Uncommon Descent Serving The Intelligent Design Community

ID Foundations, 14: “Islands” vs “Continents” of complex, specific function — a pivotal issue and debate

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In the current discussion on [Mis-]Representing Natural Selection, UD commenter Bruce David has posed a significant challenge:

A junkers Jumo 004 early Turbojet Engine (Courtesy, Wiki)

. . . it is not obvious that even with intelligence in the picture a major modification of a complex system is possible one small step at a time if there is a requirement that the system continue to function after each such step.

For example, consider a WWII fighter, say the P51 Mustang. Can you imagine any series of incremental changes that would transform it into a jet fighter, say the F80 and have the plane continue to function after each change? To transform a piston engine fighter in to a jet fighter requires multiple simultaneous changes for it to work–an entirely new type of engine, different engine placement, different location of the wings, different cockpit controls and dials, changes to the electrical system, different placement of the fuel tanks, new air intake systems, different materials to withstand the intense heat of the jet exhaust, etc., etc., etc. You can’t make these changes in a series of small steps and have a plane that works after each step, no matter how much intelligence is input into the process.

He then concludes:

Now both a P51 and an F80 are complex devices, but any living organism, from the simplest cell on up to a large multicellular plant or animal, is many orders of magnitude more complex than a fighter plane. If you believe that it is possible to transform a reptile with a bellows lung, solid bones and scales, say, into a bird with a circular flow lung, hollow bones, and feathers by a series of small incremental changes each of which not only results in a functioning organism, but a more “fit” one, then the burden of proof is squarely on your shoulders, because the idea is absurd on the face of it.

In responding, UD Contributor gpuccio clarifies:

consider that engineered modifications can be implemented in a complex organism while retaining the old functionality, and then the new plan can be activated when everything is ready. I am not saying that’s the way it was done, but that it is possible.

For instance, and just to stay simple, one or more new proteins could be implemented using duplicated, non translated genes as origin. Or segments of non coding DNA. That’s, indeed, very much part of some darwinian scenarios.

The difference with an ID scenario is that, once a gene is duplicated and inactivated, it becomes non visible to NS. So, intelligent causes can very well act on it without any problem, while pure randomness, mutations and drift, will be free to operate in neutral form, but will still have the whole wall of probabilistic barriers against them.

[U/d, Dec 30] He goes on to later add:

NS acts as negative selection to keep the already existing information. We see the results of that everywhere in the proteome: the same function is maintained in time and in different species, even if the primary sequence can vary in time because of neutral variation. So, negative NS conserves the existing function, and allow only neutral or quasi neutral variation. In that sense it works againstany emergence of completely new information from the existing one, even if it can tolerate some limites “tweaking” of what already exists (microevolution).

I suppose that darwinists, or at least some of them, are aware of that difficulty as soon as one tries to explain completely new information, such as a new basic protein domain. Not only the darwinian theory cannot explain it, it really works against it.

So, the duplicated gene mechanism is invoked.

The problem is that the duplicated gene, to be free to vary and to leave the original functional island, must be no more translated and no more functional. Indeed, that happens very early in the history of a duplicated gene, because many forma of variation will completely inactivate it as a functional ORF, as we can see all the time with pseudogenes.

So, one of the two:

a) either the duplicated gene remains functional and contributes to the reproduction, so that negative NS can preserve it. In that case, it cannot “move” to new unrelated forms of function.

b) or the duplicated gene immediately becomes non functional, and is free to vary.

The important point is that case a) is completely useless to the darwinian explanation.

Case b) allows free transitions, but they are no more visible to NS, at least not until a new functional ORF (with the necessary regulatory sites) is generated. IOWs, all variation from that point on becomes neutral by definition.

But neutral variation, while free of going anywhere, is indeed free of going anywhere. That means: feedom is accompanied by the huge rising of the probability barriers. As we know, finding a new protein domain by chance alone is exactly what ID has shown to be empirically impossible.

In her attempted rebuttal, contributor Dr Elizabeth Liddle remarks:

I don’t find Behe’s argument that each phylum has a radically different “kernel” very convincing. Sure, prokaryotic cells and eukaryotic cells are different, but, as I said, we have at least one theory (symbiosis) that might explain that. And in any case for non-sexually reproducing organisms, “speciation” is a poor term – what we must postulate is cloning populations that clone along with their symbiotic inclusions. Which is perfectly possible (indeed even we “inherit” parental gut flora).

