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Topic: What ID Proof Must Look Like.
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zenheadache
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posted 30. March 2004 21:42
It is not enough to point out the inadequacies and failures of Neo-Darwinism. We must also have something solid to substitute for it, or we commit the same error of pushing intriguing arguments which settle nothing. Unlike Darwinism, we must have something more convincing to show, or we are doing little more than taking sniper shots at vulnerable Darwinist targets. It is my hope that we can do something more constructive than that.
But what exactly must we look for to prove intelligent design?
I believe what we must look for is a biological analog of the production line.
Consider Behe’s mousetrap as illustrative. The mousetrap is made by a series of steps. It is first blueprinted, and then each part is made. On the assembly line each part is added until the mousetrap is complete. When it is complete, it is functional and pressed into service to do what it is made to do, and it is not functional at all if each of the steps in the process are not completed first.
Once it is complete it can be used for the purpose it was intended: catching mice. The irreducible complexity of the mousetrap has a condition: The mousetrap must be assembled step by step before it can work, and then after it is assembled it is pressed into service and starts functioning.
That is to say, the mousetrap cannot BOTH be assembled step by step AND function as a mousetrap at the same time. The mousetrap has a function, and it cannot perform its function before it is complete, just as a ship cannot sail in drydock.
This means two things:
1. A step by step assembly process is an unavoidable historical fact of every thing we know has been designed.
2. It is not necessary to postulate the sudden appearance of irreducibly complex biochemical structures, completely intact and operable, in order to prove design.
It may be that irreducibly complex structures cannot be assembled gradually by Darwinian evolution, but this is not to say that they cannot be assembled gradually by OTHER THAN Darwinian evolution, just as they are in the world of manufacturing. The name by which I prefer to call this process is UNnatural selection.
If it can be shown that parts which do NOT improve the function of the organism in which they occur, which do not render it better able to survive in a “survival of the fittest” world are retained anyway, if it can be shown that such immediately useless parts are transmitted to succeeding generations, if it can be shown that the succeeding generations then add other useless parts, which fit together nicely with the previous useless parts and that these are transmitted together to new generations, if it can be shown that these immediately useless pieces continue to collect and assemble in each generation, until a generation arrives where an entirely NEW system has been produced and activated by some final piece falling into place, and that this NEW assemblage is BOTH an irreducibly complex system AND an improvement in the function of the organism which enhances its ability to survive—IF all this can be shown, THEN the theory that such mechanisms were forming by design on a cosmic biological assembly line, would be solidly proved.
This would be evidence, not of accident, but of orchestration.
It would be proved that things do NOT evolve by random mutation with natural selection, only by what is beneficial to them at the given moment, but that they have a FUTURE "in mind," a future that is not produced BY the pressure of natural selection, but despite it.
Finding solid evidence of this will send the theory of random mutation off to keep permanent company with other once prevailing theories, like spontaneous generation.
If different parts of a given mechanism can be dated to show which came first, we might develop a timeline for the assemblage of the unit. Developing a timeline for the assemblage of the unit might help us determine if the features being generated were actually immediately useful to the organism, an immeditate benefit which would have increased its odds of survival. Knowing the probable sequence in which the various parts collected and assembled would also give us a clue as to the lone importance of each part and each successive assembly to the organism, telling us whether some immediately useful function were developed at each step, or if the steps were not immediately useful.
Remember, all that is necessary to prove design is one incontrovertible case. If it can be proved that ONE complex biological structure did not arise by chance, then it destroys the very foundation of Darwinism. Darwinism has a lot of territory to protect, and in all that territory Darwinism cannot afford to be wrong even once, not even on so small a matter as a single bacterial flagellum.
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RBH
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posted 31. March 2004 17:52
zenheadache wrote quote:
If it can be shown that parts which do NOT improve the function of the organism in which they occur, which do not render it better able to survive in a "survival of the fittest" world are retained anyway, if it can be shown that such immediately useless parts are transmitted to succeeding generations, if it can be shown that the succeeding generations then add other useless parts, which fit together nicely with the previous useless parts and that these are transmitted together to new generations, if it can be shown that these immediately useless pieces continue to collect and assemble in each generation, until a generation arrives where an entirely NEW system has been produced and activated by some final piece falling into place, and that this NEW assemblage is BOTH an irreducibly complex system AND an improvement in the function of the organism which enhances its ability to survive?IF all this can be shown, THEN the theory that such mechanisms were forming by design on a cosmic biological assembly line, would be solidly proved.
