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Author
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Topic: Structure of Scientiifc Anlalysis
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warren_bergerson
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Member # 262
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posted 24. February 2003 10:02
Intelligent Design, whether ID as a non-materialistic process, or ID as a materialistic process, relies on the belief or expectation that Darwinian or neo-Darwinian concepts and principles are inadequate to ‘scientifically explain’ observed biological designs and biological design processes. It seems obvious from the discussion to date, that the issue of Darwinian adequacy or inadequacy will not be resolved until some agreement can be reached on what constitutes an objective verifiable standards for determining the adequacy of scientific explanations.
I propose as a starting point for discussion the following four general criteria and three specific criteria.
GENERAL CRITERIA FOR EVALUATING SCIENTIFIC ADEQUACY
1. The criteria used must be consistent with generally accepted concepts and principles of scientific analysis.
2. The criteria used must be applicable to the scientific analysis of complex processes and systems (since biological systems are obviously complex.)
3. The criteria used must determine adequacy given incomplete knowledge.
4. The criteria used must be objective and verifiable.
SPECIFIC CRITERIA
1. DEFINE VARIABLES- A scientific explanation must provide precise definitions that make it practical to identify and quantify cause and effect variables.
2. MODEL AND TEST CAUSAL RELATIONSHIPS- A scientific explanation must provide quantifiable and testable models of cause and effect relationships
3. DEFINE STRUCTURE- A scientific explanation must provide a verifiable and testable structure for the interrelationship between different causal relationships.
The above criteria are based on the assumption that the operation of a complex system may involve a number of causal relationships. A scientific explanation can be adequate without explaining all the causal relationships involved, but an explanation must define a structure making it possible to test the logical consistency of different causal relationships.
Comments?
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warren_bergerson
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posted 25. February 2003 04:26
It may be useful to note that the primary objectives of ‘structured scientific analysis’ as proposed above, are to 1)separate data gathering procedures (procedures at which biologists are highly proficient) from the mathematical modeling, theory construction, and theory testing procedures (areas where the procedures currently in use may be inadequate and of questionable rigor) and 2) to open mathematical modeling, theory construction, and theory testing in biological sciences up to techniques and concepts used in other fields of analysis.
It seems clear from many of the posting here that the need for new, independent, objective modeling and theory evaluation techniques in the life sciences is not a ‘need’ recognized by most scientists. The vast majority of individuals involved in the biological sciences, and even, it seems the majority of those advocating some form of ID are satisfied with existing peer review standards and techniques. The proposal for new standards and techniques is obviously not a response to a popular demand.
Despite what might be labeled general satisfaction with existing techniques, there are identifiable inadequacies in existing modeling and theory construction techniques. I would cite as specific examples:
1. The inability to model and reverse engineer information processing in neurons.
2. The inability to agree on techniques for measuring complexity, volume of information processing, and/or volume of information required to generate a given level of complexity.
3. Inability to generate predictive models of evolutionary change.
While undoubtedly more controversial, questions have been raised regarding the rigor of some of the modeling and theory evaluation techniques in current use. There are general questions/accusations about the use of unsubstantiated ‘hand wave’ explanations. And more specific questions such as the use of unrealistic and misleading assumptions and questions regarding the legitimacy of ‘GA design’ claims.
The purpose of this thread is to discuss the possibility of new, objective, verifiable techniques and standards for mathematical modeling, theory construction, and theory validation. While it is recognized that relatively few individuals may see a necessity for new techniques, it is hoped a somewhat larger audience will recognize the potential benefits of considering the new techniques and standards.
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Moderator
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posted 25. February 2003 07:19
Hi Alan,
Welcome to our board. In the future, if you post a link, please also post a summary of what one will find at the link and why it is relevant to the thread.
Thanks.
[ 25. February 2003, 07:24: Message edited by: Moderator ]
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warren_bergerson
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posted 26. February 2003 10:00
Alan- I don’t see that what you suggest has any relationship to what I am proposing, but maybe you can explain the relevance.