I think you are making the mistake of assuming that because “phyla” is a term that refers not only to the earliest exemplars of each phylum but also to the entire lineage from each, that those earliest exemplars were as different from each other as we, for example, are from trees, or bacteria. It’s really important to be clear when we are talking longitudinally (adaptation over time) and when laterally (subdivisions of populations into separate lineages).

This was largely in response to Dr V J Torley’s listing of evidence:

What evidence [for the distinctness of main body plans and for abrupt origin of same in the fossil record], Elizabeth? Please have a look here:

http://www.darwinsdilemma.org/pdf/faq.pdf
http://www.darwinsdilemma.org/
http://www.nature.com/news/eni…..ria-1.9714
http://www.arn.org/blogs/index.php/literature

In “The Edge of Evolution”, Dr. Michael Behe argues that phyla were probably separately designed because each phylum has it own kernel that requires design. He also suggests that new orders (or families, or genera – he’s not yet sure which) are characterized by unique cell types, which he thinks must have been intelligently designed, because the number of protein factors in their gene regulatory network (about ten) well exceeds the number that might fall into place naturally (three).

This exchange pivots on the central issue: does complex, multi-part functionality come in easily accessible continents that can be spanned by an incrementally growing and branching tree, or does it normally come in isolated islands in beyond astronomical spaces dominated by seas of non-function, that the atomic level resources of our solar system (our effective universe) or of the observed cosmos as a whole cannot take more than a tiny sample of?

Let’s take the matter in steps of thought:

1 –> Complex, multi-part function depends on having several well-matched, correctly aligned and “wired together” parts that work together to carry out an overall task, i.e. we see apparently purposeful matching and organisation of multiple parts into a whole that carries out what seems to be a goal. The Junkers Jumo 004 Jet engine in the above image is a relevant case in point.

2 –> Ever since Wicken posed the following clip in 1979, this issue of wiring-diagram based complex functional organisation has been on the table as a characteristic feature of life forms that must be properly explained by any successful theory of the causal roots of life. Clip:

‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems.  Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

3 –> The question at stake in the thread excerpted from above, is whether there can be an effective, incremental culling-out based on competition for niches and thence reproductive success of sub-populations that will create ever more complex systems that will then appear to have been designed.

4 –> Of course, we must notice that the implication of this claim is that we are dealing with in effect a vast continent of possible functional forms that can be spanned by a gradually branching tree. That’s a big claim, and it needs to be warranted on observational evidence, or it becomes little more than wishful thinking and grand extrapolation in service to an a priori evolutionary materialistic scheme of thought.

5 –> I cases where the function in question has an irreducible core of necessary parts, it is often suggested that something that may have had another purpose may simply find itself duplicated or fall out of use, then fit in with a new use. “Simple.”

6 –> NOT. For, such a proposal faces a cluster of challenges highlighted earlier in this UD series as posed by Angus Menuge [oops!] for the case of the flagellum:

For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

8 –> The number of biologically relevant cases where C1 – 5 has been observed: ZERO.

9 –> What is coming out ever more clearly is this:

when a set of matching components must be arranged so they can work together to carry out a task or function, this strongly constrains both the choice of individual parts and how they must be arranged to fit together

A jigsaw puzzle is a good case in point.

So is a car engine — as anyone who has had to hunt down a specific, hard to find part will know.

So are the statements in a computer program — there was once a NASA rocket that veered off course on launch and had to be destroyed by triggering the self-destruct because of — I think it was — a misplaced comma.

The letters and words in this paragraph are like that too.

That’s why (at first, simple level) we can usually quite easily tell the difference between:

A: An orderly, periodic, meaninglessly repetitive sequence: FFFFFFFFFF . . .

B: Aperiodic, evidently random, equally meaningless text: y8ivgdfdihgdftrs . . .

C: Aperiodic, but recognisably meaningfully organised sequences of characters: such as this sequence of letters . . .

In short, to be meaningful or functional, a correct set of core components have to match and must be properly arranged, and while there may be some room to vary, it is not true that just any part popped in in any number of ways can fit in.