Current evolutionary theory, and in particular its mathematical population genetics component, tells us that the first clause of the OP, that "parts which do NOT improve the function of the organism" should not be "retained" (presumably in the population) given normal evolutionary processes, is false. All kinds of "immediately useless" mutations are transmitted from parents to offspring in a very high proportion of reproductive events in metazooans.
It might be useful for to zenheadache take into account the known role of neutral mutations in evolution before getting too far downstream with this line of thought. Here are some references to get started on:
Discussions of applications of neutral mutations in artificial evolution in various contexts:
A review of the role of neutral mutations in the evolution of evolvability at the molecular level.
An analysis of biological mutation operators that discusses the role of neutral mutations in expanding the space available to the evolution of scale free genetic regulation networks.
For instances of deleterious mutations that subsequently are incorporated into irreducibly complex structures, see here.. (Yes, mildly deleterious mutations can persist in a population at low frequencies for some time. Again, see pop gen's equations.)
There are doubtless better references out there - "Kimura" is a name to keep in mind. My point is that the premise of the OP needs work.
RBH
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zenheadache
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posted 31. March 2004 18:23
If "neutral" means having neither benefit nor disadvantage, then "neutral" is exactly what I mean by "immediately useless." However, that is merely one component that must be present. Neutral features must be conjoined with other neutral features, and this must continue through generations wherein a completely new system is developed and then activated by some final feature falling into place.
This would be VERY strong evidence that matter is following some invisible blueprint in a cosmic assembly line where LIFE is the product falling off the conveyor belt.
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Rex Kerr
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posted 01. April 2004 00:18
Since you're requiring multiple neutral factors to acquire specific interactions with each other with no selection, I'd say that this falls outside of what evolution can accomplish via neutral mutation.
Of course, in any particular case, you'd want to be sure that the interaction strengths really were much stronger than expected by chance given the variety of proteins present in a cell, but I think the general idea is correct: a molecular machine does not assemble component by component over many generations without any positive selection, and then fall into place all at once at the end.
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Pim van Meurs
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posted 01. April 2004 01:37
As far as neutrality is concerned, neutrality is an essential feature for both robustness as well as evolvability. In fact as Toussaint has shown neutrality is expected to evolve
Link
quote:
Abstract. Neutral genotype-phenotype mappings can be observed in natural evolution and are often used in evolutionary computation. In this article, important aspects of such encodings are analyzed. First, it is shown that in the absence of external control neutrality allows a variation of the search distribution independent of phenotypic changes. In particular, neutrality is necessary for self-adaptation, which is used in a variety of algorithms from all main paradigms of evolutionary computation to increase efficiency. Second, the average number of fitness evaluations needed to find a desirable (e.g., optimally adapted) genotype depending on the number of desirable genotypes and the cardinality of the genotype space is derived. It turns out that this number increases only marginally when neutrality is added to an encoding presuming that the fraction of desirable genotypes stays constant and that the number of these genotypes is not too small.
Zen: If it can be proved that ONE complex biological structure did not arise by chance, then it destroys the very foundation of Darwinism. Darwinism has a lot of territory to protect, and in all that territory Darwinism cannot afford to be wrong even once, not even on so small a matter as a single bacterial flagellum.
I assume that you mean chance and/or regularity. But the task to show this is non-trivial since it requires to show that no known or unknown pathways can explain a particular system. SO far however there is no reason to believe one way or the other. In fact wrt the flagellum our increased scientific knowledge seems to fill in some of the gaps. I am not sure what you mean by 'cannot afford to be wrong' though. Isn't that what science is all about?
To come back to neutrality however, the fact that RNA and DNA networks seem to consist of vaste neutral networks throughout sequence space seems quite relevant since most motifs are 'close' in sequence space. In fact these characteristics, including the scale free nature of these networks, seems able to explain a lot of observations. RObustness: many mutations are neutral in nature. Evolvability: mutations can 'explore' sequence space, leading to perhaps long periods of phenotypical stasis followed by one or more selective mutations leading to quick innovations.
