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Author
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Topic: Front Loading
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Frances
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Member # 169
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posted 09. January 2003 11:56
I believe that Warren confuses permanence of laws with no variation. While the law of gravity is permanent, its effects depend strongly on the circumstances. Similarly while mutations are a given for variations, there are many circumstances which make the outcome highly variable. In fact what may be a detrimental mutation in one environment may be a benificial mutation in another environment. Thus the permanent and universal assumption can be succesfully combined with RM&NS to describe the evolution of life. And not surprisingly it has been applied as such quite succesfully. It seems to me that Warren's claims are not only counter intuitive but also fail to address and recognize that while laws can be universal and permanent their effects need not be identical.
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Nel
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posted 09. January 2003 17:19
Actually, this quote is not by Charlie D, it is simply Morris continuing with one of my quotes.
Conway Morris continues:
quote:
This, however, is a distorted view. First, many of the basic building blocks and processes found in the metazoans are very widespread among eukaryotes and must have originated much earlier than the first animals. Second, sponges are well adapted, abundant, and diverse. They are highly organized, capable of coordinated response, and despite the relative simplicity of their bodyplan, some sponges demonstrate a radical reorganization concomitant with a shift to carnivory.
Note that this quote ignores my other two points, which this formed a bridge to in Conway's article:
quote:
Just as phenotypic diversity of life excites the imagination of the naturalist, so the range of molecules and the sophistication of their biochemistries impress the molecular biologist. In comparison, the underlying constraints on form and the inevitability of convergences have received less emphasis. Why should this be so? There seems to be two reasons. The first is that if evolution is in some sense channeled, then this reopens the controversial prospect of teleology; that is, the process is underpinned by a purpose.
Note that this contradicts any notion that front-loading is nothing but methodological naturalism.
When I wrote this, I did not merely say "front loading may exist", I posted what I think is good actual evidence of front loading. That all the hardware needed to evolve metazoan life had already existed in unicellular organisms, and it is hard to understand what selective pressure would drive an organisms to take the difficult and dangerous path towards inventiveness and complexity.
That is, our interpretation of evolutionary change, according to the data, seems to be that changes in animal morphology, whether great or small, are generated largely by alterations in developmental regulatory sequences that were reshuffled. The differences between animals displaying different body plans are not likely to be explained in general by differences in these proteins. Many remarkable examples of diverse usage of similar genes and gene families in the develompment of organisms supports Mike's point:
quote:
Secondly, our perception of evolution has been skewed over the last century. This is not surprising, as science is limited by the perceptions its tools can deliver. Yet how has the perception been skewed? From a morphological and behavioral perspective, life is immensely diverse. But the molecular perspective shows such diversity to be "skin-deep." Thus evolution, as evidence by the fossil record, has not been about developing novel hardware to solve adaptive problems. It has been more about reshuffling, testing, and deploying the molecular endowments it has been given. Put bluntly, all the evolution contained in the entire fossil record and inferred by our phylogenetic trees has been largely a footnote in the development of life. The really interesting and important questions concern the origin of this "animal in waiting" hardware that was infused into protozoan life forms.
Francis:
And your comment about the eyes of the lobster seem to be relying on outdated information. I found much of such information on a variety of websites all referencing Sarfati.
Nelson:
Then surely you can be specific with me about how my discussion on Lobster eyes is outdated. Simply saying so is not demonstrating so.
Francis:
What is the reality of eye evolution? Your question Why would these creatures take an extremely dangerous road from refraction to reflection when it's eyes are functioning quite well as they are? seems to have turned the world upside down. Present theory and evidence suggests that refracting and reflecting eyes both evolved from a common ancestor.
Nelson:
What "present theory" says about refracting eyes and reflecting eyes is quite irrelevant to my discussion as I was speaking of the power of Front-Loading and not about whether refracting and reflecting eyes both evolved from a common ancestor. I was specifically addressing the powerlessness of natural selection to explain this phenomenon.
Since Francis failed to address my quandary I'll add to my point by describing another example, this is an addition to my lobster eye example, and not a replacement of.
Dakin writes of the Pecten maximus:
quote:
Whatever may have been the origin of the eyes of the Pecten group I do not hold that utility explains their evolution...in the case of Pectinade there is no evdience of the elimination of types with less complex eyes as unfit...in view of the diverse conditions existing in the lamellibranchs there is no evidence that a reduction in the efficiency of the eyes of Pecten would lead to unfitness...We cannot escape from the conviction that in one particular series of bivalves, all intimately related genetically, a distinct type of visual organ arose, independent of other visual organs, and that apart from adaptation , and apart from utility or advantageousness, it attained a certain extraordinary complexity " (emphasis mine)
As Denton points out, these eyes do have some selective advantages over bivalve eyes, however, they survive just fine on there own and have no selective advantage in taking the long arduous road to these incredibly sophisticated eyes. Within Mollusca, all the eyes are simple variations of the camera-type eye scheme.
Francis quotes a paper:
Pax6:
quote:
Our work on Pax6 as a master control gene for eyemorphogenesis and the implications for eye evolution have been summarized for Trends in Genetics (Gehring & Ikeo, 1999). Pax genes from various animal phyla are capable of inducing ectopic eye morphogenesis, indicating that Pax6 is a master control gene for eye development. It is proposed that contrary to the dogma, the various eye-types found in metazoa, are derived monophyletically, from a common prototype. In order to explain the evolution of the different types of eyes, we have advanced the hypothesis that different genes are intercalated into the prototypic eye developmental pathway in the various animal phyla.
See Gehring, W.J., and Ikeo, K.: Pax 6. Mastering eye morphogenesis and eye evolution. Trends in Genetics 15, 371-377 (1999).
Nelson:
Thank you for quoting this paper as it also supports Front-Loading.
For example, crystallin proteins have been coopted in evolution from prior uses as enzymes, and they have in common only that in high concentration they process the requisite optical properties. The alphaA crystallins are found in all vertebrate lenses. They are there as a result of the evolutionary recruitment to an eye differentiation gene battery of genes encoding proteins of the heat shock/chaperone family. The chicken lens delta1 crystallin is similarly the product of gene encoding arginosuccinate lyase enzyme that was recruited for function within the eye lens, but only in the bird/reptile branch of the vertebrates.
These cooptions to eye lens differentiation gene batteries may have been the product of front-loading, i.e., the presence of Pax6 in the appropriate domain of the eye anlage during development.
However, I fail to see it's relevance to my lobster eye discussion.
[ 09. January 2003, 17:44: Message edited by: Nelson_Alonso ]
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Nel
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posted 09. January 2003 17:38
Mike said:
quote:
Now, please name one person in the entire global MN community who objected to this argument (that no engineer would have included cytosine in the DNA) and tackled it head on.
This is a good point. If MN is equivalent to Front-Loading, then Mike's hypothesis should be equivalent to Poole's hypothesis about cytosine deamination. And yet, Poole's hypothesis is the exact opposite of Mike's front-loading hypothesis, that an intelligent engineer would use cytosine. Thus the claim that all Front-Loading ideas are equivalent to non-teleological inferences is false.
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Frances
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posted 09. January 2003 23:44
Nelson
quote:
Note that this contradicts any notion that front-loading is nothing but methodological naturalism
Indistinguishable from methodological naturalism.
That evidence of common descent may be evidence of front loading as well suggest that Murray is correct. Changes in developmentary pathways hardly is evidence for front loading or against Darwinism either. That front loaders would like to take the evidence for common descent (such as Pax 6 hox genes) as evidence of front loading is interesting but it fails the Dembski test namely that intelligent design is infered through rejection of chance and regularity.
Your comments about the lobster suggested that you were not familiar with the proposed pathways of evolution for the eye. You seemed to suggest that the lobster went from a refractionary system to a reflectionary systems and that such a pathway seemed unimaginable. In fact lets quote your words Why would these creatures take an extremely dangerous road from refraction to reflection when it's eyes are functioning quite well as they are?.