As a direct result, in our general experience, and observation, if the functional result is complex enough, the most likely cause is intelligent choice, or design.  

This has a consequence. For, this need for choosing and correctly arranging then hooking up correct, matching parts in a specific pattern implicitly rules out the vast majority of possibilities and leads to the concept of islands of function in a vast sea of possible but meaningless and/or non-functional configurations.

10 –> Consequently, the normal expectation is that complex, multi-part functionality will come in isolated islands. So also, those who wish to assert an “exception” for biological functions like the avian flow-through lung, will need to  empirically warrant their claims. Show us, in short.

11 –> And, to do so will require addressing the difficulty posed by Gould in his last book, in 2002:

. . . long term stasis following geologically abrupt origin of most fossil morphospecies, has always been recognized by professional paleontologists. [The Structure of Evolutionary Theory (2002), p. 752.]

. . . .  The great majority of species do not show any appreciable evolutionary change at all. These species appear in the section [[first occurrence] without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants.” [p. 753.]

. . . . proclamations for the supposed ‘truth’ of gradualism – asserted against every working paleontologist’s knowledge of its rarity – emerged largely from such a restriction of attention to exceedingly rare cases under the false belief that they alone provided a record of evolution at all! The falsification of most ‘textbook classics’ upon restudy only accentuates the fallacy of the ‘case study’ method and its root in prior expectation rather than objective reading of the fossil record. [[p. 773.]

12 –> In that context, the point raised by GP above, that

. . .  once a gene is duplicated and inactivated, it becomes non visible to NS. So, intelligent causes can very well act on it without any problem, while pure randomness, mutations and drift, will be free to operate in neutral form, but will still have the whole wall of probabilistic barriers against them.

. . . takes on multiplied force.

___________

In short, the islands of function issue — rhetorical brush-asides notwithstanding — is real, and it counts.  Let us see how the evolutionary materialism advocates will answer to it. END

PS: I am facing a security headache, so this post was completed on a Linux partition. Linux is looking better than ever, just now. as a main OS . . .