Neutrality, evolvability, robustness all seem to come together theoretically as equivalent issues. Combined with the scale free nature of networks and likely mechanisms that explain these observations make for a powerful argument for evolution.
As far as the genetic code itself see The Darwinian Genetic Code: An Adaptation for Adapting?
[ 01. April 2004, 01:57: Message edited by: Pim van Meurs ]
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zenheadache
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posted 01. April 2004 22:43
Saying it is non trivial is an understatement.
Ideally, science is not supposed to care about what the facts are, but as human beings with emotions we do become attached to ideas, in the absence of proof, substituting our belief for proof. Because we have a very human yearning to ask questions and for their answers, which gives rise to science, we can easily blur the distinction between science as method, and science as answer. It is in this way that I believe Darwinism has become The Answer. We make this mistake because the hardest thing to do is to AVOID coming to a conclusion too soon. Sometimes when we jump to conclusions, we end up being right in the conclusion we jump to, but that occasional success does not sanction the practise of leaping. When we want an answer so strongly, it is an indication that we need it for reasons other than scientific ones. We begin making science fulfill some of the needs unmet by a religion we have no faith in. In addition, we tend to become so emboldened by our successes that we regard with outrage the discovery of some fact which turns out to be contrary to what we expected.
The discovery of the Big Bang, and the resultant discord amongst atronomers who felt certain about the beginninglessness of the universe is a good example of this.
Regarding neutrality, it is one of the stages of proof I would expect to find in the assembly line theory, but it is not the only one. Serial endo symbiosis could also function as a means whereby the machinery of life is made by design, as much as each can represent the absence of design.
The test of the ID proof I am thinking of would be to observe or make very strong inferences from the evidence that show irreducibly complex systems being built step by step and THEN set to working. The liklihood that such a system can be explained through gradual and random processes decreases in proportion to the distinct number of components and functions making up that system. The more complex the system, the more we shall have to repeat to ourselves "There is no designer, there is no designer, there is no designer..."
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Pim van Meurs
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posted 03. April 2004 17:22
Zen: The more complex the system, the more we shall have to repeat to ourselves "There is no designer, there is no designer, there is no designer..."
Since the issue is not really the design in nature but the nature of the designer, I would say that your argument should be rejected. In addition complexity itself is NOT sufficient for an 'intelligent design' inference either.
Zen: The liklihood that such a system can be explained through gradual and random processes decreases in proportion to the distinct number of components and functions making up that system.
Again an interesting assertion that could certainly benefit from a supporting calculation.
Unless you limit yourself to systems which "show irreducibly complex systems being built step by step and THEN set to working."
Are there any such systems that you are aware of? How does one establish if such systems exist in biology?
[ 03. April 2004, 17:26: Message edited by: Pim van Meurs ]
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zenheadache
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posted 03. April 2004 21:09
Pim: Since the issue is not really the design in nature but the nature of the designer, I would say that your argument should be rejected.
I'm not sure what this means. I am not speculating about the designer. I'm not even speculating about whether nature and the designer are two different things.
Pim: In addition complexity itself is NOT sufficient for an 'intelligent design' inference either.
What is "complexity?" What does it consist of? It isn't just the number of individually distinct parts of some object that makes a thing complex. When we are talking about "complexity" in living systems, regardless of the mechanical complexity of the specific organism, we must also mean the purpose of the organism. How this sense of purpose which we have and which is reflected in all living systems came to be from inanimate, non living matter, which has no purpose, is the million dollar question. When you use the word "complexity" and say that it is not sufficient for an ID inference, that is true. But the purpose which is present in all living things needs explanation, and to date there is none via accidental evolutionary theory. Nor can it be ignored as inconsequential simply because there is no explanation. This then seems to indicate that random mutation, natural selection, serial endo symbiosis have to date NOT been sufficent to account for a NON design inference.
If we were to honestly list the facts, and add them all up, the only conclusion we could draw from the body of the evidence in answer to the question about how we got here, by ID or random evolutionary processes, is: We don't know.