The answer is remarkably simple, first the road was hardly that 'extremely dangerous' secondly the eyes were not function 'quite well as they were'.
What I find most fascinating is your use of the lobster eye as evidence of what? Surely front loading would not explain your strawman lobster eye problem either?
Then you follow up with the Pecten Maximus and to my surprise you use a reference which after some research was found to be a 1906 (?) reference DAKIN, W. J., 1909. Pecten. The edible scallop. Proc. Trans. Liverpool Biol. Soc., 23: 333-468 or perhaps Dakin, W. J. (1909)
Pecten. Memoirs on typical British marine plants and animals, XVII. Liverpool Marine Biology Committee. or perhaps Dakin, M. L. 1906. Habits, anatomy, and embryology of the giant scallop (Pecten tenuicostatis, Mighels). Univ. Maine Stud. 6:1-71, . It is hard to tell since my local antique store was not carrying this book :-) I am sure that most people on this thread would appreciate that some research may have been done since last century that may help us understand Dakin's 'problems'. One need but to look about half a century later, 1967 when Barber et al showed in The fine structure of the eye
in the mollusc Pecten maximus. Z. Zellforsch. mikrosk. Anat. 76:295–312. how the Pecten eye in fact is well adapted to its environment. I am not sure if Nelson is aware of the fact that Pecten Maximus spends its time in the tidal zones and thus is exposed to both water and air. Remarkably, Pecten Maximus evolved an eye that can work in both environments, in water is works as a catadioptric system while in air the eye works as a dioptric system. The dioptric system is the original optical system while an adaptation of the tapetum led to a secondary imaging element. See also 105Land, M. (1965) Image formation by a concave reflector in the eye of the scallop, Pecten maximus. J.
Physiol. (London) vol. 179, pp.138-153
But there is more
quote:
Pecten took advantage of an opportunity. It pushed its original retina away from the aperture, and backfilled with a new retina near the argentea. The result is a mollusc with two reverse retinas in each eye. More careful measurements might locate the two focal surfaces differently. This result would be consistent with two direct retinas in each eye. As indicated earlier, the transmission efficiency of this eye is poor because the unfocussed light must pass through one retina before imaging at the proper image surface. A probable 50% of the light is lost in this process.
From PROCESSES IN BIOLOGICAL VISION:including, ELECTROCHEMISTRY OF THE NEURON by James T. Fulton
Of course according to Nelson's argument one should conclude that if his comments about the Pecten or the lobster were correct that neither front loading nor evolutionary processes could be responsible for these systems. But interestingly enough more recent data than from the beginning of last century shows that science does move forward in its knowledge. I guess we may even refer to this as a Front loading of the gaps argument :-)
Now to the next posting by Nelson
quote:
This is a good point. If MN is equivalent to Front-Loading, then Mike's hypothesis should be equivalent to Poole's hypothesis about cytosine deamination. And yet, Poole's hypothesis is the exact opposite of Mike's front-loading hypothesis, that an intelligent engineer would use cytosine.
Nelson is confusing the assumptions with the actual evidence. Both hypotheses are the same, one is reached from a teleological perspective the other one from a non-teleological perspective. Of course the teleological perspective should not be confused with evidence of front loading, especially since so far it has not been shown that front loading can be distinguished from methodological naturalism. As Mike has shown what happened since the front loading event is indistinguishable from common descent and evolutionary mechanisms. Since no evidence is provided that front loading was a requirement, the addition of a front loading or front loader seems highly extraneous. In fact since natural processes cannot be eliminated, Dembski would surely not have infered design here.
for those interested in more information about the Pecten Maximus (aka the great scallop) see for instance
Marine Life Information Network for Britain and Ireland - MarLIN
And for the seafood lover
See also trilobite eyes and [Survey of Modern Counterparts of Schizochroal Trilobite Eyes: Structural and Functional Similarities and Differences in Historical Biology 12, 229-263 (1997) by Gábor Horváth et al
[ 10. January 2003, 00:04: Message edited by: Frances ]
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warren_bergerson
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posted 10. January 2003 07:42
Quote Frances: That evidence of common descent may be evidence of front loading as well suggest that Murray is correct. Changes in developmentary pathways hardly is evidence for front loading or against Darwinism either.
Frances and Nelson seem to be using a definition of front loading which means something like ‘hidden information introduced into a system in the distant past which has a significant, even controlling impact on the production of a specific design’. Using such a definition, it could be argued that finding an obscure example of front loading would be equivalent to finding evidence that some external designer did or could have controlled the creation of specific biological designs. This is not a sound scientific interpretation or definition of front loading.
If a design process is defined as a process to find a member of Nf from a set of N possibilities, then the existence Nf, N, and the mechanisms of the search process are all examples of front loading. The existence or occurrence of any design process implies the existence of massive and very complex front loading.
It is easy to show that an element of front loading is necessary to the design process. This is accomplished by removing or changing the component and showing the design process will not occur. There are undoubtedly millions of different and easily identifiable ‘front loading’ components that would disrupt a cells development or which could have disrupted the creation of the Mona Lisa.
The initial and somewhat trivial interest in front loading is its relevance to Darwinian theories and to testing Darwinian theories. Any scientific theory which addresses a design process must logically also address front loading. Design process theories, and evolutionary theories are design process theories, can be disproved either by showing that there are systematic changes in front loading where none should have occurred(evolution of either evolutionary processes or evolution of developmental processes) or by showing that the existing front loading by itself is inadequate to produce what the theory claims can be produced(inadequacy of front loading in development) .
I read yesterday what was described as a quote from Dembski to the effect that Darwin was the promise of predictive scientific theories that have never been produced. The combination of front loading and the permanent and universal interpretation of scientific determinism explain in large part why evolutionary science has found it impossible to produce the promised theories.
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Evan
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posted 10. January 2003 08:02
Warren writes that
quote:
Frances and Nelson seem to be using a definition of front loading which means something like "hidden information introduced into a system in the distant past which has a significant, even controlling impact on the production of a specific design".
Yep, I think that is what front-loading means as it has been used by people like Behe and Mike Gene. As I've read this thread, my suspicion has been that Warren is taking "front-loading" to mean something very different than what everyone else does, and now my suspicion is confirmed.
Whatever Warren means by front-loading (and I'm not sure what that is), it's not the same as what everyone else in the discussion means (which is approximately what Warren describes in the quote above.)
[ 10. January 2003, 08:28: Message edited by: Evan ]
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warren_bergerson
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posted 10. January 2003 10:49
I think the discussion here could benefit from illustrations of some well known and well documented examples of powerful and highly effective forms of front loading. The examples here are from human problem solving, but it is not unreasonable to assume the same front loading mechanisms are involved in essentially all biological design processes. In my initial post, I proposed defining front loading as follows:
WHAT IS FRONT LOADING
The mathematical concept of front loading can be defined in terms of complexity (N/Nf) or improbability(Nf/N) and search processes. For simplicity in discussion let Nf=1. For a complexity of N, a random trial and error search will find the functional or teleological form in .5*N trials or cycles. Front loading or non-random search means that the functional or teleological form can be found in less than . 5*N trials.
The following are three well known types of front loading from human problem solvingt behavior.
STORED SOLUTION
When faced with a problem involving finding one of a small number of Nf solutions from
a very large set of N solutions, one highly effective type of front loading is the stored solution. It is much faster to access a solution stored in memory rather than search for the solution by some lengthy trial and error process.
It is recognized that stored solutions plays an important role in passing adaptive solutions between generations, but does it seems reasonable to suggest that stored solutions play a role in long term adaptive change (adaptation to changing climate for example). Note that while common sense and the available evidence both suggest that stored solutions play a role in adaptive evolution, there is no existing theory which includes such mechanisms.
STORED ALGORITHM
A second highly effective and very common type of front loading is the stored algorithm. Rather than storing the solutions to a very large array problems the system or person stores a ‘simple’ algorithm which allows the system or person to easily calculate a solution to very complex problems. It is obvious that humans routinely use this very effective form of front loading.
