PS: The attempt just above to claim that the digital processing using discrete symbols in the cell is not that because it uses smart polymer chains, is inadvertently so revealing that it backfires via reductio ad absurdum. The genetic code is a code and that one has to distract from that is telling. The genetic code is plainly a code, accept that and come to terms with it. Just as with the algorithmic clockwork like assembly of body plans. Paley wins this one. kairosfocus
October 14, 2011
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Dr Liddle, I have repeatedly explained what hill climbing in the wider sense is about; I used this descriptively long before I noted on the specific set of algors called hill climbing, some of which are in fact highly relevant to GAs and evolutionary claims, just follow the link in the OP and read the part on varieties. I do not appreciate the distraction and piling on tactic. This is something that is simple and that is easy to understand. At least, until it was turned into a neat talking point to strawmannise. I am decidedly not amused. Please do better next time. GEM of TKIkairosfocus
October 14, 2011
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Dr BOT: Pardon, but there is a tone problem again, sufficiently serious that I note first of all. Please, adjust tone. On substance, the term hill climbing has a more narrow sense of a particular class of optimisation algorithms, and a broader sense that would capture algors that move uphill to a target, including by tossing our a spray of samples and moving uphill. On the expectation built into the algor that that is where the hot zones lie. This was thrashed out in gory details months ago with MG et al over Ev. Next, the issue of a narrow island of function is a direct matter of the nature of coded algorithms vs the set of possibilities for strings of digits of the same length not so constrained. If you want to see just how precise and narrow this is, why not look at the UD post today on body plan unfolding stepwise on Hox Genes and the onward article in the science daily site? notice especially these SD clips, that I will soon add to the OP:
Why don't our arms grow from the middle of our bodies? The question isn't as trivial as it appears. Vertebrae, limbs, ribs, tailbone ... in only two days, all these elements take their place in the embryo, in the right spot and with the precision of a Swiss watch. Intrigued by the extraordinary reliability of this mechanism, biologists have long wondered how it works. Now, researchers at EPFL (Ecole Polytechnique Fédérale de Lausanne) and the University of Geneva (Unige) have solved the mystery . . . . During the development of an embryo, everything happens at a specific moment. In about 48 hours, it will grow from the top to the bottom, one slice at a time -- scientists call this the embryo's segmentation. "We're made up of thirty-odd horizontal slices," explains Denis Duboule, a professor at EPFL and Unige. "These slices correspond more or less to the number of vertebrae we have." Every hour and a half, a new segment is built. The genes corresponding to the cervical vertebrae, the thoracic vertebrae, the lumbar vertebrae and the tailbone become activated at exactly the right moment one after another. "If the timing is not followed to the letter, you'll end up with ribs coming off your lumbar vertebrae," jokes Duboule. How do the genes know how to launch themselves into action in such a perfectly synchronized manner? "We assumed that the DNA played the role of a kind of clock. But we didn't understand how." . . . . Very specific genes, known as "Hox," are involved in this process. Responsible for the formation of limbs and the spinal column, they have a remarkable characteristic. "Hox genes are situated one exactly after the other on the DNA strand, in four groups. First the neck, then the thorax, then the lumbar, and so on," explains Duboule. "This unique arrangement inevitably had to play a role." The process is astonishingly simple. In the embryo's first moments, the Hox genes are dormant, packaged like a spool of wound yarn on the DNA. When the time is right, the strand begins to unwind. When the embryo begins to form the upper levels, the genes encoding the formation of cervical vertebrae come off the spool and become activated. Then it is the thoracic vertebrae's turn, and so on down to the tailbone. The DNA strand acts a bit like an old-fashioned computer punchcard, delivering specific instructions as it progressively goes through the machine. "A new gene comes out of the spool every ninety minutes, which corresponds to the time needed for a new layer of the embryo to be built," explains Duboule. "It takes two days for the strand to completely unwind; this is the same time that's needed for all the layers of the embryo to be completed." This system is the first "mechanical" clock ever discovered in genetics. And it explains why the system is so remarkably precise . . . . The process discovered at EPFL is shared by numerous living beings, from humans to some kinds of worms, from blue whales to insects. The structure of all these animals -- the distribution of their vertebrae, limbs and other appendices along their bodies -- is programmed like a sheet of player-piano music by the sequence of Hox genes along the DNA strand.