What I am proposing is essentially engineering models of biological systems and the operations of biological systems expressed in formal mathematical/logical notation. It will be noted that engineering type models and simulations have been developed for many features of biological systems. Consider models and simulations of heart pumps as an example. What I am advocating as formal or structured scientific analysis is the development and testing of formal engineering type models. What I am advocating is being done, but it is not generally being considered in terms of the development and testing of scientific theories.
Since this isn’t attracting much comment, it may be useful to briefly review a couple of general features of the proposed formal analysis:
CURRENT STATUS
Formal analysis of the type I propose is being performed for many of the functional features of biological systems. Obvious examples include the modeling associated with simulating physical functions such as heart pumps and the modeling associated with simulating brain function such speech recognition.
The major factors limiting development of the type of formal analysis I recommend are complexity and dynamics. The more we learn about biological systems, the more we realize that the level of complexity involved is far greater than originally anticipated. The greater than originally expected level of complexity is obvious.
Engineering analysis is applied most easily to static phenomena. Engineering models and simulations are developed to satisfy a fixed or static set of conditions. It is relatively easy to model and simulate the pumping of a heart at a point in time under fixed conditions, and it is easiest to model and simulate speech recognition under static conditions. The task of modeling and simulating becomes increasingly difficult, (much more difficult) as you attempt to model and simulate changing conditions and systems that adapt to changing conditions. Attempts to model and simulate dynamic or adaptive systems quickly run up against current technological limitations.
As a simple example, consider models and simulations of the heart. It is not terribly complex to model and build a mechanical pump that can simulate pumping blood at a point in time. It becomes increasing difficult to model and build a pump that can simulate adaptation to changes in pumping requirements. Given current technology, it becomes impossible to build a pump that can automatically adjust to changes in the size of the organism and can automatically repair damage.
As another example, we can model and simulate speech recognition, but the task becomes increasingly complex as we attempt to deal with changing speech patterns. Building a system that could ‘learn to recognize a new language’ is, I believe, well beyond current capabilities.
It should be obvious that it is not currently possible to develop models and simulations of high level adaptive or evolutionary change processes that meet the formal or rigorous standards of analysis proposed here. As has been discussed extensively elsewhere, models that purport to represent evolutionary processes are descriptive and/or based on unrealistic assumptions. It is in fact possible to perform formal analysis on Darwinian and neo-Darwinian processes using the formal processes being proposed here. But when such analysis is performed using ‘simplistic interpretations’ of the concepts, the models are invalid or do not work. No one, to my knowledge, has yet found a way to perform this type of formal analysis and produce a valid model based on Darwinian concepts.
TECHNICAL ISSUES
The type of formal structured scientific analysis I am proposing requires addressing a number of challenging technical issues. There are, I believe, a variety of effective techniques for addressing these issues, but knowledge of these techniques may be limited to certain somewhat obscure technical areas. Consider the following:
1. Defining and quantifying variables- A variety of techniques are used in a variety of fields for precisely defining and quantifying both complex variables and large sets of interrelated variables. Accounting, as an interesting example, provides powerful techniques for quantifying complex behavior.
2. Defining structure- Again, a wide variety of highly effective techniques exist for defining complex logical structures. Defining structure is essentially a technique for breaking a large complex phenomena into a set of more elementary units (or for combining elementary units to form more complex phenomena). Given the ability to define or model structure, complexity per se should never in itself prevent the analysis of complex phenomena. The assertion, for example, that evolutionary processes or biological systems are too complex to be subjected to formal analysis, is simply not valid.
3. Modeling and testing causal relationships- At first blush, it might seem that the scientific techniques for modeling and testing causal relationships are those associated with ‘grand’ theories like those of Newton and Einstein. But if one looks closely at fields like engineering and computer simulation, one finds a lot of modeling and testing of simple causal relationships. Of particular interest in life sciences are dynamic or controllable causal relationships (causal relationships where the effect, result or response associated with a cause, input or stimuli can be changed or controlled). The formal analysis of biological systems also requires analyzing the processes or causal relationships which produce or cause changes in dynamic causal relationships.