It is also abundantly clear that something logically similar to stored algorithms play a major role in evolutionary change. A change in a single factor such as brain size, within limits, is translated into a wide range of corresponding changes in skull size, body size etc. Again, although the evidence clearly supports the existence of stored algorithms in evolutionary change, no existing theories accounts for the phenomena.
SHARED INFORMATION
A third highly effective form of front loading is shared information. Faced with solving a complex problem, one very effective technique is to ‘get the information or solution from an external source’. As should be obvious, humans routinely use the ‘ask an expert’ technique to solve complex problems. Note that using this relatively simple design generating technique requires that very elaborate information sharing processes and mechanisms must be present or front loaded.
Biological systems have very complex processes and mechanisms for sharing information. It seems almost certain that these information sharing processes play a role in evolutionary change. Again no existing theory incorporates information sharing as a mechanism of evolutionary change.
SUMMARY
Science being what it is, there is no reason a scientist like Mike Gene shouldn’t find the study of very weak and obscure front loading processes and mechanisms interesting and productive. To keep such research in perspective, however, it is important to note that there are many well known and very powerful forms of front loading which impact not only human problem solving but also long term evolutionary change. The important issue with front loading, as I have stated from the beginning, is not the obvious and trivial existence of front loading, but the implications front loading has for the development of evolutionary and design process theories.
If Evan is correct and most of the participants here are using the ‘beginning of time’ concept of front loading, then it might be productive to consider in some detail the logic underlying the concept. The beginning of time concept of front loading suggests a multi-billion year, hidden, almost undetectable chains of causation which end in producing a complex biological designs. I personally find it hard to believe that scientists would take seriously any proposal based on such mechanisms.
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Mike Gene
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posted 10. January 2003 11:07
Warren,
I really enjoyed your break down of ways to front-load, as I do think you can make the case that evolution reflects each one.
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Nel
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posted 10. January 2003 15:34
Francis,
In my post I mentioned that one of the fingerprints of front-loading, wrt to my particular examples (and not necessarily Gene's), is that natural selection seems to be sterile in explaining a particular event. So in this respect it is a rejection of chance and regularity.
My question concerning decapod eyes referred to the evolution from refraction to reflection and not what gene for eye development existed in the common ancestor. So I'm still confused as to what you mean when you say my information is oudated.
Now, you say that the answer is "remarkably simple" wrt my Lobster eye example, and then you assert that the road was quite simple and that the early animal's eyes did not function well, without any evidence or justification. You simply leave it at that as if the question was answered by a simple handwave.
The fact is that reflecting eyes can only focus an image if the optics of the system are just right. Front-loading evolution with the ability to take the road to more complexity would certainly explain not only the how but the why of lobster eye evolution.
With respect to the Scallop, you go into a discussion that, it seems as if you are trying to contradict something in my post, but fail to do so. You make the following points:
1. My reference is dated 1908
This is irrelevant as new research has only confirmed Dakin's sentiments and not contradicted it. For example, in the one of the references you cite, M.F. Land (1965) "Image Formation by a Concave Reflector in the eye of theScallop Pecten maximus", and also cited by Michael Denton, shows that it has 60 eyes which reflect from the hemispheric surface onto the retina.
2. You say: "I am not sure if Nelson is aware of the fact that Pecten Maximus spends its time in the tidal zones and thus is exposed to both water and air."
Actually I am quite aware of this. What I am not aware of is what significance this has to anything I discussed. What is interesting about this with respect to one of Mike's points about Front-Loading is that the Spondylus do not swim but are attached to rocks and yet they have developed the same ability as the Pectin. This makes it all the more mysterious for evolution as well, since "adaption to the environment" seems quite irrelevant in this respect.
3. You state:
"In the water the eye works as a catadioptric system while in air the eye works as a dioptric system. The dioptric system is the original optical system while an adaptation of the tapetum led to a secondary imaging element."
Which adds all the more to the complexity of this system. All the scallop's relatives have either photosensitive pits, or primitive camera-type eyes.It is hard to see how natural selection alone, or undirected evolution alone evolved a photsensitive pit to the reflecting image-forming eye of the scallop.
Francis then quotes:
quote:
Pecten took advantage of an opportunity. It pushed its original retina away from the aperture, and backfilled with a new retina near the argentea. The result is a mollusc with two reverse retinas in each eye. More careful measurements might locate the two focal surfaces differently. This result would be consistent with two direct retinas in each eye. As indicated earlier, the transmission efficiency of this eye is poor because the unfocussed light must pass through one retina before imaging at the proper image surface. A probable 50% of the light is lost in this process.
From PROCESSES IN BIOLOGICAL VISION:including, ELECTROCHEMISTRY OF THE NEURON by James T. Fulton
First of all, this does not answer Dakin's concern. Dakin's concern was:
quote:
Whater may have been teh origin of the eyes of the Pecten group I do not hold that utility explains their evolution...We cannot escape the conviction that in one particular series of bivalves, all intimately related genetically, a distinct type of visual organ arose, independent of other visual organs, and that apart from adaptation, and apart from utility or advantageousness, it attained a certain extraordinary complexity.
I agree that Pectin took advantage of an opportunity, but this is more likely due to front-loading rather than undirected evolution. The eye is quite efficient for the need of the scallop. The rays of light are reflected such that the eye perceives them as origination from a point in space. The concave mirror then focuses the light rays inwards, so that they cross. It seems as though scallops were way ahead of their time, the same principle is used in reflecting telescopes, invented by Newton. ![[Wink]](wink.gif)
Now to the next posting by Nelson
I wrote:
quote:
This is a good point. If MN is equivalent to Front-Loading, then Mike's hypothesis should be equivalent to Poole's hypothesis about cytosine deamination. And yet, Poole's hypothesis is the exact opposite of Mike's front-loading hypothesis, that an intelligent engineer would use cytosine.
Francis:
Nelson is confusing the assumptions with the actual evidence. Both hypotheses are the same, one is reached from a teleological perspective the other one from a non-teleological perspective.
Nelson:
Again, I fail to see how this addresses the point. Both hypothesis are absolutely not the same. One states that an intelligent engineer would not use cytosine, and Mike's hypothesis states that the engineer would use cytosine. How are they the same? By the way this is using the data, not assumptions. Francis then repeats his assertions that front-loading is equivalent to non-telological mechanisms without addressing the fact that Poole's hypothesis is the complete opposite of Mike's. Poole wants to say that cytosine is the product of evolution tinkering with the genetic code. Whereas, Mike's hypothesis states that it was an efficient decision of the intelligent agent.
[ 10. January 2003, 15:46: Message edited by: Nelson_Alonso ]
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Mike Gene
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posted 10. January 2003 21:23
Frances: Nelson is confusing the assumptions with the actual evidence. Both hypotheses are the same, one is reached from a teleological perspective the other one from a non-teleological perspective.
Now let's recall the context. Frances originally stated, You seem to suggest that your approaches are unique to ID but so far I would say that your approaches are for all practical purposes non distinguishable from methodological naturalism.
First, the "approaches" are indistinguishable. But now Frances admits the perspectives behind the hypotheses are different. Well, different perspectives are likely to give rise to different approaches (after all, we 'approach' things from a 'perspective'.) In this case, the non-teleological perspective takes an approach that often terminates in the realm of "just happened" (so-called frozen accidents, in this case). The teleological perspective, in contrast, looks for patterns, connections, and relationships. Thus, it should not be surprising that Poole et al. don't really explain why cytosine is part of the genetic material, it's something that just happened and thus something that evolution just had to deal with as best as it could. The only questions worth thinking about is how evolution had to handle it. The teleological perspective can certainly entertain such hypotheses, as it is under no obligation to force every data bit into a teleological mold, but it is able to contemplate things that are out-of-bounds for the non-teleologist, namely, that some things about life were designed to facilitate specific evolutionary events. The teleologist thus enjoys something that compensates for the "extraneous considerations" that concerns Frances - an additional perspective.