Now, compose such by chance variations and survival of the fittest. Ouch, Paley's watch is a bear to stumble over -- including his self-replicating watch. (Yup, Paley has been routinely strawmannised.) Finally, you know or should know that Lewontin documents, in a way that reflects the views of a dominant sector of the science and sci edu elites [cf. here on], the a priori materialism that has driven the demand that we see algorithmic programming like this as a product of blind chance and mechanical necessity. GEM of TKIkairosfocus
October 14, 2011
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Well, there are self-replicating peptides and self-replicating RNA molecules as well. But they are still all molecules, just as DNA is a molecule.
Ink, paper fibers, and stone don’t have minds either. You’re making an arbitrary distinction. If you know the source of the symbols, they are symbols, because symbols originate with minds. But if they look like symbols and function like symbols but you don’t know the source, then they aren’t symbols.
But symbols in Ink, paper fibers etc are read by things with minds! Indeed they are read by the same kinds of minds that assigned symbol to referent, and without a shared knowledge of the assignment, the symbol cannot be read. The analogy with the reaction between molecules completely breaks down. DNA and RNA sequences are not "read" by things with minds, and, moreover, the "reader" would be totally unable to "read" the sequence were it to be rendered in any other medium. In other words there is simply no symbolic layer in either translation or transcription processes in the cell. Argument-by-analogy is unsound anyway, but when the analogy is stretched to breaking point at the exact point that bears the weight of the argument, then it becomes seriously fallacious!Elizabeth Liddle
October 14, 2011
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Elizabeth, Are you talking about your hypothetical self-replicator again?
When it comes to a self-replicating molecule, we are not talking about some abstraction at the level of a “system”.
All the ones we know of that exist have DNA.
In contrast, a symbol transcends the material it is rendered in, because it is interpreted by a mind, and that mind doesn’t care whether the thing is printed in ink or etched in stone. A molecule has no mind.
Ink, paper fibers, and stone don't have minds either. You're making an arbitrary distinction. If you know the source of the symbols, they are symbols, because symbols originate with minds. But if they look like symbols and function like symbols but you don't know the source, then they aren't symbols. What sounds like logic often ends up as arbitrary and preferential.ScottAndrews
October 14, 2011
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kairosfocus, can we just establish one point and get it out of the way: Do you agree that evolution is not a hill-climbing algorithm?Elizabeth Liddle
October 14, 2011
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Petrushka, pardon but you are just repeating yourself in the teeth of having already being corrected. All this shows is that when targetting is implicit many people won't see it for what it is, hence the success of switcheroo. And, months ago we had to dissect Ev and the targetting for that notorious case was not even implicit, so soon as you read the details. GA's start within target zones and walk in to hot spots by using trends, while being fine tuned to do just that. GEM of TKIkairosfocus
October 14, 2011
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Scott:
Whether it’s bits and bytes or ink molecules interacting with paper fibers, everything is chemical or electrical. By your reasoning, what isn’t “chemistry?”
A thought isn't "chemistry", Scott, nor is "reading" and "speaking" and writing. Chemical interactions underlie the processes, but the symbol use, the representatations, the abstraction are only explicable at the the level of the system not at the level of specific chemical reactions. That's why we talk about "systems neuroscience" btw. When it comes to a self-replicating molecule, we are not talking about some abstraction at the level of a "system". We are talking about lock-and-key type interactions that can be perfectly well understood at the level of chemical bonds. You do not need to model the process at some higher "systems" level ot understand it, and there is no "symbolic" process going on. The clearest indication of this is that the alleged "symbols" cannot be rendered in any other material and still "represent" what it is supposed to represent. In contrast, a symbol transcends the material it is rendered in, because it is interpreted by a mind, and that mind doesn't care whether the thing is printed in ink or etched in stone. A molecule has no mind.
Apparently the only way you can reason around “representations and protocols” in biology is to negate all of them everywhere and render the very words meaningless. I call it reading, responding, and typing a post. What do you call it, “electronics?”