Comments
Response to champignon:
Are you aware that the monophyly of life on earth has been established to odds of better than 10^2680 to 1, and that all of the front-loaded genetic information you’re referring to would have to have been crammed into the single UCA?
Well, actually, if eukaryotes and archaea arose from a pool of early bacteria, the genetic data couldn't really tell if eukaryotes and archaea arose from a single cell or from a population of cells, if that population is homogenous. There wouldn't be any cramming of genetic information either. I'm not suggesting that every single gene found in life forms was placed into the initial cells. I am suggesting that major genes that would shape future evolution were designed into the initial cells. You can get a lot from a single gene, especially if overlapping genes are used. By the way, I'd like to point out that you just changed the topic on me. We were originally discussing if front-loading predicts a nested hierarchy as much as non-telic evolution. Kindly respond to my points on (a) endosymbiosis and the origin of modern eukaryotes, and (b) lateral gene transfer. Also, you said:
Under front-loading, nothing prevents major identical changes from happening in unrelated species. This will also destroy the nested hierarchy.
Similarly, nothing is preventing major identical changes from happening in unrelated species under non-telic evolution. Why? Lateral gene transfer can cause a "major identical change" in unrelated species.Genomicus
January 13, 2012
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Chas D: If you think that “gradual modifications would produce a blending of defining characteristics”, then you missed it – it is the reason that is not the case. Joe: LoL! Defining characteristics means phenotypic traits.
Double Lol! You are aware that the central displine in cladistics these days is molecular phylogenetics - DNA? That is, genotype, not phenotype? Non-blending. Hierarchies in DNA are what I refer to throughout my posts. Morphology is used as well, but molecular phylogenies are the standard.
And Mendell was a creationist.
So bleeding what?
ChasD: Fixation is observed whenever a rare allele becomes extinct, and only one allele remains in the population. Joe: So we have never observed it.
You are a strange, strange man. I guess a species has never been observed to go extinct, either. You think you saw the last die, but you don't KNOW that there isn't another one somewhere. Fixation of one allele or another is inevitable in any finite population of replicators, unless selection intervenes to prevent it. I could demonstrate the principle mathematically, or observe it in a lab population, or in a simulation using a bag of M&Ms ... but no: observe it. In the wild. Capture every individual of the species, gene-sequence them and then watch the last X die. "Hey Joe, over here, I observed it!". "Really? Show me.". The Prince of Denial. ID is not anti-evolution, but you deny every single aspect of it. You sure you're not a creationist?
And strange taht you agree that a nucleotide can mutate more than once and then say I need a brush-up. Obviously you don’t undertsand the implication, which is there isn’t any expected pattern.
Ah, now I get your point. Yes, multiple serial substitutions can occur. Surprisingly, molecular systematists are one step ahead of you on this one - they have already appreciated the point. Honestly, you think people who work on this are unaware of such things? That is one reason why recovered trees, particularly on SNPs, are not always fully congruent. Fortunately, there are many, many different kinds of marker one can use. Mutation is more than SNPs. 1. History is bunk. 2. Historf is bunk. (substitution) 3. Historo is bunk bunk. (duplication) 4. Histori is blunk bunk. (insertion) 5. Historg is blunk nk. (deletion) 6. Histort bluisnk nk. (transposition) 7. History biulsnk nk. (inversion) During this genuine lineage of copying and mutation, the last letter of "history" undergoes multiple SNP mutation back to y, which obscures the intermediates. But there is information elsewhere in the 'genome' that can help resolve this source of incongruence. The insertion at 3 has been quite degraded by the time you get to 7, but that is because I had several mutations to get into the illustration. It does not demonstrate a universal issue for all phylogenies. Your expectation (hope) is that, because of the phenomena of multiple serial substitutions, and degradation, ALL molecular phylogenies are useless. That does not follow.Chas D
January 13, 2012
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Chas D 'When a replicating process is set in train, however caused, then whenever designers stop interfering, the natural process rolls on, and has consequences – intentional or not' Perhaps. But with massive limitations. As the fossil record clearly shows.PeterJ
January 13, 2012
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KF: Beside the point. What you decide that evolution, or abiogenetic chemistry, historically did and did not achieve all by their little selves, they remain two separate phenomena. When a replicating process is set in train, however caused, then whenever designers stop interfering, the natural process rolls on, and has consequences - intentional or not. These consequences are investigated by the discipline known as evolutionary theory.Chas D
January 13, 2012
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Genomicus, Welcome aboard. Some rather interesting points. I observe how repeatedly, the focal issue that functional specificity and complexity point to tight constraints on possible configs in the space of possibilities, and how the sort of increments you highlight raise questions about built-in capabilities. Like for instance, if Eukaryotes enfold mitochondria, how do mitochondria get coded for in making a new cell? How does such a mechanism originate by chance plus necessity in a lucky case where one unicellular organism engulfs another? Or are we looking at intentional modularity here? KFkairosfocus