And this goes to my question is asked Frances. Poole et al. made a very strong claim. They could have argued that cytosine is in apparent tension with the notion that an engineer designed life. But they go much further, declaring, in an unqualified manner, "Any engineer would have replaced cytosine." That, of course, is a rather presumptuous and strange claim, giving that Poole et. al have no experience designing life forms from scratch. Nevertheless, I asked Frances if he could cite one scientist, in the entire world, who took this assertion on because I knew Frances could not cite a single word from a single person. Even on Brainstorms, where there is no shortage of highly intelligent skeptics among the non-teleologists, there was not one single syllable of doubt. And this all goes back to perspectives. If you are a non-teleologist, stopping at the level of "just happened" is natural. Thus, clearly the approaches are not indistinguishable.
Of course the teleological perspective should not be confused with evidence of front loading, especially since so far it has not been shown that front loading can be distinguished from methodological naturalism.
I can simply repeat from above:
For example, you ask me for evidence that distinguishes between front loading and methodological naturalism. But front-loading is a particular view of ontology while methodological naturalism is a particular form of epistemology. Your request is thus inherently confusing.
As Mike has shown what happened since the front loading event is indistinguishable from common descent and evolutionary mechanisms.
Again I can repeat:
You claim you are not asking for unnatural evidence, yet your problem with evidence for front loading is "all these examples of 'front loading' have played out through, no surprise there, natural, evolutionary mechanisms." Why is this a relevant observation? Of course front loaded evolution is going to play out by natural evolutionary mechanisms. The only way to make sense of your observation is to conclude you want something other than "natural evolutionary mechanisms." Ergo - unnatural evidence.
Since no evidence is provided that front loading was a requirement, the addition of a front loading or front loader seems highly extraneous.
Again, I can repeat:
You continue to work under the impression that design must be a supernatural process and we thus invoke it only when it is "required," that is, when someone can prove it is impossible that natural processes could produce something. But there are many other ways to think about design and front-loading is one of them. Front-loading entails a simple question - how could you design the future through the present? My focus is on this question and determining how plausible this is.
I am under no burden to explain why I need to demonstrate that intelligence is required . You are free to ignore the "extraneous additions." I personally find them to be quite helpful for generating novel testable hypotheses. They also serve as a good check against the intellectual inertia that leads many to stop at the level of "just happened." And the fact that science ignores an alternative perspective is sufficient reason alone to explore it.
In fact since natural processes cannot be eliminated, Dembski would surely not have infered design here.
Correct me if I am wrong, but I don't think Dembski is concerned if his approach generates false negatives.
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Frances
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posted 11. January 2003 13:02
Mike argues that teleology and non-teleology works from different perspectives. I agree that there may be different perspectives from which research is started but in the end they work with the same methodology namely 'methodologicalim naturalism'.
Mike seems to agree when he states that 'But front-loading is a particular view of ontology while methodological naturalism is a particular form of epistemology. Your request is thus inherently confusing.' Thus we seem to agree that methodology wise his approach and Poole's approach are indistinguishable. The question really is, if the ontology proposed by Mike is required and as I have shown it isn't since Poole's ontology led to the same conclusions. One may argue that neither Mike nor Poole have shown how cytosine may have become incorporated but they did both 'discovered' the effects of deamination. Mike is suggesting that there was some pre-existing purpose to this. While it is hard to determine if such a hypothesis has any value after all I have not seen a description of what this 'purpose' may have been? In fact as far as I can tell from other threads, the purpose seems to be indistinguishable from what would be expected from evolution.
May I also point out that while 'methodological naturalism' may be an epistemology, naturalism itself is also an ontology. But these terms only serve to confuse rather than to elucidate what the differences would be between Mike's approach and a non-teleological approach. Both seem to reach the same conclusions although they may be based on different presumptions. So in other words has Mike shown that the deamination of cytosine is evidence of front loading? Without a clear understanding of the hypothesis of front loading, its mechanisms, its purpose, its limitations front loading is a meaningless concept that merely accepts a given initial state without describing how it arose.
Mike objected to Poole's statement that an engineer would not have done it this way by showing that cytosine deamination was used by evolution. But that is not surprising per se, evolution uses whatever is available. The question is: Would an engineer have done it this way. Mike has yet to show that this is the case.
Mike objects that Poole did not provide for an explanation why cytosine is present in the genetic material but I would like to point out that neither does Mike really. Both assume that cytosine was present albeit for different reasons but neither one provides for a testable mechanism.
Mike still seems to believe, incorrectly I may add, that I argue that design needs to be supernatural. Mike believes that front loading is an alternative to Dembski's filter (although it seems that according to Dembski front loading is covered by his approach of elimination).
If the issue of front loading is simple 'how does the present determine the future' then we are basically working from the concept that given the initial state, can we determine how natural processes would play out. But then front loading is not a concept of intelligent design either unless we can eliminate natural processes having led to the initial state or show positive evidence of the design event.
Of course you are not required to show that intelligence is required but then we should not consider front loading to be a useful concept in the arguments surrounding intelligent design.
As far as a naturalistic scenario how cytosine may have become part of the genetic code I refer to the work of Joyce et al who showed how a binary code (D/AU) and a ternary code (GUA) could have existed and how additions of bases did seem to be selectable. The question now remains, why cytosine? I have given a possible scenario in which the binary code arose in the deep thermal vents where cytosine was absent, when however cytosine arose on the same beaches where fox protocells may have arisen, an opportunity was provided for the genetic code to gain a selective advantage.
Of course the scenario is highly speculative but provides for some tests which seem to be absent in the scenario of the 'engineer'.
quote:
The amino acids glycine, alanine, aspartate, serine, glutamate, isoleucine, lysine, proline, valine and leucine are produced at 150ş C in the presence of hydrothermal hydrogen, though in sharply descending order of yield [glycine yield ~2% with respect to KCN + NH4Cl + HCHO with excess CO2 + H2; conditions comparable to those obtaining at the seepage (Hennet et al. 1992)]. It so happens that the most stable RNA triplets
form the codons for just these simple abiotic amino acids (Trifonov 2000).
quote:
If the wobble and transition mutations were dominant a sufficiently long time, the newly formed codons of the strand initially encoding
only glycines and, one step later, aspartic acid, would almost all contain purines G or A in the middle.
and
quote:
Notably, the G alphabet consists largely of polar and charged residues, whereas the A alphabet consists of primarily hydrophobic residues.
Distinct Stages of Protein Evolution as Suggested by Protein Sequence Analysis by Edward N. Trifonov et al
Nic Tazmek provides us with a useful 'analogy' of front loaded design
The ternary code (lacking C) from Joyce
quote:
During the past year, we obtained several novel RNA and DNA enzymes through in vitro evolution. In one instance, starting with the RNA enzyme just described that catalyzes the joining of oligonucleotide substrates, we evolved a variant enzyme that contains only 3 of the 4 nucleotides. It completely lacks cytosine, yet achieves a catalytic rate enhancement of more than 105-fold. Cytosine was chosen for elimination for 2 reasons: First, RNAs that contain only adenine, guanine, and uracil can still form 2 different base pairs (adenine-uracil Watson-Crick and guanine-uracil wobble pairs). Second, cytidine is the least stable of the 4 nucleosides, so much so that it has been argued that cytosine was not present in the first genetic material. From the point of view of RNA catalysis, clearly cytosine is expendable. The evolved cytosine-free RNA enzyme manages to get by with adenine-uracil, guanine-uracil, and purine-purine pairs, as well as various secondary and tertiary structural interactions.
An interesting supporting papers is A supersymmetric model for the evolution of the genetic code J. D. BASHFORD, I. TSOHANTJIS, AND P. D. JARVIS. They show a hypothetical evolutionary scenario in which the first step involves three families, A, C/G and U which would coincide with the ranges of hydrophobicity/hydrophilicity
Nelson.