On the contrary, Scott, my objection to UBP's use of the word representation is that it is far too broad, and renders the word meaningless. I am aiming for a precision that I find lacking in UBP's post, a lack of precision that I think is fatal to his argument. A molecule is not a symbol.Elizabeth Liddle
October 14, 2011
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Elizabeth, Whether it's bits and bytes or ink molecules interacting with paper fibers, everything is chemical or electrical. By your reasoning, what isn't "chemistry?" Apparently the only way you can reason around "representations and protocols" in biology is to negate all of them everywhere and render the very words meaningless. I call it reading, responding, and typing a post. What do you call it, "electronics?"ScottAndrews
October 14, 2011
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a system of representations and protocols
This, as always, UBP, is question-begging. There are already in existence some self-replicating molecules. Whether you call what they do a "representation" or a "protocol" is up to you. The fact is that they do it, and what they do when they do it is called by most people "chemistry".Elizabeth Liddle
October 14, 2011
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Pardon, but have you considered the implications of starting in a narrow island of specific function in a large space of possible configurations, and then proceeding within that island by hill-climbing, and contrasted that with the claimed mechanisms of origin of life and of body plans?
No, you are not pardoned. Yes, I've considered the implications. A GA is not a hill climbing algorithm. What claimed mechanisms of OOL? Can you try and be clear about exactly what you are talking about - Evolution OR Origin of Life - they are not the same thing. Now you make a claim there - 'starting in a narrow island of specific function in a large space of possible configurations' - I agree that the space of possible configurations is large but how do you know that it is starting on a narrow island of function - by making this statement you imply that you know what the topology of the landscape for a proto-replicator is. If you do know, as you constantly imply, then publish your data because the entire field of biology would like to know!
That is why “acknowledgement” is so important, as the beginning within such an island of function in a space of vastly more configs that are non-functional is a matter of being targetted from the outset.
Another claim without evidence. And again - what acknowledgement? To me this reads like this: I have made an aeroplane Can it fly to the moon? No, it is an aeroplane. Ha! you admit then that it is not actually capable of spaceflight! No, I said it was an aero plane, I never said it was a rocket. Try and be clear about the topic being discussed: Evolution OR Origin of Life. They are not the same thing.
Hill climbing is then moving by successive increments to hot spots within the island. (Think about what proportion of strings of ASCII characters of the same length will be GA algorithms, and what fraction will be non-functional gibberish>)
Yes, but a GA is not a hill climbing algorithm - get your facts straight - and then you suddenly switch mid paragraph to talking about what fraction of possible code configurations would be a GA. Replication is what we are talking about.
In short GA’s — properly addressed — are about what is not in dispute, not even by Young Earth Creationists.
The problem is you have never properly addressed them, I'm not even sure you really understand them, if you did you wouldn't keep confusing genetic algorithms with hill climbing algorithms.
And, specifically, GA’s therefore tell us nothing about how we get to islands of function with nice trendy uphill slopes pointing the way to peaks of function.
No, they don't, as we keep saying again and again and again. How many times will we have to repeat to you - Evolution, and GA's are not ever proposed as explanations for the origin of evolution or GA's. GA's are not hill climbing algorithms - they can deal with much more rugged landscapes than hill climbing algorithms, that is why they are not called hill climbing algorithms, that is why they are called Genetic Algorithms!
So, the use of GAs and related algorithms as icons of evolution, since Dawkins’ Weasel, is yet another fundamentally misleading icon that makes unwarranted extrapolation driven by Lewontinian a priori materialism in the dominant sectors of science education, popular education and the school room.
Why do you keep on about WEASEL - it is a toy example from a pop-sci book, it is only an 'Icon' to you. If you want to talk about GA's to scientists (like me) then please referr to published science, not coffee table books because it just reinforces the already strong impression that your understanding of GA's is entirely based on pop-science and not real academic literature. Try starting with Holland's work and look at the vast body of other actual science that has been done in this area (to which Dawkins has contributed almost nothing!). What has this guy Lewontin got to do with anything (apart from feeding your paranoid conspiracy theories). GA's are based on observed phenomena - reproduction with variety leading to differential survival rates of members of a population in an environment.DrBot
October 14, 2011
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evolutionary search is usually driven by measuring how close the current candidate solution is to the objective.