Nor does the evidence FAVOR random evolution, since the entire notion of what is and is not random is entirely subjective. Is it random because it really is, or because it just LOOKS that way to US? These are NOT trivial questions to answer, and we may not be able to answer them at ALL. And since science cannot and SHOULD not make promises it cannot keep, and since science in all reality MAY NOT be able to give us all the answers we want—I am sorry to say—then we may simply have to live with that vacuum, rather than fill it with the wrong answers. This will be difficult to do because there is a LOT of pressure on science to "come up" with answers that put all the religious questions to rest.
Pim: Zen: The liklihood that such a system can be explained through gradual and random processes decreases in proportion to the distinct number of components and functions making up that system.
Again an interesting assertion that could certainly benefit from a supporting calculation.
Unless you limit yourself to systems which "show irreducibly complex systems being built step by step and THEN set to working."
Are there any such systems that you are aware of? How does one establish if such systems exist in biology?
Has the blood clotting cascade been explained? Have the molecular machines been explained? If they have not been, then they are the type of systems that I mean. If they have been—REALLY have been I mean, not just WISHFULLY—then the argument is over. In that case, there is no reason for either of us to be here having this discussion. But if they have NOT been, then it must be explained HOW such systems can come to be gradually. I have not seen evidence of "scaffolding," and in any case, any discovered scaffolding is something I would expect to find in the ID hypothesis as well, particularly in the assembly line theory I have proposed.
Remember, my purpose in writing this was that I saw no reason to accept Behe's initial conjecture that such IC systems might have come into being whole and intact, completely operable. Particularly since NOTHING in our experience which we KNOW has been intelligently designed follows such a model. Every thing that is designed and built by intelligence is done so step by step. But it cannot perform the function for which it is designed AS it is being built, and THIS is the crucial difference that proves design rather than accident.
Now, am I aware of the mentioned IC systems being built in this way? No, that is why I wrote this article. I simply tried to provide a different approach to thinking about the problems that might lead to some discovery.
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Pim van Meurs
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posted 04. April 2004 00:16
Zen: If we were to honestly list the facts, and add them all up, the only conclusion we could draw from the body of the evidence in answer to the question about how we got here, by ID or random evolutionary processes, is: We don't know.
You forgot another possibility namely non-random evolutionary processes.
Zen: Has the blood clotting cascade been explained?
In what sense? Yes we know quite a bit about the blood clotting cascade. Some excellent research exists The Evolution of Vertebrate Blood Clotting and Is the Blood Clotting Cascade "Irreducibly Complex?". Then there is the EvoWiki
and Kevin's Obrien article.
What has ID contributed to our knowledge of the blood clotting cascade?
What is the ID hypothesis according to Zen?
And then the following statement caught my eye "Nor does the evidence FAVOR random evolution, since the entire notion of what is and is not random is entirely subjective."
All that is argued for evolutionary theory is that mutations do not arise preferentially beneficial to their environment.
I feel that I am being trolled here. Please tell me it ain't so...
[ 04. April 2004, 00:20: Message edited by: Pim van Meurs ]
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Scott
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posted 04. April 2004 03:25
quote:
All that is argued for evolutionary theory is that mutations do not arise preferentially beneficial to their environment.
I think that perhaps zen is on to something wrt randomness, though I would not be surprised to find that it has been brought up before.
Are mutations really "random" with respect to whether they are beneficial given the current environment, if whether they are beneficial or not is not equiprobable?
If we classify mutations as beneficial, deleterious, and neutral, are each of these outcomes equiprobable?
If not, are the mutations really random?
This brings up another question, which is how do we establish that mutations are IN ACTUALITY random?
Scott
[ 04. April 2004, 03:27: Message edited by: Scott ]
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Pim van Meurs
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posted 04. April 2004 13:47
Scott, these are good questions so let me see if I can address them
Are mutations truely equiprobable, that is are neutral, deleterious and beneficial mutations equally likely? The answer is simple: No.
Most mutations are neutral, because the base pair substitutions lead to the same amino acid. This redundancy in the genetic code is an important factor for both robustness as well as evolvability.
Now coming to evolvability, one should not be surprised if evolution itself evolves or in other words, if evolutionary strategies can arise which tend to be more likely to be beneficial to the organism.