If I understand your comments correctly, you were quoting from Denton and do not have direct access to the original sources quoted by Denton? Your claim that new research has confirmed Dakin's claims seems to be in stark contradiction with the reality. In fact it has been shown that there can be identified selective pressures to explain the evolution of the eye as found in Pecten. The fact that there are 60 eyes in no way complicates or simplifies matters.
So lets see what we have so far discovered. Nelson quotes from Denton an early 20th century paper which wonders how the Pecten eye may be explained.
First some references to reviews of Denton
Reviews:
"Evolution: A Theory In Crisis" by Michael Denton
Michael Denton - Evolution: A Theory In Crisis
Evolution: a theory in crisis?
Nature's Destiny.
From the impossibility of evolution to the inevitability of evolution: Anti-Evolutionst Michael Denton turns into an 'Evolutionist'.
Observations
1. Front loading would not explain the Pecten eye either.
2. Selective pathways have been identified that may explain the Pecten eye. Dakin stated Whatever may have been the origin of the eyes of the Pecten group I do not hold that utility explains their evolution... but as shown in more recent research a. utility may indeed explain function namely the ability to see well both in and outside water.
Now Nelson seems to be switching to the Spondylus (superfamily Pectinacea). I assume that Nelson refers to Dakin, W. J. 1928b. The eyes of Pecten, Spondylus, Amussium and allied lamellibranchs, with a short discussion on their evolution. Proc. R. Soc. Lond. B, 103: 355-369.. Does Nelson have the original copy or is his argument totally based on Denton's claims?
Lets look at some of the details of Spondylus and Pecten to understand their evolutionary relationships.
Superfamily Pectinacea
Family Pectinidae
Family Spondylidae
In the Spondylus and Pectinidae, the eyes are quite well developed consisting of a cornea, lens and retina. These eyes most likely cannot form a well - focused image but they can detect changes in light intensity with the photoreceptor cells found in the ocelli.
Spondylus squamosus Schreibers, 1793.
The spondylid, te koikoinanti, lives firmly attached to dead coral in intertidal and shallow subtidal regions on the ocean side of the motu and in the lagoon where it is found on sandbars.
From here quote:
ability to produce spines in the family Spondylidae, however, was already apparent in ancestral Pectinacea in the late Palaeozoic.
So it seems from this that the pectinacea were ancestral to Spondylidae. I have not been able to find much about the eyes in the Spondylidae but a likely explanation seems obvious if indeed Spondylidae have similar dual inverted retinas as the Pecten Maximus.
quote:
Numerous tiny black eyes rim the opening of the Atlantic thorny oyster (Spondylus americanus) (left). The eyes sense changes in light intensity and help the oyster, a bivalve (two-shelled) mollusk, detect predators such as sea stars. (Photo by Jessie Cohen/NZP
Source
So it seems that the two live in similar areas but as far as I can tell Pecten is the only one with the dual retinas.
Nelson then claims that quote:
All the scallop's relatives have either photosensitive pits, or primitive camera-type eyes.It is hard to see how natural selection alone, or undirected evolution alone evolved a photsensitive pit to the reflecting image-forming eye of the scallop.
It may be hard to see but others have done quite an excellent job in explaining the possible evolutionary paths from photosensitive pits to the eyes of the scallop or the human. Of course if it is hard to explain then it surely is hard to explain when assuming front loading as well :-)
And then a quantifiable statement
quote:
I agree that Pectin took advantage of an opportunity, but this is more likely due to front-loading rather than undirected evolution
I encourage Nelson to show that it is indeed more likely due to 'front loading' than through selective evolution.
I have provided many references to resources which in detail explain the hypothetical pathways. So far evolutionary hypotheses seem to outperform 'front loading' in this area.
Perhaps Nelson could share with us his hypothesis of front loading that would explain the Pecten and other eyes found in nature?
As far as the lobster eye is concerned, I have shown how the initial confusion on Nelson's part from refractive to reflective is no problem for a pathway in which refractive and reflective eyes have a common ancestor in the form of a light sensitive pit.
Evolution compound eye
Two types
Apposition:
Superposition
From Evolution of eyes Russell D Fernald
Evolutionary pathway
Evolution simple eye
Three types
Evolution simple eye
Pax-6
quote:
Homologues for both Pax6 and Sine oculis have been found in flatworms, a phylum whose members have one of the simplest types of photoreceptors (Pineda et al., 2000). It seems that nature only figured out how to make an eye once, and these basic instructions may underlie the formation of eyes of vertebrates and invertebrates, despite the enormous differences between the structure of these eyes.
Source
quote:
The eyes of squids, flatworms, flies (top row) and vertebrates (bottom row: trumpet fish, human, heron) use
different optical principles and visual pigments and are constructed from different materials, but their development
is always initiated by the same pax6 gene. (Animal photos courtesy BioMEDIA ASSOCIATES, www.ebiomedia.com.)
quote:
The Pax-6 gene encodes a transcription factor containing both a paired domain and a homeodomain and is highly conserved among Metazoa. In both vertebrates and invertebrates, Pax-6 is required for eye morphogenesis; for development of parts of the central nervous system, and, in some phyla, for the development of olfactory sense organs. Ectopic expression of Pax-6 from insects, mammals, cephalopods (phylum Chordata), and ascidians (phylum Urochordata) induces ectopic eyes in Drosophila, suggesting that Pax-6 may be a universal master control gene for eye morphogenesis.
Source
A good Reference
[ 13. January 2003, 00:32: Message edited by: Frances ]
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warren_bergerson
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posted 11. January 2003 13:37
Mike,
I am glad you enjoyed the examples of front loading and I am glad to see you agree that some powerful forms of front loading do appear to play important roles in evolutionary processes. I now want to address the use of front loading in modeling evolutionary or design processes.
To begin, it will be recognized that it is not difficult to construct mathematical models or computer programs that can simulate various types of front loading. You can, for example, start with a simple genetic algorithm search routine that finds adaptive solutions using a basic random variation/selection mechanism. You can then construct alternative models using various front loading processes and mechanisms such as stored solutions or calculation algorithms. It is, or should be, obvious that in most instances it is easy to construct front loaded simulation models that dramatically outperform genetic algorithm programs.
The performance differences between a simple systems based on ‘random variation and natural selection’ and a system using front loading are dramatic. A complex adaptive/evolutionary change that can take billions of years with a simple random variation process can be achieved in a handful of years/generations using front loading mechanisms and processes.
It is important to note that all models and simulations of evolutionary or design processes will involve high levels of front loading. As is often pointed out, even the simplest random variation/selection genetic algorithm model requires/involves huge amounts of front loading.
It is also important to note that even simple genetic algorithm systems involve complex causal processes or machines and involve a variety of causal factors or processes in addition to selection and variation. The lack of conventions for distinguishing different types of genetic algorithm systems and front loaded variations of genetic algorithm systems can often hide the significance of different types of front loading in simulating evolutionary processes.
Once you recognize different types of front loading evolutionary models, one can start looking at the question of predictive theories of evolutionary and biological design processes.
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Mike Gene
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posted 12. January 2003 16:49
Frances: Thus we seem to agree that methodology wise his approach and Poole's approach are indistinguishable.
Wrong. As I just explained, "different perspectives are likely to give rise to different approaches (after all, we 'approach' things from a 'perspective'.) In this case, the non-teleological perspective takes an approach that often terminates in the realm of "just happened" (so-called frozen accidents, in this case). The teleological perspective, in contrast, looks for patterns, connections, and relationships."
The question really is, if the ontology proposed by Mike is required and as I have shown it isn't since Poole's ontology led to the same conclusions.
Wrong again. If you read their paper, there is no mention of the genetic code and something akin to the IHE. It is simply false that the "same conclusion" was reached.
One may argue that neither Mike nor Poole have shown how cytosine may have become incorporated but they did both 'discovered' the effects of deamination.
Wrong again. Poole et al. did not "discover" that cytosine deamination tapped into a codon pool that almost exclusively draws from hydrophobic amino acids (along with effects that choose residues often involved in secondary structure formation) and thus could facilitate protein evolution.