January 12, 2012
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ChasD: And when have we observed 500 or more bits of functionally specific complex information actually originating by blind chance and equally blind mechanical necessity, as opposed to by intelligent action? Why is that so, per the accessible quantum state resources of the 10^57 or so atoms of our solar system across say 10^17 s, and the number of possible configs of 500 bits? KFkairosfocus
January 12, 2012
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P: And when have we observed 500 or more bits of functionally specific complex information actually originating by blind chance and equally blind mechanical necessity, as opposed to by intelligent action? Why is that so, per the accessible quantum state resources of the 10^57 or so atoms of our solar system across say 10^17 s, and the number of possible configs of 500 bits? KFkairosfocus
January 12, 2012
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Chas D:
If you think that “gradual modifications would produce a blending of defining characteristics”, then you missed it – it is the reason that is not the case.
LoL! Defining characteristics means phenotypic traits. And Mendell was a creationist.
Fixation is observed whenever a rare allele becomes extinct, and only one allele remains in the population.
So we have never observed it. And strange taht you agree that a nucleotide can mutate more than once and then say I need a brush-up. Obviously you don't undertsand the implication, which is there isn't any expected pattern.Joe
January 12, 2012
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Genomicus,
Methinks that someone on this thread doesn’t know what front-loading is.
Methinks someone doesn't realize that his preferred front-loading hypothesis isn't the only one.
The front-loading hypothesis simply posits that the earth was seeded with life forms which contained the necessary genomic information such that future evolution could be shaped and constrained.
Are you aware that the monophyly of life on earth has been established to odds of better than 10^2680 to 1, and that all of the front-loaded genetic information you're referring to would have to have been crammed into the single UCA?
BTW, I would like to point out that you didn’t even try to answer my point about organism complexity also resulting in a nested hierarchy.
That's because I didn't understand what you were trying to say. Could you try again?champignon
January 12, 2012
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How did I miss it and when has it been observed?
If you think that "gradual modifications would produce a blending of defining characteristics", then you missed it - it is the reason that is not the case. In fact, you may have missed the whole thing about Mendelian genetics. Start in 1902 or thereabouts. Bateson. Certainly cleared the 'blending' thing up for early critics. Remember that we are talking about molecular phylogeny - DNA. Fixation is observed whenever a rare allele becomes extinct, and only one allele remains in the population. The remaining allele is de facto fixed. An allele, in this instance, being one variant of the set of DNA sequences occupying the same location on the set of chromosome copies in a population. Where do rare alleles come from? Common alleles whose day is past, or new alleles in their early stages. Once a particular variant is fixed, all descendants of that population will have that same variant at that locus - including branched species - barring further mutation.
BTW there isn’t anything that latches a nucleotide so one that has mutaed can mutate again and even back to the original.
Not sure I fully comprehend. But if a nucleotide can mutate once, that is proof enough that it can mutate. All it is is a point error. There is nothing to stop it mutating again. Nothing 'latches nucleotides'. There are many reasons why mutations occur. I hate to say it, but your grasp of basic biology - the stuff you need to know to make a sensible critique - could do with a brush-up.Chas D
January 12, 2012
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Chas D:
You miss a central result of evolution – fixation in populations.
How did I miss it and when has it been observed? BTW there isn't anything that latches a nucleotide so one that has mutaed can mutate again and even back to the original.Joe
January 12, 2012
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Scott,
I’m going to bookmark this exchange because of what it demonstrates.
Please do. I hope you'll refer to it often, until it starts to sink in.
If you can debate a point with someone and completely filter someone’s words so that you only observe the parts where they agree with you and discard the rest as if they never happened, even when you know the person disagrees with you, that speaks volumes to your perception of other evidence.
Don't pretend that I haven't directly addressed our points of disagreement. You claimed that the nested hierarchy doesn't confirm evolution if we can't "derive" specific instances of genetic variations from it and demonstrate why they were selected. I responded:
It’s like saying to a physicist, “If you can’t derive quantum mechanics solely from the spectra of elements and compounds, then those spectra — and the fact that they match the predictions of the theory — do not in any way confirm the theory.”
Or like saying to Einstein, "If you can't derive general relativity from gravitational lensing and the precession of Mercury's orbit, then those are not confirmatory -- even if they exactly match the predictions of the theory." It's ludicrous. I also responded directly to your assertion that evolutionary theory can explain the existence of "varied cells" but not "the variety of multicelled organisms that form the hierarchy":