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Janitor@MIT
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posted 26. February 2003 15:50
“The taxpayer is looking for 66% of the universe that the astronomers have lost.”—Alan Creswell
LOL I think you’ve underestimated. The astronomers can’t account for ~98%.
What we know must be ~<?
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Cornelius G. Hunter
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posted 02. March 2003 03:02
Warren:
I think you are bringing up an important point. First, the question of whether or not Darwinism is a fact (or even adequate) is a key issue. So we need some accepted standards for theory assessment. I know philosophers of science are deep into this, and there are no easy answers. But I appreciate your attempt here.
I wonder how your approach would handle an example case. How about the universal genetic code? The situation is that evolution has little more than speculation about how it could have evolved. The speculation involves the code arising from simpler codes. And since, according to evolution, the code can evolve, we obviously could have a world with multiple codes. So evolution doesn't give anything beyond speculation as to how it could have evolved, and it doesn't predict a universal code. Nonetheless, the fact that the code is universal is claimed as extremely powerful evidence.
To my way of thinking there is a problem here with the theory. I wonder how would your criteria handle this situation?
--Cornelius
[ 02. March 2003, 03:04: Message edited by: Cornelius G. Hunter ]
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warren_bergerson
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posted 02. March 2003 09:59
Cornelius,
Quote: I wonder how your approach would handle an example case. How about the universal genetic code? The situation is that evolution has little more than speculation about how it could have evolved.
I believe the approach I outlined could be used to evaluate models and theories based on genetic code. The first basic question the proposed approach would address is the existence of a viable model or theory.
Clearly genetic code or genetic code variables can be precisely defined or precisely modeled in terms of base 4 integers. I assume when you refer to universal genetic code you are referring to a system with at least three key operations: 1)transform genetic code to living/functioning organism, 2)modify or evolve genetic code, and 3)create or evolve genetic code system from pre-genetic code system.
It is not terribly difficult to construct simple models and theories of each of these key operations. It is, however, far more difficult, I would suggest impossible using conventional techniques and concepts, to develop a valid model or theory of any of these processes.
You can, for example, propose that there is a one to one mapping from genotypes to phenotypes. But if you use an approach such as the automated assembly instruction approach which makes it possible to precisely define phenotypes, you find that phenotypes are far too complex to be compatible with a one to one mapping. Any scientist is free to propose some alternative type of genotype to phenotype mapping which could be tested and validated. Since no such model or theory has been proposed and validated, my approach would conclude that at this time there is no valid mapping model or theory. Since there is no valid mapping model, there is not currently a valid ‘universal genetic code theory’.
By the standards I propose, anyone is free to propose a genotype to phenotype mapping. There are, I believe, relatively standard techniques which could be used to test and validate any explicitly defined mapping. The only ‘new’ feature in the approach I am proposing is that claims of ‘there exists a valid genotype to phenotype map’ or ‘there exists a valid universal genetic code theory’ would not be permitted unless such models and theories could be explicitly presented and validated.
Just as there is currently no valid genotype to phenotype model or theory, there does not appear to be any existing valid ‘genetic change models’ or ‘genetic creation’ models or theories. Again the approach I am proposing allows anyone to develop models and theories of the key processes associated with a genetic code theories. The approach simply disallows claims the such models and theories exist when such models and theories can not be explicitly produced for testing and validation.
Quote: . I know philosophers of science are deep into this, and there are no easy answers. But I appreciate your attempt here.
Philosophy of science, when rigorously applied, is useful in evaluating the soundness of techniques used by scientists. Philosophy of science is useful for finding logical flaws in techniques and concepts. Philosophy of science is useful in explaining what does not work, and almost entirely ineffective at coming up positive suggestions for addressing the unsolved problems of science. A valid, predictive, scientific model or theory of evolutionary change processes does not exist. I have always been under the impression that this lack of a valid predictive theory was, at least in the past, recognized in the philosophy of science.