Mike is suggesting that there was some pre-existing purpose to this. While it is hard to determine if such a hypothesis has any value after all I have not seen a description of what this 'purpose' may have been?
Wow, it's there for all to see. It is explicitly spelled out in my original essay.
In fact as far as I can tell from other threads, the purpose seems to be indistinguishable from what would be expected from evolution.
So you are saying that the concept of evolution itself led you to expect what I describe in my original essay? Please explain, in some detail, the basis for this expectation.
May I also point out that while 'methodological naturalism' may be an epistemology, naturalism itself is also an ontology.
So? As we all know, methodological naturalism is not dependent on metaphysical naturalism. Use of the former says nothing about the latter.
Both seem to reach the same conclusions although they may be based on different presumptions.
The same conclusion was not reached.
So in other words has Mike shown that the deamination of cytosine is evidence of front loading? Without a clear understanding of the hypothesis of front loading, its mechanisms, its purpose, its limitations front loading is a meaningless concept that merely accepts a given initial state without describing how it arose.
Obviously, it is not a meaningless concept given that it allowed me to make connections not made by those viewing cytosine as part of a frozen accident. The deamination of cytosine is just one example where mutation events are not random with respect to the residue altered and the manner in which it is altered. Clearly, this is something an engineer might exploit.
Mike objected to Poole's statement that an engineer would not have done it this way by showing that cytosine deamination was used by evolution.
This is rather meaningless, since anything could be "used by evolution." It's not a question of cytosine being "used by evolution," but the specific manner in which it can be employed and whether an engineer might want it this way.
But that is not surprising per se, evolution uses whatever is available.
Sure, but this really doesn't mean anything unless you are under the impression that design is supposed to be something that evolution cannot use. The fact that evolution depends on what is available gives a designer access to evolution, as design can provide what is available to thus guide evolution. For example, the universal genetic code didn't have to be constructed such that it could exploit cytosine deamination to facilitate protein evolution. Evolution didn't have to be built around four bases that had an unequal predisposition to change. Etc. Evolution would still be using whatever is available even if the genetic code was different and cytosine was not part of the DNA. Of course, the results of such evolution would probably be very different.
The question is: Would an engineer have done it this way. Mike has yet to show that this is the case.
Poole et al. made the claim that no engineer would have used cytosine. I have provided one reason why an engineer might have used cytosine. This is sufficient to refute the original claim.
Mike still seems to believe, incorrectly I may add, that I argue that design needs to be supernatural.
It doesn't matter what you add. Unless you believe that design needs to be supernatural, none of your criticisms make any sense. Again, you claim you are not asking for unnatural evidence, yet your problem with evidence for front loading is "all these examples of 'front loading' have played out through, no surprise there, natural, evolutionary mechanisms." Why is this a relevant observation? Of course front loaded evolution is going to play out by natural evolutionary mechanisms. The only way to make sense of your observation is to conclude you want something other than "natural evolutionary mechanisms." Ergo - unnatural evidence.
But then front loading is not a concept of intelligent design either unless we can eliminate natural processes having led to the initial state or show positive evidence of the design event.
That life itself is built around a sophisticated, universal genetic code itself is positive evidence for a design event. But that's another topic and I realize you would not consider this positive evidence. But then that takes us back to what it is that you would consider positive evidence and that will take us off in all kinds of different directions. In other words, what data would cause you to suspect evolution was front-loaded by an intelligent agent?
Of course you are not required to show that intelligence is required but then we should not consider front loading to be a useful concept in the arguments surrounding intelligent design.
This doesn't follow. First, you should only speak for yourself and not some group. Secondly, I fail to see how a concept is useful only when it proves a negative. In fact, I have demonstrated the opposite.
As far as a naturalistic scenario how cytosine may have become part of the genetic code I refer to the work....
I recognize the existence of alternative "could have happened" speculations, but those are not relevant at this point.
Nic Tazmek provides us with a useful 'analogy' of front loaded design
I responded to this years ago.
Unless I get bored or find extra time, you can have the last word, as it seems to me that my original replies to your continued objections still apply, regardless of how you reword them.
[ 12. January 2003, 16:52: Message edited by: Mike Gene ]
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Nel
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posted 12. January 2003 18:47
I'm going to quickly reply to Francis. Then, I want to make sure that I am not hijacking Warren's thread by summarizing the evidence for Front-Loading which both Warren and I agree on (some other time).
Frances links to replies to Denton's "Evolution: A theory in crisis" which has absolutely no bearing on anything I discussed. With the exception of this link:
http://home.planet.nl/~gkorthof/kortho29.htm
Which does not discuss neither the Pectin or Lobseter eye examples I brought up.
Francis then purports to make the following "observations":
1. Front loading would not explain the Pecten eye either.
No evidence or justification is given for assertion number 1.
2. a. utility may indeed explain function namely the ability to see well both in and outside water.
That these eyes can see both inside and outside water does not explain how natural selection and random mutations built the eye without any form of "channeling" evolution.
Francis said:
"Now Nelson seems to be switching to the Spondylus (superfamily Pectinacea)."
I don't understand why Francis would say that I "switched" to Spondylus. I clearly did not.More on this below.
Note that I have read both references in the library however, I originally found the citations in Denton's book. The references are cited for all to see and whether I got it from Denton's book or not is irrelevant.
Francis then writes:
"In the Spondylus and Pectinidae, the eyes are quite well developed consisting of a cornea, lens and retina. These eyes most likely cannot form a well - focused image but they can detect changes in light intensity with the photoreceptor cells found in the ocelli."
Thanks. This is simply reiterating my point. My point about Spondylus was that they do not swim but attach to rocks (and coral), and yet their eyes are as developed as the Pectin maximus which swims for short distances. Denton makes this point in his discussion of the eye of the Scallop.
Francis then says:
So it seems from this that the pectinacea were ancestral to Spondylidae. I have not been able to find much about the eyes in the Spondylidae but a likely explanation seems obvious if indeed Spondylidae have similar dual inverted retinas as the Pecten Maximus.
Nelson:
It may be obvious to Francis but it certainly is not obvious to me. As has been oft stated, evidence of common descent (i.e. similarities) is not evidence of the mechanism of evolution. Which is why I offer up Front-Loading as a mechanism responsible for the change. Perhaps a reiteration of front-loading is in order here since Francis seems to think that common descent somehow contradicts Front-Loading. It doesn't.
Francis then reiterates:
Of course if it is hard to explain then it surely is hard to explain when assuming front loading as well :-)
Nelson:
This is not necessarily true. And this stems from the mistaken notion that FL is equivalent to a non-teleological mechanism. If these biological features were poised to evolve into greater complexity through an intelligent agent then it wouldn't have been as difficult as a blind force tinkering with such a complex system.
Francis says:
I have provided many references to resources which in detail explain the hypothetical pathways. So far evolutionary hypotheses seem to outperform 'front loading' in this area.
Nelson:
I disagree. In none of the papers that Francis referenced does he show a detailed mechanism by which any of the eyes I discussed evolved.
Francis repeates:
As far as the lobster eye is concerned, I have shown how the initial confusion on Nelson's part from refractive to reflective is no problem for a pathway in which refractive and reflective eyes have a common ancestor in the form of a light sensitive pit.
Nelson:
Which is irrelevant. My concern is for the evolutionary pathway between refractive and reflective eyes and not what the common ancestor of eyes in general may have looked like. Again, FL and common descent are not necessarily mutally exclusive. In fact, this would support Mike's statement, that these organisms are in fact, poised to evolve.
Francis's first image is that of the "apposition eye". The website he references simply discusses how this eye works and does not address any of my points. For example, for the second image, the website states:
quote:
The superposition eye is characterised by the fact that the ommatidia cooperate to produce a brighter superimposed image on the retina, they are not isolated. There are three types which are illustrated in the overhead, the refracting, reflecting and parabolic eyes. The are found in nocturnal insects such as neuropteran flies and moths as well as crustacea and crabs.