Your only argument seems to be this: “What if there’s some invisible, magical barrier to evolution that stops it in its tracks after a certain amount of ‘microevolution’? If that were true, then evolution wouldn’t explain the nested hierarchy we see!” Well, yes. And if there is an invisible, magical barrier around the solar system, and if the laws of physics are completely different on the other side of the barrier, then physics no longer predicts the spectra we see from distant stars and galaxies!
champignon
January 12, 2012
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Scott says:
But now that you’ve discovered, after all this time, that ID has no symmetry with evolutionary theory and is not an opposing explanation of origins, I’ll leave you with some time to absorb that.
The Discovery Institute says:
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
"Not an opposing explanation of origins," Scott? LOL.champignon
January 12, 2012
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Woops. Double post. Apologies.Genomicus
January 12, 2012
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Another response to champignon:
Under front-loading, nothing prevents major identical changes from happening in unrelated species. This will also destroy the nested hierarchy.
Methinks that someone on this thread doesn't know what front-loading is o.o Please elaborate on the above point.
Anyway, front-loading is a non-starter because it cannot explain how unexpressed genetic information is protected from mutation for eons until the moment comes when it is finally “turned on”.
Yup. I thought so. You don't know what the front-loading hypothesis posits. The front-loading hypothesis simply posits that the earth was seeded with life forms which contained the necessary genomic information such that future evolution could be shaped and constrained. Nowhere does the front-loading hypothesis suggest that genes were simply turned off, not performing any function, and then suddenly, these genes are expressed resulting in a host of complex systems. BTW, I would like to point out that you didn't even try to answer my point about organism complexity also resulting in a nested hierarchy. Just saying.Genomicus
January 12, 2012
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But now that you’ve discovered, after all this time, that ID has no symmetry with evolutionary theory and is not an opposing explanation of origins, I’ll leave you with some time to absorb that. I do wonder what other misconceptions have been weighing you down.
"Discovered" it, Scott????? It's the point that some of us have been making for years!Elizabeth Liddle
January 12, 2012
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Another response to champignon:
Under front-loading, nothing prevents major identical changes from happening in unrelated species. This will also destroy the nested hierarchy.
Methinks that someone on this thread doesn't know what front-loading is o.o Please elaborate on the above point.
Anyway, front-loading is a non-starter because it cannot explain how unexpressed genetic information is protected from mutation for eons until the moment comes when it is finally “turned on”.
Yup. I thought so. You don't know what the front-loading hypothesis posits. The front-loading hypothesis simply posits that the earth was seeded with life forms which contained the necessary genomic information such that future evolution could be shaped and constrained. Nowhere does the front-loading hypothesis suggest that genes were simply turned off, not performing any function, and then suddenly, these genes are expressed resulting in a host of complex systems.Genomicus
January 12, 2012
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The same evidence that applies to OOL applies to further evolution. It’s as simple as that.
No it isn't. The process of evolution continues today; the process of "OOL" does not. If you take any current population, it will, according to some very concrete mathematical, empirical, computational and theoretical work, evolve. Blindly, by natural means. We do not need to insert a designer to keep this process ticking over; it happens all by itself. You have to interfere to stop it. So you are segregating out the unavoidable, natural process of evolution through mutation and selection/drift (as I find myself repeating, the thing ID is not anti), and asserting that there was historic interference with it, even though a 'blind' process of evolution can and does occur all by itself. We can argue about what it can create, but essentially, left to its own devices, a population experiencing birth and death will evolve, inexorably. Mutations will become fixed, and there is no going back. So when you talk of 'further evolution', you have to offer some means to distinguish that which can occur naturally from the interference. IC is one such attempt. But it remains entirely in accord with the ID inference, as stated, to allow for an ID OOL, and then NO further interference. The two are not subject to identical considerations.Chas D
January 12, 2012
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Response to champignon:
Unlike evolution, front-loading is not restricted to gradual changes. If massive changes occur (which is possible under front-loading), then the pattern of the nested hierarchy will be destroyed. The nested hierarchy is not merely an indicator of descent with modification; it’s an indicator of descent with gradual modification.