Apparently, and I certainly don’t claim to be an expert on the subject, a number of philosophy of science professionals have made a significant effort to rationalize treating imprecisely defined descriptive theories as real scientific theories. Apparently, a number of philosophy of science professionals have also attempted to exclude ‘dynamic and teleological causation’ as legitimate and useful analytical concepts. IMO, both efforts are seriously misguided.
SUMMARY
The scientific analysis of biological systems is the analysis of systems involving complex causation. I am proposing that in developing and testing models and these of these complex systems we need to return to rigorous ‘one failure falsifies’ standards that would result in the rejection of most existing models and theories. I am also proposing that if we look to engineering concepts and principles, it will actually be possible to construct models and theories that satisfy the more rigorous validation standards.
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Frances
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posted 02. March 2003 15:23
Cornelius.
Your questions seem quite relevant and it may be helpful to see what evolutionary science has to say about your claims.
There are many papers on the origins and evolution of the genetic code which may be helpful here.
Freeland Lab: Genetic Code Evolution : evolution
The Early Evolution of the Genetic Code by Robin D. Knight and Laura F. Landweber
See also REWIRING THE KEYBOARD: EVOLVABILITY OF THE GENETIC CODE by Robin D. Knight, Stephen J. Freeland and Laura F. Landweber quote:
The genetic code evolved in two distinct phases. First, the ‘canonical’ code emerged
before the last universal ancestor; subsequently, this code diverged in numerous nuclear
and organelle lineages. Here, we examine the distribution and causes of these secondary
deviations from the canonical genetic code. The majority of non-standard codes arise from
alterations in the tRNA, with most occurring by post-transcriptional modifications, such as
base modification or RNA editing, rather than by substitutions within tRNA anticodons.
A good review paper "Selection, history and chemistry: the three faces of the genetic code" Robin D. Knight, Stephen J. Freeland and Laura F. Landweber
And of course Knight's thesis
[ 02. March 2003, 15:30: Message edited by: Frances ]
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Cornelius G. Hunter
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posted 02. March 2003 23:23
Warren and Frances:
Warren:
I agree with you, but I wanted to take it a step further. You note that there is no current theory for the evolution of the DNA code. And of course evolution doesn't require there to be a single code. Yet, the fact there is a single code is cited as powerful evidence.
So, yes, I agree that we cannot evaluate the merit of the hypothesis that the code evolved because there is, currently, no such explanation. But that is not my question. My question is how do we evaluate the merit of a theory (namely, evolution) which claims Observable X (the universality of the code) as powerful supporting evidence when it neither requires X to be true, nor can explain X (ie, evolution can't explain how the code evolved, universal or not).
Frances:
You provided several URLs but I'm not sure what signficance you are attaching to them. They serve to illustrate that explanations (beyond speculation) for the evolution of the code do not exist and that the theory of evolution does not predict there to be a single code -- perhaps that was your point.
What intrigues me is the fact that evolutionists claim the code as the most powerful evidence (that's how one evolutionist put it; in any case it is consistently presented at least as *one* of the most powerful evidences) for their theory. Theories have (i) explanations and (ii) evidence supporting the explanations.
The fact that the DNA code is universal may be one of evolution's best evidences, but clearly it is not very strong evidence on an absolute scale. I'm wondering if Warren's approach can be used to evaluate this situation.
--Cornelius
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Frances
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posted 03. March 2003 01:16
Dear Warren,
What I beleive the evolution of the genetic code shows is that evolution did seem to have made some 'small' changes to it but that the code itself is quite universal.
The theory of common descent surely would predict a common code (with possible variations of course due to evolutionary mechanisms).
As far as speculations are concerned, that's how science works and in this case has to work since the actual event is hundreds of millions if not billion years away.