Well no. Biological evolution, like the traveling salesman problem, does not have a goal or target. It has a way of comparing variants with each other, but not a way of measuring them against a goal. That is not a trivial difference. It is why the probability argument is irrelevant. There is nothing about biological evolution that knows whether it is making progress. There is nothing to calculate the probability against. The population survives or it doesn't. Populations do not see hills and do not attempt to climb them. If they happen to take a route that seems unlikely, it is only so in retrospect. It did not intend to take any particular route, and each is is likely as the next.Petrushka
October 14, 2011
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Dr BOT: Pardon, but have you considered the implications of starting in a narrow island of specific function in a large space of possible configurations, and then proceeding within that island by hill-climbing, and contrasted that with the claimed mechanisms of origin of life and of body plans? That is why "acknowledgement" is so important, as the beginning within such an island of function in a space of vastly more configs that are non-functional is a matter of being targetted from the outset. Hill climbing is then moving by successive increments to hot spots within the island. (Think about what proportion of strings of ASCII characters of the same length will be GA algorithms, and what fraction will be non-functional gibberish>) In short, GA's if they can be said to mimic anything evolutionary, mimic adaptations of an existing body plan, under actually artificial selection based on a defined trend and a well-tuned algorithm. In short GA's -- properly addressed -- are about what is not in dispute, not even by Young Earth Creationists. And, specifically, GA's therefore tell us nothing about how we get to islands of function with nice trendy uphill slopes pointing the way to peaks of function. So, the use of GAs and related algorithms as icons of evolution, since Dawkins' Weasel, is yet another fundamentally misleading icon that makes unwarranted extrapolation driven by Lewontinian a priori materialism in the dominant sectors of science education, popular education and the school room. GEM of TKIkairosfocus
October 14, 2011
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Thanks for your acknowledgement that a GA works within an island of function; which has been highlighted from the beginning of the discussion, by the design side:
Good grief KF: evolution, and GA's require systems that replicate and are therefore already have those functions - this is not an admission, this is what we have always said! I don't understand why you keep harping on about it, we have always made this crystal clear, along with the distinction between evolution and OOL, one which you insist on equivocating over.DrBot
October 14, 2011
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Petrushka, Thanks for your acknowledgement that a GA works within an island of function; which has been highlighted from the beginning of the discussion, by the design side:
It’s central to understanding that a GA requires a connected landscape in order to navigate incrementally . . .
I note that in the case cited at the head of the p. 1 of the OP, I showed how Stanley and Lehman wrote:
. . . evolutionary search is usually driven by measuring how close the current candidate solution is to the objective. That measure then determines whether the candidate is rewarded (i.e. whether it will have offspring) or discarded . . . . surprisingly, sometimes not looking for the goal in this way leads to finding the goal [--> notice, an admission of goal- directedness . . . ] more quickly and consistently. While it may sound strange, in some problems ignoring the goal outperforms looking for it. The reason for this phenomenon is that sometimes the intermediate steps to the goal do not resemble the goal itself. John Stuart Mill termed this source of confusion the “like-causes-like” fallacy. In such situations, rewarding resemblance to the goal does not respect the intermediate steps that lead to the goal, often causing search to fail . . .
In short, there are issues of following a hill climbing trend as implicit goal-seeking based on carefully selected fitness functions and search procedures, as well as the issue of needing several things to be in place at once for function to appear, i.e. an implied case of irreducible complexity. [NB: Did you cross-reference no 3 in the ID founds series (as linked in OP), on this issue, and did you read the J Bartlett paper on analysing IC on a Turing machine? Also, kindly note that the strawman fallacy of caricaturing the other party -- as you have done (how can you act as though we have not addressed the precise problem that GA's work on hill climbing requiring a continuous and well behaved zone with nice not "deceptive" trends, cf. the illustration at the top of the post), is a species of red herring distractor, that works precisely by being a distractive tangent.] Now, too, we have repeatedly put on the table [start with p. 2, OP] and linked relevant information on why we should expect and on evidence do observe such islands of function separated by vast seas of non-function in config spaces. Having provided evidence and citations from the biological world [on the tree of life], kindly explain to us how we are supposedly begging questions by asserting a disconnected landscape of life "axiomatically," which sounds suspiciously like a turnabout argument attempt, given the Lewontinian a prioris noted for evo mat. It seems to us rather that on abundant evidence, we should expect that complex, specific, information-rich function, starting from the joint metabolic systems and vNSR in first cell based life, will be disconnected. We find that: 1 --> the difficulty of elaborating algorithmic digital codes incrementally while preserving function at each step, 2 --> the observed status of the fossil record [note the