Front-loading is not restricted to gradual change, but nor is undirected, non-teleological evolution directed to gradual change. E.g., the endosymbiotic theory of the origin of eukaryotic cells is entirely non-gradual. It involves a primitive eukaryote engulfing a bacterium belonging to alpha-Proteobacteria, resulting in cells with mitochondria. That's not gradual evolution. It's incorporating a considerably different genome into an organism with significantly different characteristics. Then, of course, there are instances of lateral gene transfer whereby molecular machinery belonging to one species can be transferred "over night" to another species. This can hardly be considered "gradual evolution." Further, the front-loading hypothesis, is pretty restricted when it comes to unfolding biological states that were front-loaded. For example, if the cilium was front-loaded, the front-loading designers would have to design the initial cells on earth with homologs of the ciliary proteins in order to make such an evolution plausible. So, when we find prokaryotic homologs of ciliary components, a nested hierarchy will result even if the cilium was front-loaded. Front-loading involves gradual evolution to a very large extent, thus a nested hierarchy is expected. In summary, a. Non-teleological evolution is not restricted to gradual change, as evidenced by the endosymbiotic theory for the origin of modern eukaryotes and by the lateral transfer of molecular machines from one species to another. b. As the front-loading hypothesis incorporates gradual evolution to a large extent, nested hierarchies are expected for many protein families.Genomicus
January 12, 2012
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The nested hierarchy observed is not an expected outcome of accumulations of random mutations. Gradual modifications would produce a blending of defining characteristics and nested hierarchies cannot have that.
You miss a central result of evolution - fixation in populations. The 'gradual modifications' commence as single mutations and then some, through selection and drift, become the sole allele at their locus, population-wide. Then, the 'gradual modification' of the entire population has moved on one allele, and all descendants must descend from the originally mutated sequence at that locus. There is no blending at that locus; there is just one sequence. There are, of course, more subtle issues of intervening mutation before fixation and multiple loci, but best get your head around that one first.Chas D
January 12, 2012
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Champignon, I'm going to bookmark this exchange because of what it demonstrates. Even as I respond to you conceding certain obvious points and disputing others, you apparently only see the former and don't even notice that the body of my post disagreed with you. If you can debate a point with someone and completely filter someone's words so that you only observe the parts where they agree with you and discard the rest as if they never happened, even when you know the person disagrees with you, that speaks volumes to your perception of other evidence. Apparently you apply this filter to absolutely everything.ScottAndrews2
January 12, 2012
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I have, and going by the FAQ it is not a theory in the sense that the theory of evolution is a theory.
There has been enough equivocation with the word that it's pointless to split hairs over it. You pick the word you like and maybe I'll use it. I don't think nitpicking over the word is relevant.
But you were treating it as though it symmetry with the theory of evolution. You can’t have it both ways! If ID isn’t a theory in the sense of explaining anything, then it’s not comparable with a theory that is.
Just now, after a thousand people have asked how ID explains this or that and a thousand responses explain that's not what ID is, just now you're noticing that ID is not an explanation of how something is designed, created, or formed? Perhaps you should run through the FAQ one more time. Detecting a thing and explaining it are not the same. When one observes that a small amount of mercury has expanded or contracted within a thermometer they infer that its volume reflects, among other factors, its current temperature. This detection is based upon sound science. What does it explain? Does it tell you where mercury came from? Does it tell you where the heat is coming from, or where it went? But now that you've discovered, after all this time, that ID has no symmetry with evolutionary theory and is not an opposing explanation of origins, I'll leave you with some time to absorb that. I do wonder what other misconceptions have been weighing you down.ScottAndrews2
January 12, 2012
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Scott,
Are you sure you’re thinking this through?
Yes. Are you? 1. You've conceded that evolutionary theory predicts a single nested hierarchy. 2. You've conceded that the prediction is confirmed: we observe a single nested hierarchy, to an astounding degree of precision. 3. You've conceded that no other theory predicts a single nested hierarchy. Your only argument seems to be this: "What if there's some invisible, magical barrier to evolution that stops it in its tracks after a certain amount of 'microevolution'? If that were true, then evolution wouldn't explain the nested hierarchy we see!" Well, yes. And if there is an invisible, magical barrier around the solar system, and if the laws of physics are completely different on the other side of the barrier, then physics no longer predicts the spectra we see from distant stars and galaxies! I guess we'll have to ditch both physics and evolutionary theory.champignon
January 12, 2012
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Champignon, Are you sure you're thinking this through? 1. Natural selection and drift occur. OK.M 2. They predict the nested hierarchy. Of course they don't. They predict a nested hierarchy. Does the nested hierarchy they predict bats and spiders and humans and sea cucumbers? Not at all. Assuming that the starting point is a reproducing cell, they predict an assortment of varied cells. There is no observation relevant to drift or natural selection leading to a prediction that they would produce the variety of multicelled organisms that form the hierarchy. Those organisms cannot be explained by drift and selection, so how can drift and selection predict them? 3. The prediction is confirmed to better than one part in a trillion trillion trillion trillion. See the above. That's some fantastic imagination. The way you're blowing through these talking points suggests that you're repeating something you heard but clearly never thought through. 