You may check out Rob Knight's work on the genetic code and how the various hypothetical scenarios are being investigated allowing us to understand in more detail a likely pathway that explains the genetic code.
Explanations do exist, we just do not know which one is the best one.
The theory of evolution once again does not require there to be a unique code, after all even a unique code for the common ancestor may have evolved. What the data suggest is that the code is for all practical purposes frozen. From an evolutionary perspective that is not totally surprising.
Reading this actual research on events that have taken place so far in our past are fascinating and show how science may be able to unravel even such distant events.
For instance "Table 3 Theories explaining variation in the code" and "Table 4 Testable predictions of the various models" in REWIRING THE KEYBOARD: EVOLVABILITY OF THE GENETIC CODE Robin D. Knight, Stephen J. Freeland and Laura F. Landweber show how science moves forward in this area.
in "Knight, R. D. and L. F. Landweber (1999). "Is the genetic code really a frozen accident? New evidence from in vitro selection." Ann N Y Acad Sci 870: 408-10." concludes that
quote:
We conclude that arginine shows specific affinity for its codons in the context of arginine aptamers, and that this affinity may have played some role in determining which codons encode arginine in the universal genetic code. More general conclusions await structural data for multiple aptamers to other amino acids. Recently reported aptamers to isoleucine contain conserved isoleucine codons at the binding site [18], indicating that codon-amino acid recognition may be a general phenomenon.
various theories seem to be proposed
quote:
The genetic code might be a historical accident that was fixed in the last common ancestor of modern organisms. ‘Adaptive’, ‘historical’ and ‘chemical’ arguments, however, challenge such a ‘frozen accident’ model. These arguments propose that the current code is somehow optimal, reflects the expansion of a more primitive code to include more amino acids, or is a consequence of direct chemical interactions between RNA and amino acids, respectively. Such models are not mutually exclusive, however. They can be reconciled by an evolutionary model whereby stereochemical interactions shaped the initial code, which subsequently expanded through biosynthetic modification of encoded amino acids and, finally, was optimized through codon reassignment. Alternatively, all three forces might have acted in concert to assign the 20 ‘natural’ amino acids to their present positions in the genetic code.
Knight et al also propose variants of primordial code evolution quote:
Three models of early code evolution. The ‘universal’ genetic code found in the last common ancestor (pink circle) might or might not be
similar to the first genetic code that evolved (blue circle). (a) The primordial genetic code is maintained by lineage merging in a reticulate
network: there is little competition between lineages, and lineages that share the majority genetic code have the advantage of using novel
proteins from other lineages when protocells merge. (b) Strong selection for increased code efficiency among lineages drives the code in the
last common ancestor far from the primordial code. Most lineages with variant codes become extinct, but a few successfully reach new local
optima. (c) Despite competition among lineages, the chemical factors leading to the establishment of the original genetic code are much the
same as the factors that influence the error in a given amino acid substitution; therefore the final code remains similar to the initial code.
Aptamer experiments can distinguish (b) from (a) and (c) by providing evidence for a primordial code that might or might not be similar to the
code in the last common ancestor.
How?
quote:
Compelling evidence (see above) supports the idea that arginine, and perhaps isoleucine, interacts with its codons in RNA aptamers and that the
genetic code is highly optimal with respect
to error minimization. When sequences for aptamers for more amino acids are available, we will be able to test whether chemical factors influenced the choice of amino acids and their codon assignments in the canonical genetic code. Assuming that each amino acid was originally assigned those codons for which it has greatest
chemical affinity, it would be possible to reconstruct this primordial genetic code. The divergence between this primordial code and the code found in the last common ancestor of all life could test models of early code evolution (Fig. 4).
Science has proposed what seems to be very testable hypotheses of early genetic code evolution.
Something else:
Bob Knight:
quote:
My conclusion, though, it that it's an exciting time to be doing bioinformatics. None of this work would have been possible five years ago: the combination of increased compuing power and huge sequence databases make these fundamental questions about evolution accessible for the first time.