extensive cite on the Cambrian revolution and the remarks by Gould], 3 --> the evidence that points to discrete protein fold domains, deeply isolated in AA sequence space [of order about 1 in 10^70], 4 --> the evident presence of irreducible complexity tracing to multiple core necessary factors, 5 --> The mutual ruin of genes first and metabolism first OOL models, etc . . . all point to serious and unresolved problems with the evolutionary materialist paradigm that have persisted for decades or even more than a century in some cases. In that context, we think it is time for a paradigm shift to one that does not have an evidently insuperable problem surmounting search challenges in a config space with isolated islands of function in an exponentially growing domain as complexity increases. Namely, design, which is known to routinely produce FSCO/I rich entities, and which in the case of Venter etc. is showing proof of concept of direct applicability to cell based life. Can you -- by way of supplying correction to our implied ignorance (or worse, a la Dawkins et al) -- demonstrate, on observation, why the Darwinian connected continent of viable forms traversed by a tree of life model at OOL, OO body plans etc, is empirically well warranted? Is it not the case that each argument in science must account for all the credible facts, and that it must have such facts on the table? And if you cannot supply unambiguous facts rooted in actual observation, then do we not instead have divergent schools of thought, which should have the right to proceed on their own terms, seeking support? [As in, no censorship in education on strengths and limitations of origins science theories, and no career busting in institutions for practitioners; cf. recent and classic cases in point.] GEM of TKIkairosfocus
October 14, 2011
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Dr Bot: Pardon, I will ignore the patent hostility of tone, simply noting that I have monitored carefully and that our evaluation of comments is plainly very different. If you know comments that in fact demonstrate how, on observation: (a) OOL from plausible prelife circumstances and through mechanisms of chance and/or necessity, and/or (b) OO major body plans or significant body subsystems through incremental chance variations and differential reproductive success . . . have been warranted, kindly identify the specific comments. Note, I am interested in observationally anchored evidence, not speculations, simulations that show instead targetted search algorithms that result in hill-climbing within an island of function [i.e. the novel body plan is already implicitly assumed, and we are dealing with variations within the body plan], etc. In short, where has the proposed darwinian mechanism, and/or where have chem evo mechanisms been shown to be adequate for the major claims being made. As a bonus, kindly explain why to date those who have shown these things have not been awarded say the Nobel Prize. (Prigogine's Prize for far from equilibrium systems does not count, as he admitted; cf. remarks in say Thaxton et al, TMLO, 1984.) GEM of TKIkairosfocus
October 14, 2011
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It's not at all tangential. It's central to understanding that a GA requires a connected landscape in order to navigate incrementally. Without discussing the attributes of actual landscapes there can be no useful discussion of whether evolution is possible or impossible. A (good) cryptogram is specifically designed to defeat incremental attacks. So the argument about hill climbing and such is going to boil down to the empirical question of whether the actual biological sequence landscape can be navigated. It's not something that can be known axiomatically.Petrushka
October 14, 2011
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Have you not read any of the comments in this thread? You are constantly being presented with the evidence you demand, then performing rhetorical back flips to avoid dealing with it.DrBot
October 14, 2011
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Dr Liddle, Grabbing a moment, first, please warrant on observation tracing to plausible prelife circumstances, the concept:
if you are talking about how the first minimal Darwinian-capable self-replicator came about (OOL) – fine. Darwinian mechanisms can’t explain the origins of a Darwinian-capable population.
The only observational evidence of life I am aware of is of cell based organisms that integrate metabolism and vNSR, digital code based self-replication that also codes for the metabolic subsystem. Such an entity is irreducibly complex per having multiple necessary causal factors to account for the two key facilities, and is also well beyond the FSCI threshold, just on the known stored info of at least 100,000 - 1 mn bits or so. If my information is incomplete on this matter, kindly enlighten me. However, if my information is accurate to what we know, it highlights that the only credible explanation of such is design, especially through the use of language, codes, algorithms, and data structures coupled to implementing machinery (expressed in turn based on said coded information). So also, once design is on the table, I have no reason to dismiss the significance of complex, integrated systems, that they normally contain many interacting, causally necessary core components. That starts with the need for heat, fuel and oxidiser to make a fire, and goes on from there to a pervasive phenomenon in the world of multiple component systems. So, I EXPECT to find islands of function as the characteristic pattern for cell based multicellular complex life forms that develop by cell multiplication and specialisation into tissues, structures, organs and an integrated body plan for each organism and individual. In some cases, there are two complementary sexes, both of which are required for reproduction, i.e. the minimum for reproduction is two individuals, of diverse sex. As p 2 of the OP highlights, the actual