4. No other theory predicts the nested hierarchy, including common design, front-loading, and ID generally. So what? Not everything needs to be a prediction. There is no logical inconsistency between any of these things and nested hierarchies. And, as pointed out, nothing at all, period explains the nested hierarchy. 5. This confirmation of a distinctive prediction is strong evidence in support of evolutionary theory. As I've pointed out, the diversity in biology is consistent with some expectations of evolutionary theory (nested hierarchies for example) but inconsistent with others (such as the specifics of the organisms that make up the hierarchy.) The theory that the sun revolves around the earth predicts that I'll see the sun cross the sky every day. Sure, some evidence harmonizes with evolutionary theory. Lots of evidence contradicts it, and lots can't be explained by it. For one thing, all of your evidence omits natural selection. You include just about every living thing on earth as evidence of selection and yet you cannot cite the selection of so much as a single variation. You cannot explain A using B and C while omitting either B or C. It's so mind-numbingly simple that I can't believe I have to put it into words once, let alone make the point over and over.ScottAndrews2
January 12, 2012
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Petrushka: Thank you for the usual cathechism. It is always good to be remembered of the "cognitive strength" of the darwinian position...gpuccio
January 12, 2012
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Perhaps you should read the FAQ. I had simply assumed from your participation in so many discussions that you were better acquainted with it.
I have, and going by the FAQ it is not a theory in the sense that the theory of evolution is a theory. But you were treating it as though it symmetry with the theory of evolution. You can't have it both ways! If ID isn't a theory in the sense of explaining anything, then it's not comparable with a theory that is. If it is a theory in the sense of explaining things, then clearly it needs to do some explaining. But whenever we ask for an ID explanation of something, we are told to read the FAQ. And then whenever we explain something in terms of the theory of evolution, we are told that the explanation is a "just-so story". It's heads you win, tails we lose! And the reason for that is equivocation with the word "theory". ID is not a "theory" in a scientific sense (which is not to say it isn't science) of a postulated explanation. It's a default conclusion in the absence of an explanatory theory which IDists find persuasive. That's why, IMO, it is bad science.Elizabeth Liddle
January 12, 2012
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We therefore showed how the video in fact — inadvertently — demonstrated processes of intelligent design and goal-directed intelligent selection, as an instance of an intelligently designed Genetic Algorithm.
No, KF. No, no, no, NO. I thought you might be above that hollow sophistry. The algorithm was intelligently designed. Its result was not, except inasmuch as its designer knew - from observation of natural processes - how nature operates on genes and phenotypes, and so knew how to mimic those processes. It used only mutation and selection. The end result was apparent design and complexity, by incremental selection without a particular design in mind. Hey ho. I don't doubt that both sides will retain their prejudices intact. An 'own goal'? What do you think my goal actually was? To convert souls for Darwinism? Or simply to discuss an interesting scientific and philosophical point wrt design, complexity and the limitations of mutation/selection? Your agenda may be political; mine is not (but then, that's exactly what a crypto-political darwinist would say). I will leave it to your 'astute onlookers' to determine their own take on the matter.Chas D
January 12, 2012
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Scott, Your demand that we derive cases of variation and selection from the nested hierarchy is bogus. It's like saying to a physicist, "If you can't derive quantum mechanics solely from the spectra of elements and compounds, then those spectra -- and the fact that they match the predictions of the theory -- do not in any way confirm the theory." The double standard is glaring. You set the bar much higher for evolutionary theory than for other sciences that don't challenge your religious preconceptions. Science is about coming up with theories to explain and predict our observations. We know that: 1. Natural selection and drift occur. 2. They predict the nested hierarchy. 3. The prediction is confirmed to better than one part in a trillion trillion trillion trillion. 4. No other theory predicts the nested hierarchy, including common design, front-loading, and ID generally. 5. This confirmation of a distinctive prediction is strong evidence in support of evolutionary theory. ID's lack of confirmed observations, by contrast, is embarrassing.champignon
January 12, 2012
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There is no informational problem regarding the origin of protein domains. You have created a science fiction fantasy out out of missing history. There is no scientific mystery about missing history. It is quite obvious that protein evolution will tend to fix the most useful variants very quickly, resulting in the extinction of cousin variants. This will happen because unlike small differences in size and shape, differences in proteins will affect metabolism. Any allele that provides an advantage will fix quickly in a population. Which goes some way to explaining why variations on modern proteins are unlikely to be as functional as wild proteins.Petrushka
January 12, 2012
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GP: Very well put, as usual! KFkairosfocus
January 12, 2012
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