I don't see any relevance here to what I discussed.
Francis then links to several "pathways", which are obviously images from undetailed lecture notes from here:
http://www-psychology.concordia.ca/SCOL398/L1_398/Evo1.JPG
This site simply says:
quote:
1st stage: simple eye spots: receptors in open cup, limiting pigments. Evolved independently 40 - 65 times.
Very limited. Shadows, no pattern recognition, no prey-predator distinction, good to find congenial environment.
2nd stage: optical system: lens or mirror or other. Evolved only 6 times in the 33 metazoan phyla (96% of species).
There are at least 10 ways to produce images, all known in technology.
Francis then quotes irrelevant material about Pax-6. I have no idea what point he was trying to make with this.
Again, none of this shows how blind natural forces would, nor does it even explain why, natural selection would guide the organism down the difficult road of refraction to reflection in my particular examples. That pathways may exist is not under contention, so the above is again, irrelevant. However, what I would expect from a Front-Loading persepective is that every step of the way was every bit more complex then the last, however, through the help of pre-positioned elements the evolution of these eyes was directed through intelligent agency. Because, as I stated for the lobster eye, the eyes are perfect squares that are fine-tuned for the vision of lobster.
I gave a model for what a Front-Loading perspective might bring to the table concerning these systems. Crystallin proteins have been coopted in evolution from prior uses as enzymes, and they have in common only that in high concentration they process the requisite optical properties. The crystallins are found in all vertebrate lenses. They are there as a result of the evolutionary recruitment to an eye differentiation gene battery of genes encoding proteins of the heat shock/chaperone family. The chicken lens crystallin is similarly the product of gene encoding arginosuccinate lyase enzyme that was recruited for function within the eye lens, but only in the bird/reptile branch of the vertebrates. These cooptions to eye lens differentiation gene batteries may have been the product of front-loading, i.e., the presence of Pax6 in the appropriate domain of the eye anlage during development.
Let me bring this home and remind everyone participating why I even brought up Denton's examples (and he has numerous ones, including the avian lung, and the human brain). These kind of examples are what Morris had in mind, that people like Conway Morris and Denton -think that evolution is such that we will get a particular result. In Morris' ariticle discussed by Mike Gene, with respect to channeling evolution, Morris cites Denton's book.
Crabs, which operate in the same niche as the lobster have refracting eyes and do just fine. So why go on the difficult journey towards the more complex reflective eye? That organisms have an underlying "floor-plan" might be the answer. It may be that there are what Dennett tagged "Good Tricks" in specific cases: and that these will be independently reached but this only applies to traits and not whole configurations.
[ 12. January 2003, 19:49: Message edited by: Nelson_Alonso ]
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Frances
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posted 13. January 2003 01:52
Mike seems to have avoided addressing the real issues and instead focused on some minor issues. First of all Mike objects to me stating that his approach and Poole's approach led to the same conclusion. Mike correctly points out that I confused Poole's paper with the papers in which the link between cytosine deamination and increase hydrophobicity was made. While I thank Mike for correcting my minor error he seems to have ignored the real issue namely that he used methodological naturalism to explain the tendency of cytosine deamination to incrase hydrophobicity. In fact from the moment he defined the instance of 'front loading' his approach is indistinguishable from methodological naturalism. Neiter Mike nor others may have explained or shown how cytosine became incorporated but both work from the assumption that it was. Mike suggests that his approach allowed him to address the claim that 'an engineer would have replaced cytosine' but nothing in his approach supports this argument. All he has shown is that natural processes seem to have led to cytosome deamination and a corresponding increase in hydrophobicity. No effort was made to show that an engineer would or would not have used cytosine or would or would not have replaced cytosine. In fact Mike has made no effort to show any link between his findings and the idea of front loading. Looking back in time and then saying that it must have been front loaded because it seems to have been selected for is begging the question. Mike complains the evolutionary approach claims that it must have been chance/evolution but that is not very different from 'it must have been design'. Both are assumptions which would require some supporting evidence. The fact that cytosine deamination leads to increased hydrophobicity is no evidence of the premise that 'chance did it' nor 'an intelligent designer did it'. Mike wants to argue that different perspectives give different approaches but I'd argue that these approaches are not distinguishable from methodological naturalism. No teleology is required to explain what happened t>t_0 and no evidence of the need of teleology at t=t_0 has been provided.
Mike does suggest that he provided a description with 'purpose' but that seems to be like painting the bulls eye around the arrow, to use a common metaphore. Mike suggests that his approach allowed him to pre-specify that deamination of cytosine increased hydrophobicity but that seems hard to imagine. The concept of evolution would also predict that if cytosine deamination were an important contributor to the increase of hydrophobicity and that if such increase would be increasing fitness that cytosine deamination events would be common.
It has been argued that Mike's approach canm not been distinguished from methodological naturalism approach and that the findings do not help us answer the question of the presence of cytosine at instance t_0, the moment of front loading. Thus either chance/necessity or intelligent design may have been responsible for what happened at time t_0 but after time t_0 it was all methodological naturalism and not intelligent design.
Mike suggests that since cytosine inclusion was not a frozen accident his premise may be preferable. But lets point out that Mike does not explain anything about the 'frozen design incident' thus leaving it for all practical purposes indistinguishable from a 'frozen accident'. Additionally Mike may have created a strawman of 'frozen accident' when the actual mechanisms may have been a combination of availability and selective advantages. That an engineer may exploit the same pathways that evolution may exploit also does not help us address the issue of front loading. Front loading/origins are separate from the evolution t>t_0. Mike however has not provided any evidence that the event at t=t_0 involved front loading. Mike did initially suggest that there was some problem with cytosine formation in prebiotic world which would have been a way to eliminate chance/regularity as a possibility and thus strengthening a design inference but as I have pointed out our knowledge has increased and potential and realistic pathways may have been identified.
Mike seems to agree that from t=t0 forward evolution did play a role, so now the question is if t=t_0 requires an intelligent designer or preferably involved an intelligent designer. So far no evidence has been provided that this is the case. If Mike wants to limit his claims to just refuting Poole then his efforts may have helped towards this goal but then the issue of front loading seems irrelevant. But I would say that Mike has not shown how the engineer is in any way limited in what he/she would or would not do.
Mike still seems to be confused when insisting that I claim that design has to be supernatural. I am pointing out that t>t_0 does not help resolving the intelligent design claim and that t=t_0 has not been addressed. You suggest that at t=t_0 some event took place without really defining the moment t=t_0, the circumstances of the event, the goals of the event. Mike merely claims that at t=t_0 there was an initial state namely cytosine was present as one of the four bases in DNA. Unless Mike wants to argue that at t=t_0 a supernatural design event took place, he has no reason to suggest that I am requiring a supernatural design.
Mike now suggests that the existence of a 'sophisticated, universal genetic code' is positive evidence of a design event but Mike once again fails to show this to be the case. In fact no positive evidence of such a design event has been provide, merely claimed. But that sounds like a 'front loading of the gaps' explanation. Since Mike seems to agree that from this moment forward everything was fully explainable in natural terms, and no need for intelligent design was required he basically has used the data which supports common descent to argue for 'common design' without really explaining anything about this 'design'. Countless papers and hours of research have been involved in providing for and actually finding plausible pathways to explain the origins of the genetic code and none so far seem to have found any evidence of this intelligent design event, in fact what may have been a good point to place t_0 seems to have been pushed back over time from the Cambrian to the prebiotic RNA world.
Mike wants to know what data would cause me to suspect that evolution was front loaded. This would require the following 1. Mike needs to define what the purpose or goal(s) are of the intelligent agent 2. Mike has to show that given the chaotic and unpredictable nature of the world around us, this goal can be reliably reached 3. it can be shown that natural processes without intelligent design could not have achieved the state at t=t_0 4. it can be shown that there was indeed an intelligent agent present at t=t_0.