fossil record -- long since known to be dominated by sudden appearance, stasis and disappearance and/or continuation into the modern world -- reflects a non-gradualistic plan, i.e it supports the expectation. (I first saw that with marine fossils from my grandparents' farm in St Elizabeth, Jamaica, and this continued with the similar pattern of marine fossils in Barbados. So, the remarks by Gould et al are not a great surprise to me.) Complex, functionally specific, integrated systems with many necessary components are a "natural" and expected pattern in designed systems. Multiply, by the informational challenges to get to a viable body plan and implementing embryological development algorithm for a new type of organism, dozens of times over, on earth. Mix in mosaic creatures that look a lot like code reuse through a library. Also, so called convergent evolutions -- echo location with whales and bats jumps up. Think on how large sections of the human genome seem to be just sitting there in kangaroos, where on the usual timeline, the divergence for these types of mammals is said to be about 150 MYA, about the time often suggested for emergence of/dating of early birds and well back in the dinosaur period. All of this points, in my mind, to a pervasive pattern of what we should expect from the activities of designers. Direct molecular manipulation and code writing, use of viri as injectors of novel genetic programs, forms of frontloading, etc, are all possibilities on ways and means. But, we must know there are different ways to skin a catfish, and TRIZ gives a useful framework for thinking about the known challenges of engineering development. But of course, in raising themes like just above, I am widening the scope of reflections. Strictly speaking design theory is about the inference from empirically tested and reliable sign to key causal factors, across chance and/or necessity and/or design. GEM of TKIkairosfocus
October 14, 2011
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Distractively tangential. Please focus on the primary issues in the OP, pp1 & 2.kairosfocus
October 13, 2011
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Joseph, can you tell us more about how you used GAs to find solutions to encryption issues?dmullenix
October 13, 2011
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Onlookers and participants: First, please read p. 2 of the OP. Second, note how: a--> after 1 1/2 days, 1,000+ views and 100+ comments, b--> including from the former PR man for NCSE, c --> we still have yet to see empirical observational data on the origin of FSCO/I by blind chance and necessity, d --> or how on empirical observations we have a C + N pathway from Darwin's pond or a modern equivalent to a cell based, metabolising and vNSR self-replicating, cell based organism. e --> We know that the only empirically known source of FSCO/I is intelligence. f --> Similarly, Venter has given proof of concept that designers can use nanotech techniques to design elements for a living cell. g --> And, we know that designers form holistic systems, crossing vast config spaces to reach islands of function. h --> So, as of now the empirically best warranted account for OOL with such vNSR and metabolism, is design. i --> Where, there is a whole panoply of relevant design techniques and strategies [cf TRIZ], so, that new line of objections is a distractor. j --> With design on the table at OOL, it is on the table all along the rest of the way, and so it is quite significant that objectors from the darwinist side have been unable to show observational basis for the claimed power of chance variations incremented through differential reproductive success. k --> Design is known to be empirically adequate to account for complex functionally specific systems and structures, as can be seen from the world of technology we inhabit. l --> It is being asked, why don't we see designer trash around. Actually, what is more relevant is that we see known strong signs of design, fingerprints if you will: digital, coded algorithmic info in the heart of cell based life stands out as a case in point. m --> In any less ideologically loaded context, to suggest that such info, in the millions of bits, wrote itself out of accumulated lucky noise feeding trial and error, would be dismissed as a patent absurdity, with excellent reason in light of the space of possibilities for complexity of that order. So, let us see if the darwinist objectors are now able to warrant, on credible observation, why they stick to their model for origin of life and of major body plans. GEM of TKIkairosfocus
October 13, 2011
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You have been with us so long and do not follow the threshold of complexity with functional specificity issue?
kf, I find it a little frustrating that you assume that if I do not agree with something it is because I do not "follow it", despite having been "told". This is not a justified assumption. I have repeatedly said that I do not accept your evidence for these "thresholds" and "islands" that you talk about. It is my position (and the position of standard evolutionary biology) that the "thresholds" and "islands" you allege are illusory, or, at least, can be reached by incremental change.
Have you shown, empirically how darwinian incrementalism can bridge spontaneous info generation challenges?
Yes, many times, not least by AVIDA, but also through the evidence from "microevolution" i.e. evolution that can be observed happening from generation to generation. Each generation passes "information" from itself to the next, and differential reproduction means that that that information that leads to more offspring is selectively reproduced, resulting in the accumulation of information as to how best to build an organism fit for that environment.
By contrast, designers, notoriously, work holistically and by integrating components to achieve overall function. They face no problem in traversing vast config spaces to islands of function.