What evolutionary theory argues is not that mutations are equiprobable but rather that mutations do not arise to be beneficial to the environment as a response to the environment. In other words, there is no direct link between the mutation that arises and its effect on the environment.
Random does not mean that we do not understand the mechanisms of mutation, random merely describes the assumption and observation that organisms do not direct their mutations to match the changing environment. Does this mean that mutations cannot be biased? Nope.
Some relevant experiments includde Luria and Delbruck
They showed that random mutations exist. They did not show that nonrandom mutations did not exist. In fact recently there has been some excitement about adaptive mutations which seemed to initially suggest that non-random mutations arose. But on closer inspection the mechanism was that of hypermutation and selection.
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Rex Kerr
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posted 04. April 2004 15:09
zen, while I agree in principle with most of your points, there are a couple in your last post that seem questionable.
The first is that "science cannot and should not make promises that it cannot keep". It's important to remember that science doesn't guarantee truth, and that there are more options than certainty or vacuum. So while the scientific study of, say, the origin of the flagellum is likely to always be fairly speculative, we can learn more than nothing. And in some cases there is a good deal of data out there (e.g. about primate and hominid evolution) and we can potentially be fairly confident in our conclusions. (Even if we perhaps aren't yet because we haven't collected enough data.)
The second is the apparent unwarranted slipping between uncertainty regarding details and the equal probability of alternative hypotheses. If you want a complete story with all the i's dotted and t's crossed, then random mutation, natural selection, genetic drift, etc. etc., aren't going to give it to you. However, that doesn't mean that other hypotheses are on an equal footing--they may be either shot down by existing data or unnecessarily complicated or unwarrented.
This seems to underly the comments about purpose--and I think you're mistaken that evolution can't lead to behavior and function that we classify as purposeful!--and evidence not favoring random evolution. (Pim has addressed the latter point.)
(With regard to purpose, selection for survival imposes a non-negotiable, non-arbitrary goal, and thus provides a mechanism for consolidating function that increases the chance of attaining that goal. We tend to call this purpose.)
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zenheadache
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posted 04. April 2004 16:10
Pim: Random does not mean that we do not understand the mechanisms of mutation, random merely describes the assumption and observation that organisms do not direct their mutations to match the changing environment. Does this mean that mutations cannot be biased? Nope.
Some relevant experiments includde Luria and Delbruck
And here is Luria and Delbruck: In 1943 Luria and Delbrück [7] performed a cornerstone experiment to prove that random mutations (i.e. mutations that are not related to the environment) do exist. They exposed bacteria to a lethal selective pressure -- bacteriophage T1. As this bacteriophage immediately kills non-resistant cells, only cells with a pre-existing specific mutation to resist the bacteriophage could survive the treatment (the selective pressure). Luria and Delbrück exposed populations of bacteria to such lethal environment, and analyzed the number of surviving cells in the different populations (different petri-dishes). From the distribution of surviving cells they concluded that the relevant mutations had occurred randomly before the bacteria wereexposed to the selective pressure, i.e. the mutations arose randomly and were not induced by the environment.
As Delbrück himself pointed out [10], only cells with a pre-existing specific mutation could survive the experiment, as the non-adapted cells died immediately without an opportunity to mutate in response to the pressure. The experiments did prove the existence of random mutations, but it did not rule out the possibility that there are also non-random mutations.
The argument here is that the bacteria could not have survived by producing mutations in response to the pressure, therefore the surviving bacteria had already mutated randomly before the experiment.
What is missing here? What is wrong with the conclusion? Well, it’s a false disjunction. Our alternatives are that the bacteria survived either by a)random mutation prior to the experiment or b)evolutionary pressures produced by the experiment. Not B, therefore A.
The problem with the disjunction is that it settles upon a defintion of “random” in a context which is itself highly questionable.
Anticipation is an indication of intelligent design. Intelligence anticipates what might or could occur and then designs a response to survive what might happen BEFORE—BEFORE—the anticipated event. What is assumed to be random in this experiment fits perfectly what we would expect to find if evolution is being guided by intelligence.
Therefore, contrary to what is claimed, the question I asked remains unanswered: Is it really random, or does it simply look that way to us? unfortunately, the experiment cannot answer the question.