Mike objects to my scenarios of how cytosine may have become part of the genetic code as irrelevant but they are very relevant in understanding what happened at t=t_0. Mike does not seem to have any evidence of front loading at t=t_0 to required intelligent agent. Thus it is very relevant to show that the front loading at t=t_0 can be explained from a naturalistic perspective without the need for ID. At t>t_0 Mike and I seem to agree that it was purely natural processes at work without the need for intelligent design.
As far as Nic's analogy, Mike may have responded but that may be far from having addressed Nic's observations. In fact I would argue that you did not even address Nic's claims.
I hope that Mike will not feel to bored to address the arguments I raised rather than dismiss them by discussing some irrelevant side issues.
Dear Nelson.
It seems clear to me that you are ignoring the details provided by me about possible pathways for evolution.
If you claim that front loading explains Pecten then you accept that evolution can generate the eye as found in Pecten unless you are not talking really about front loading but intervention.
Perhaps you can first share with us your front loading hypothesis wrt for instance Pecten and the Lobster? In fact you suggested that Pax-6 gene 'supports front loading' but if that is the case your argument seems to be that given the existence of Pax-6 at an instant t=t_0 you expect evolution to lead to the large variety of eye 'designs' as found in nature. Is that correct or are you backtracking your claims that let's say every species/family/genus/ or at whatever level was 'front loaded' independently at different instances in time/space?
I doubt that one can make a logically consistent claim of front loading that is not contradicted by the data other than through the Pax-6 gene. But Pax-6 seems to be going back in time quite some distance, long before the family Pectinidae arose.
To me it seems that you are not arguing for front loading but rather intervention since your objections seem to be terribly ad hoc and seem to refuse to recognize natural pathways to these structures. If that is the case then you cannot be arguing for front loading since teleological front loading is defined to be at t=t_0 the necessary information was inserted so that at a given time t1, with t1>t0, a certain feature arises in a certain family/species. Non teleological front loading would be that at a certain instance t=t_0 an initial state exists and we can trace back to such an initial state showing how the various eye 'designs' all seem to trace back to ancestral forms.
As far as the references to Korthof et al, they are meant to help the interested reader understand many of the problems found in Denton's work.
It seems evident to me that Nelson has not familiarized himself with the papers he quotes but rather that he is relying on second hand information which may or may not be relevant or even accurate. As I have shown, Dakin's 1908 statements are explained in more detail in 1967 and onwards where it was shown that the Pecten eye is very likely an evolutionary continuation of the single retina eye with the addition of a reflecting layer. The transition is even better to understand from a selective evolutionary viewpoint when realizing the advantage of these changes namely the ability to see both in and outside water. Combine this with the fact that the Pecten resides in a tidal affected area and thus may be exposed to both water and air and one realizes the selective advantage of the Pecten eye. Thus we have found the answer to Dakin's uncertainties. Nelson complains that I do not provide sufficient detail how natural selection and mutation built these eyes but if Nelson were to argue for front loading he would have no choice but to accept that natural forces can lead to the Pecten eye or Nelson should drop his claims about Pecten and front loading. Surely our ignorance of certain details should not be taken as evidence for front loading. In fact although we have not yet obtained all the necessary evidence a plausible pathway has been provided. Nelson may be complaining about 'sufficient details' but the amount of detail so far already exceeds any alternative hypothesis. And since Nelson seems to want to argue front loading he also by default has to accept some time period in which evolutionary processes shaped the eye of Pecten to what it is right now.
Nelson then raises the spectre of Spondylus, which attaches to rocks as if this forms a problem. Until Nelson can show us from the original research papers what the eye of the Spondylus looks like as compared to Pecten we have no real way to discuss this. Secondly until Nelson shows that there is actually a problem explaining the evolution of the eye in Spondylus and Pecten, we merely can speculate about what Nelson's 'argument may be'. Since Nelson seems to accept the evolutionary history of Pecten and Spondylus one may wonder why he seems to oppose that evolutionary processes led to the eye 'designs' since he does seem to accept front loading and common descent. Perhaps Nelson believes that another mechanism than evolutionary mechanisms played a role? He mentions front loading but as I have shown that merely states that at a given stage in time t=t_0 information was injected into the genome to allow Pecten and Spondylus to form their respective eyes. The fact the pectinacea were ancestral to Spondylidae surely supports the evolutionary pathway. So it is not clear to me how Nelson suggests front loading could have helped Pecten and Spondylidae. In fact, if Nelson is correct about the location of the Spondylus and its eyes (so far the data seem to be vague on either aspect) then Nelson may have to explain why a front loader would lead to a system which is now defunct namely the ability to see in air.
Nelson then confuses the issue of front loading and intervention even further when he states quote:
If these biological features were poised to evolve into greater complexity through an intelligent agent then it wouldn't have been as difficult as a blind force tinkering with such a complex system.
Is Nelson suggesting that evolution is guided through an intelligent agent. Then he should not be arguing for front loading but instead for intervention.
Nelson still seems to be unwilling to deal with the available evidence which includes intermediate stages for the varieties of simple and compound eyes. Perhaps Nelson wants to argue that the details are not sufficient but that's just a matter of time for science to find all the common genes and variations that have led to the variety of eyes as found in nature. So far the evidence strongly suggests both evolutionary mechanisms and at least for many basic components a common ancestor.
If Nelson had taken the time to look at the pictures then he would have noticed how these portray the variety of intermediate paths likely to have been taken in the evolution of the various eye forms.
Nelson still repeats his so far unsupported assertion that quote:
Again, none of this shows how blind natural forces would, nor does it even explain why, natural selection would guide the organism down the difficult road of refraction to reflection in my particular examples
1. Could Nelson show that the road of refraction to reflection is difficult
2. Could Nelson show that the road of refraction to reflection is even relevant for the lobster?
Nelson confuses the situation even further by claiming that
quote:
However, what I would expect from a Front-Loading persepective is that every step of the way was every bit more complex then the last, however, through the help of pre-positioned elements the evolution of these eyes was directed through intelligent agency.
So is it front loading or is it intervention? If it is front loading then we have the situation that at a certain time the information needed for evolution to play out was injected into the genome of a common ancestor and that from this common ancestor all the descendants arose with the large variety of eyes. Ignoring for the moment the grasping at straw nature of such a front loading scenario which would have to play out through an inherent chaotic and thus unpredictable system and interactions to eventually lead to the eye of the Pecten. Nelson presents no more evidence than that a some moment the basic building blocks were present that eventually would allow the Pecten or any other organism to evolve an eye design. No effort is made by Nelson to show that the eyes of the lobster are optimal for the functioning of the lobster. In fact Nelson merely argues that for the lobster eye, the eyes are perfect squares that are fine-tuned for the vision of lobster. No further information is presented to support this case. And if Nelson wants to consider fine-tuning and continue to argue for front loading then Nelson de facto has accepted the fine tuning power of evolutionary processes.
Given the contradictory stance of Nelson on the issue of front loading I would encourage Nelson to address the following issues.
1. Explain the hypothesis of front loading as it applies to Pecten.
2. If Nelson accepts front loading then does Nelson accepts that natural processes are responsible for the shaping of the eyes of Pecten? In absence of such an acceptance, Nelson cannot be talking about front loading here.
3. Can Nelson explain in detail the similarities and differences between Pecten and Spondylus and can Nelson provide us with the arguments proposed by Dakin? Do the findings apply to the whole family of Spondylus or just some particular species? After all the various species of Spondylus do seem to occupy a large variety of ecological niches
4. Can Nelson show that the lobster eyes are perfect squares or is Nelson using stylized drawings to reach these conclusions?
Perhaps Nelson may want to explain why the squares in the following picture are all but perfect?
Perhaps Nelson was confused by the resulting drawings?
Perhaps Nelson can also appreciate what perfect squares really would look like?
Finally since these squares are crystals why is it not a surprise that they tend to be geometrical? As far as the 'problem of refraction versus reflection' it may be noticed that there are few differences between a refracting and reflecting ommatidia.
[ 13. January 2003, 07:27: Message edited by: Moderator ]
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