What is the exiting findings that were made possible by increased computing power?
quote:
These calculations let me figure out how surprising it should be to find particular motifs. Here's a plot of the length of the motif against the number of random sequences you'd need to search to have a 99% chance of finding it, for the solid lines, and a 1% chance of finding it, for the dashed lines. The isoleucine motif has two modules and 12 bases, and you'd need to search about 100,000 sequences to find it; the hammerhead has three modules and 11 bases, and you'd need to search about 1000. Note that this is just for the sequence requirements: there's no guarantee that they'd fold into the right structure. However, the amazing thing is that this is about a billion-fold fewer sequences than the 10^15 typically used in SELEX!
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Cornelius G. Hunter
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posted 03. March 2003 02:58
Frances:
You wrote:
quote: "The theory of evolution once again does not require there to be a unique code, after all even a unique code for the common ancestor may have evolved. What the data suggest is that the code is for all practical purposes frozen. From an evolutionary perspective that is not totally surprising."
Indeed, the universality of the code is certainly not at all surprising from the evolutionary perspective. I would go further and say evolution accommodates it quite well. This, of course, assuming that one has already presupposed evolution to be true and so isn't bothered by the fact that evolution doesn't explain how it evolved.
But the fact that evolution accommodates the universality of the code misses the point. The point is, as you say, that evolution doesn't require the code to be universal. This, along with the lack of an explanation for its origin, is what makes evolution's exaltation of this finding so intriguing.
Regarding the lack of explanation, the point is not that there is *no* explanation. As you point out, those who presuppose evolution can always come up with speculations. The point is the explanations are really nothing more than speculations. You write:
"Explanations do exist, we just do not know which one is the best one."
Indeed, there are dozens of such "explanations" which are so vague there is no way to evaluate their feasibility (aside from judging them infeasible since they give no details). Even Knight, who is working *within* the paradigm and as such presupposes evolution, admits the evolutionary history of the code is obscure (to say nothing of the actual pathway and details of its evolution).
So how do we reconcile this state of affairs with evolution's high claim of evidential confirmation? Can you help explain this situation?
By the way, this same situation repeats itself over and over. I'm merely using the DNA code as an example because it is so obvious. Take another example. In 1951 George Simpson said that "there really is no point nowadays in continuing to collect and to study fossils simply to determine whether or not evolution is a fact. The question has been decisively answered in the affirmative." Likewise, Tim Berra wrote "Fossils provide hard evidence that evolution has occurred," and Ken Miller wrote that the fossil data indicate that "descent with modification, which most of us prefer to call evolution, really happened."
I won't go back over the fossil evidence which I assume most readers are familiar with. The bottom line is they simply don't prove evolution is true as claimed. Same thing with other evidences: high evidential claims amidst ambiguous evidences.
We could discuss the evidential details and how bad this or that evidence really is, but that is not the question here. The question is, how do we explain and understand the disparity between the evolutionists claims and the empirical data?
--Cornelius
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warren_bergerson
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posted 03. March 2003 07:41
Cornelius,
Quote: I agree with you, but I wanted to take it a step further. You note that there is no current theory for the evolution of the DNA code. And of course evolution doesn't require there to be a single code. Yet, the fact there is a single code is cited as powerful evidence.
I think you are bringing up a very good point. Scientific analysis does not begin with the development and testing of formal theories. Science begins either with a ‘how to we fix that problem’ or with interesting observations such as ‘all life forms involve DNA’ or ‘all life forms involve cell walls’ or ‘all higher animals have nervous systems involving neurons’. I have heard this ‘interesting observation stage’ referred to as pre-science.
The proposed approach to structured analysis would, I believe, show that evolutionary biology has not yet emerged from the pre-science stage. That is not an unreasonable position or conclusion.
The argument that the ‘universal presence of DNA supports the existence of evolutionary processes’ would seem to be a fundamentally flawed argument. It would be far more logical to argue that 1)if life requires DNA, and 2)DNA does not occur in nature outside life forms, there is no possible way for life to have evolved by natural processes. It seems logically that any valid evolutionary theory must postulate the existence of non-DNA life forms.