Exactly. So in human designs we see solutions transferred wholesale from one "lineage" to another. We do not see such transfers in nature, because, as you say, incremental evolutionary processes cannot do this. This is strong evidence that in nature, the "design" processes are incremental and Darwinian, not the results of a far-sighted, holistic designer.
BTW, have you read p 2 of the OP on the observed gaps?
I don't see anything in the OP about "observed gaps", apart from the well-known OOL gap. Can you give an example of a post-OOL "gap" that you think is untraversable by incremental means?Elizabeth Liddle
October 13, 2011
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KH: Once design is on the table, the panoply of methods known or plausible for engineering is also on the table -- just show us that you have looked up TRIZ as one example. The decisive issue, given institutional forces, however, is empirically tested, signs of design. Dr Liddle: You have been with us so long and do not follow the threshold of complexity with functional specificity issue? Have you shown, empirically how darwinian incrementalism can bridge spontaneous info generation challenges? By contrast, designers, notoriously, work holistically and by integrating components to achieve overall function. They face no problem in traversing vast config spaces to islands of function. BTW, have you read p 2 of the OP on the observed gaps? GEM of TKIkairosfocus
October 13, 2011
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My point is easy enough to understand from the quoted text above. Dr Bot states that "real scientist" don't appeal to evolution in explaining OOL issues. My experience is somewhat different than his/hers apparently. Dr Liddle is a brilliant "real scientist", and yet she does it repeatedly, even after being told:
LIDDLE: Yes, my answer does indeed “suggest the source the code”. And if you think that “the simplistic observation that living systems that function will exist longer than ones that don’t” is pointless, then you are missing a very important point!
BIPED: You are saying that the differential survival of a replicating system is the source of the code which causes the system to exist. But the differential survival of a physical system wouldn’t have happened until the code-driven system itself existed. (Alternatively, you can provide plausible evidence of a non-code-driven system providing inheritance, then point to the cause of a code arising within that system). In any case, differential survival is the result of an adaptive system in a variable environment, and it very obviously requires the system. This was already pointed out to you in my previous post. If something requires something else to exist before it can come into being, then it cannot logically be the cause of the thing it requires – because it doesn’t exist yet.
BIPED: The issue now is the same as it was last time. Provide some evidence for a self-replicating molecular entity which provides for its inheritance without a system of representations and protocols, then point to the rise of representations and protocols in that system.
Now, am I suggesting that Dr Liddle isn't clever enough to parse it out if pressed on the issue? No of course not. But then the next time it comes up, she goes right back to it as some fuzzy amorphous mechanism where everything works out anyway. And she is hardly the only "real scientist" who does this. It happens here all the time. ;)Upright BiPed
October 13, 2011
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I did not calculate the FSCI, but I think we can all agree that it is well beyond the universal probability limit. All I did was answer his question. Relating to biology, how can you rule in self-replication w/ heritable variation in reproductive success? No evidence anywhere of this creating FSCI. I didn't know that you had the sources to prove this mechanism to be a "potent source of functional complexity", which we have all been asking of you for months on end now.uoflcard
October 13, 2011
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Within body plans, the argument to improvement over primitive features through differential reproductive success is a hill climbing claim. Again, the challenge is to get to the body plans, i.e. shores of islands of function.kairosfocus
October 13, 2011
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All you have to do is show that body plan evo, per observation, occurs on darwinian methods and that this then best explains what we are seeing in the world of life. BTW, I think the pic of my son next to a canon is the best. But, others have their votes.kairosfocus
October 13, 2011
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I am no biologist. What I know about fish is that it breathes in oxygen dissolved in water, right? If you are a biologist, perhaps you could tell me what happens to fish after it is taken out of water into fresh air. Maybe it is a stupid question, in which case you have to forgive my ignorance, but how come a chance sequence of infinitesimal changes can enable fish to start breathing in the air and decide to become something else, e.g. a pig? How exactly?
It's not a stupid question, and it has been the subject of considerable research. One set of clues is given by extant lobe-limbed fish like lungfish which have primitive lungs as well as gills, and which resemble in many ways the lobe-limbed fossil fish that seem to have been ancestral to early tetrapods. Have you read Neil Shubin's "Your Inner Fish"?Elizabeth Liddle
October 13, 2011
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All the best with the trip!Elizabeth Liddle
October 13, 2011
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