Why do we assume that the “proven” randomness in the experiment is accidental, not produced by design? Why? It seems to me that we have beguiled ourselves with circular reasoning. The “proof “ of the random mutation of the bacteria, as given in this example, is the assumption of the random mutation of the bacteria. There is no evidentiary or purely logical reason why we must accept the pre-experimentally mutated bacteria which survived as examples of random mutation AT ALL.
Ironically, might the very mutations we consider random also double as evidence of intelligent design, because they were NOT produced by environmental pressures?
Now the title of this whole post is "What ID Proof Must Look Like." I want to emphasize the word PROOF, as opposed to the reality. The reality may not resemble what we need to prove design, and so design may NOT be provable, which does not mean that it wasn't designed anyway. What I focused on was what we would have to find for the sake of PROOF.
This is what I wrote in my original post:
If it can be shown that parts which do NOT improve the function of the organism in which they occur, which do not render it better able to survive in a “survival of the fittest” world are retained anyway, if it can be shown that such immediately useless parts are transmitted to succeeding generations, if it can be shown that the succeeding generations then add other useless parts, which fit together nicely with the previous useless parts and that these are transmitted together to new generations, if it can be shown that these immediately useless pieces continue to collect and assemble in each generation, until a generation arrives where an entirely NEW system has been produced and activated by some final piece falling into place, and that this NEW assemblage is BOTH an irreducibly complex system AND an improvement in the function of the organism which enhances its ability to survive—IF all this can be shown, THEN the theory that such mechanisms were forming by design on a cosmic biological assembly line, would be solidly proved.
Now I expect that if evidence of this were to be found, it will not be confined to one species. Rather, the various pieces of the system will be found under construction through one or several genera. The trick is to find evidence of this having occurred, and it will by no means be easy to find.
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Pim van Meurs
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posted 04. April 2004 16:45
Zen: Anticipation is an indication of intelligent design.
Yes, these smart bacteria surely saw Luria and Delbruck's experiments coming :-)
Zen: What is assumed to be random in this experiment fits perfectly what we would expect to find if evolution is being guided by intelligence.
Why? Seems a bit ad hoc to me. Are you saying that intelligent guidance can predict the future?
Zen: Therefore, contrary to what is claimed, the question I asked remains unanswered: Is it really random, or does it simply look that way to us? unfortunately, the experiment cannot answer the question.
What it can answer is that these mutations appear to be random and that such is well explainable scientifically. If Zen's claim is that science cannot eliminate some forms of intelligence which seem to be able to foresee the future then he may have a point but that's nothing new. Science looks at the data and finds the best scientific explanation.
Zen: There is no evidentiary or purely logical reason why we must accept the pre-experimentally mutated bacteria which survived as examples of random mutation AT ALL.
Of course not, we can always posit an intelligence which saw these experiments coming. But that is not much of a scientific explanation really. So is it a false disjunction that Luria's experiments had two options only? Unless one can argue that these experiments were somehow predicted and propose a scientific theory, I would say that from a scientific perspective there are no real problems here. Science may be wrong, but that requires more than the logical possibility that it is.
Perhaps Zen can help us understand what the evidence of intelligence is in this experiment? A scientific approach or a philosophical approach? If it is the latter then I agree, such intelligence can always exist since science cannot really eliminate or support it.
As far as Zen's attempt to 'prove' design, it seems that he is rejecting that science is tentative but despite pointing out that we may not understand the mechanisms of mutations which therefor make it appear random, the same may apply to his approach namely the interpretation of useless. Perhaps useless is defined best by 'that which we do not understand yet'? Any conclusions based on such ignorance should be made carefully. Certainly proof seems to be too strong a concept here.
[ 04. April 2004, 16:48: Message edited by: Pim van Meurs ]
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Scott
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posted 04. April 2004 18:29
Pim, thanks for the response. The provided link raised some interesting questions, some of which were addressed by zen.
Is it your take that the claim is not that the mutations were "random" with respect to the new environment, post introduction of the bacteriophage, but rather that they must have been "random" with respect to the environment as it existed prior to the "lethal selective pressure?"
Any idea how the authors of the article determined that it was the resistant bacteria that had experienced mutation, rather than the non-resistant bacteria?
regards
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