IMO, no proposed model or theory of evolutionary processes should be considered a serious scientific proposal unless it can 1)provide a reasonable explanation for the evolution of DNA, 2)explain the operation of pre and non DNA life forms and 3)at least predict the existence of evidence supporting the existence of pre DNA life forms.
To back up a bit, the subject of this thread is rigorous structured standards for evaluating scientific theories. I am in effect proposing a rigorous scientific theory filter. One obvious use of the filter is to demonstrate that many existing accepted theories do not really qualify as scientific theories. The purpose of the filter is not, however, to reject all theories. I believe that if you establish rigorous standards then there are ‘engineering type techniques’ which can be used to establish valid scientific theories of biological change processes.
Explaining pre DNA life forms is one of the criteria I believe can be satisfied. In very simple terms, I assume there must exist in nature self contained units or ‘bubbles’ which have the ability to 1)survive over a period of time, 2)to expand and contract and 3)to divide. These bubbles must also contain dynamic or changeable change in state causal relationships(what I call dynamic and teleological causal relationships, or ‘assembly/operating instructions’). Bubbles with certain types of ‘operating instructions’ would be more likely to survive than bubbles with other forms of dynamic and teleological causal relationships. Over time, these bubbles could evolve given the presence of storage mechanisms, selection mechanisms(not limited to natural selection), and variation mechanisms (not limited to random variation) operating on dynamic and teleological causal relationships (not DNA or phenotypes).
This teleological algorithm model would suggest or predict that ‘life’ existed and evolved long before the evolution of DNA. The model also suggests or predicts the existence in cells of ‘dynamic and teleological causal relationships or processes’ which are 1)essential to the existence of life forms and 2)which function or can function in the absence of DNA. My guess, is that we already know of a significant number of non-DNA or pre-DNA processes or mechanisms in cells, but we ignore their significance because they do not fit in with our accepted theories.
SUMMARY
The purpose of this thread is to discuss procedures and standards for evaluating and accepting/rejecting scientific theories. One goal of the proposed standards is to eliminate or reject theories which do not meet rigorous standards. This, it appears would include most of the evolutionary and genetic theories currently accepted as valid. The main goal of the rigorous standards, however, is to make it possible to introduce and validate models and theories which can meet the more rigorous standards. The ‘universal genetic code’ topic provides a useful basis for illustrating the principles involved.
Frances,
It is not clear from your comments if you are suggesting that 1)existing evolutionary theories can satisfy the criteria defined or 2)you are supporting some alternative set of theory evaluation criteria. Please clarify your position.
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Frances
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posted 03. March 2003 11:37
Cornelius: Indeed, there are dozens of such "explanations" which are so vague there is no way to evaluate their feasibility (aside from judging them infeasible since they give no details).
I suggest you read the references which not only provide for explanations but also with ways to determine their feasibility and in fact provides for ways to falsify.
Cornelius: Even Knight, who is working *within* the paradigm and as such presupposes evolution, admits the evolutionary history of the code is obscure (to say nothing of the actual pathway and details of its evolution).
And yet, if you read Knight you see him propose not only several potential pathways but also ways to formulate hypotheses and falsifications of such hypotheses. And not all hypotheses assume evolution as the mechanism responsible for the origins of the genetic code either.
This is a fascinating topic and many interesting papers explore the various concepts and hypotheses. As Knight has suggested the recent arganine aptamer and other aptamers suggest that perhaps the original universal genetic code can be reconstructed after all.
Cornelius: So how do we reconcile this state of affairs with evolution's high claim of evidential confirmation? Can you help explain this situation?
Countless examples can be provided that show strong evidence of common descent and evolution. Is that what you are refering to?
So not only are there current hypotheses of the genetic code and its evolution, science is also working hard to falsify them or reconcile them with the available evidence. To call this a pre-science stage for all practical purposes fails to accurately understand or appreciate science.
Warren's suggestions are fascinating since if one read the available literature then we notice that scientific theories/hypotheses of the evolution of the genetic code do exist; in fact I reported recent findings by Knight that seem to make the RNA (pre-DNA) world almost a certainty. What this shows is that the argument 1)life requires DNA is what is commonly known a strawman argument. More correctly one would formulate the statement to be 1) life at present requires DNA but strong evidence of a pre-DNA (RNA world) exists and some have even proposed a pre-RNA world.
I also would like to emphasize once again that the universal genetic code and its evolution once again support strongly the already plentiful evidence of common descent. That Warren, without much rigorous support, attempts to disqualify evolution merely by assertion seems to not only be irrelevant but also contradicted by actual scientific progress. What surprises me is that such statements are made despite me providing with various links that would have helped Warren investigate the current state of affairs.
[ 03. March 2003, 11:51: Message edited by: Frances ]
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Cornelius G. Hunter
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posted 03. March 2003 12:34
Frances:
Frances wrote: "I suggest you read the references which not only provide for explanations but also with ways to determine their feasibility and in fact provides for ways to falsify."
Falsification criteria need to be formulated carefully, otherwise they are essentially meaningless. I can, for example, give you ways to falsify astrology. As for ways to determine the feasibility or likelihood of the evolution of the DNA code, I haven't found anything close in the literature. I could hunt around and try to figure out what you are referring to, but perhaps you could help out and show us what it is you are referring to.
You also mention that Knight has proposed hypotheses that do not "assume evolution as the mechanism responsible for the origins of the genetic code." Again, I'm not sure what you are referring to here, as I have not seen that. I wonder if you are using a narrow definition of evolution such as "natural selection", so that pathways which are, for example, chemically driven / determined and not subject to natural selection do not fall into the category of "evolution." If this is the case, then you are drawing too fine a distinction here as such scenarios are easily subsumed within the broader view of evolution (ie, the species arising via natural means). On the other hand, if you are saying that Knight has proposed *non* natural mechanisms for the creation of the DNA code, then that is news to me. Could you please clarify?
Frances wrote: " Countless examples can be provided that show strong evidence of common descent and evolution. Is that what you are refering to?"
What I was referring to is the gap between the evidence and the evolutionist's claims. Evolution is supposed to be a fact, and the universality of the DNA code is supposed to be the best evidence, or at least among the best evidences, yet evolution doesn't require its universality or explain its evolution (beyond speculation). This situation occurs over and over. I used the fossil evidence as another example. I could give other examples. The situation is you have a theory claiming X as evidence that the theory is true, yet the theory neither requires nor explains X (beyond speculation). What gives?
Frances wrote: "So not only are there current hypotheses of the genetic code and its evolution, science is also working hard to falsify them or reconcile them with the available evidence."
No one is doubting that there are current hypotheses. But how do speculative hypotheses translate into powerful, compelling evidence; essentially proof, for evolution?
Frances wrote: "To call this a pre-science stage for all practical purposes fails to accurately understand or appreciate science."
I'm not calling this "pre-science." Again, this is not the issue. The issue is you have a theory claiming X as evidence that the theory is true, yet the theory neither requires nor explains X beyond speculation.
Frances wrote: "fact I reported recent findings by Knight that seem to make the RNA (pre-DNA) world almost a certainty."
Hmm, I can't believe that I missed such a momentous find. Can you elaborate? I will be very interested to know why the RNA world hypothesis is almost a certainty.
Frances wrote: "I also would like to emphasize once again that the universal genetic code and its evolution once again support strongly the already plentiful evidence of common descent."
OK, it sounds like you agree with the evolutionist's high evidential claim vis-à-vis the universality of the code. Then can you explain how you arrive at this remarkable conclusion given that fact that evolution doesn't require the code to be universal nor can explain how the code evolved beyond speculation?
--Cornelius
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