Microevolution vs. Macroevolution

[Student Nurse]

Last semester I took Microbiology. Before then I was a Christian and believed in creation, but what I studied and what I saw undoubtedly proved evolution - hence the "switchover" or "atheistic conversion" or whatever you want to call it.

I hear a lot of Christians say "the microbiological world proves microevolution" (i.e. evolution on the small scale such as bacteria adapting to new hosts/environments and incorporating plasmids into their DNA in order to become resistant to antibiotics), "but that doesn't prove macroevolution" (ie human evolution)

If this isn't true, then what does it prove to you? How can something be true on the small scale and not on the large? (give examples please)

[Galphanore]

otseng, do you have me on ignore?

[Galphanore]

I would like to know what you think is a complex mutation?

DNA mutations should result in a synthesis of a novel amino acid sequence which in turn produce novel and functional proteins. We can start with this. Are there any examples of a new protein that have evolved through mutations?

Yes.

[Rob]

You have to remember, evolution is incremental and accumulative. I would like to know what you think is a complex mutation?

I don't doubt the fact of organic evolution. But the theory regarding the mechanisms is open to change, kind of like evolution itself. Descent with modification does not necessarily depend upon the classical understanding of incremental and accumulative change in individual alleles (gradualism) which in themselves result in imperceptible change. There are modular genetic entities (Hox gene families, for example) which can via recombinatorial rearrangement bring about new devepmental pathways, and this is perfectly compatible with "greater leaps in evolution" of morphological features:

Gene and Genome Duplications as Resources for Genetic Pathway Evolution

(....)

A Note on Modularity and Entrainment, or What the Classic Neo-Darwinian View Missed

In the light of contemporary molecular biology, one can perceive something that was invisible to biologists during the formulation of the Modern Synthesis. It will be recalled that neo-Darwinian evolutionists in the first half of the 20th century believed that only mutations of very small phenotypic effect were likely to survive and be positively selected (Fisher, 1930). That supposition was reasonable at a time when the gene was a mysterious entity, there was little knowledge of the wide differences in functional type between different gene products, and indeed, the actual nature of gene products was ill-defined. The Fisherian assumption was reasonable in light of both general knowledge of pleiotropy, on which it was based, and the observations of developmental geneticists, who studied mutations of large effect that, in virtually all cases, made organisms less fit than the respective wild type. According to Fisher's argument, visible mutational effects could produce only disorder and dysfunction in previously well-adapted systems. (Wilkins 2002: 348)

Advances in both population genetics and molecular biology, however, have rendered Fisher's argument less compelling.... Chielf among these [advances in evo-devo and developmental genetics] is the finding that genes are not autonomous actors, but participate within functional groupings, broadly termed "modules" (Raff, 1996; Hartwell et al., 1999). The correlate of this property is that genetic alteration of of one component of a module alters the operation of the module as a whole. That, in turn, imparts a degree of order to mutant effects themselves. (Wilkins 2002: 348)

-- Wilkins, Adam S. The Evolution of Developmental Pathways. Massachusetts: Sinaur Associates; 2002; p. 347.

One of the most important sources of novel gene functions, gene duplications play a major role in evolutionary change. (....) The notion of "evolution by gene duplication" was proposed in 1970 by Susumu Ohno, who argued that gene and whole genome duplication provided the raw material for evolutionary innovations such as subcellular compartments, fins, and jaws. (....) Ohno also proposed that two rounds of whole genome duplication occurred at some point in early vertebrate evolution--a possibility that could explain the relatively large size and complexity of the vertebrate genome. (Gross 2005: 1676)

(….) Recent studies have shown that the global pattern of the physical location of homologous genes provides evidence of ancient whole genome duplications in yeast and plants, even when most of the duplicates have degraded. (….) Dehal and Boore identified over 3,500 gene duplications present in multiple vertebrates, indicating they had occurred at the base of the vertebrate tree, dating back some 450 million years. (….) When considering only this subset of 3,500-plus early vertebrate duplications, they found a global pattern of human genome segments with similar arrangements of paralogous genes and multiple chromosomes with long linear stretches of interdigitated sets of paralogous genes--evidence that the duplications occurred in large segments. Even stronger support of the 2R hypothesis comes from the observation that the collinear arrangement of these genes is predominantly in a 4-fold pattern; this repetitive pattern is seen accross almost all the human chromosomes. It’s unlikely, the authors argue, that any combination of smaller, independent duplication events could have generated the same pattern. Now that strong evidence for Ohno's hypothesis exists, researchers can investigate both the mechanism of genome duplication events and their possible effects on vertebrate evolution. It seems likely that a whole genome duplication would provide combinatorial possibilities that could permit a greater leap in evolution than could single gene duplications, even if the single gene duplications affected the complete set of genes. Studies that examine the function of these paralogous genes can explore whether these large-scale genomic events helped drive organismal complexity and diversification within the vertebrate lineage. (Gross 2005: 1676)

-- Gross, Liza. Synopses of Research Articles: Clear Evidence of Two Rounds of Vertebrate Genome Duplication. Public Library of Science (PLoS) Biology. 2005 Oct; 3(10):1676-1677.

[Goat]

Before I go on, what is your concept of what the evolutionary theory is? What is your definition of a species. I want to know your assumptions first, so we don't play the game of equivocation.

This is probably a good idea at this point.
My argument is against the commonly held belief that small, random mutations leading to gross changes capable of eventually changing a single celled organism into a blue whale is proven. Lets ignore the problem of how we got the organism for the time being.
Definition of species.... this is tough because even the scientific definition doesn't marry with real world observation. Many animals classified as distinct species have been found to be able to breed.

Would you say that a chimpanzee and a human are different species? Would you say that two strains of flys that can not reproduce seperate species?

[Goat]

You have to remember, evolution is incremental and accumulative. I would like to know what you think is a complex mutation?

I don't doubt the fact of organic evolution. But the theory regarding the mechanisms is open to change, kind of like evolution itself. Descent with modification does not necessarily depend upon the classical understanding of incremental and accumulative change in individual alleles (gradualism) which in themselves result in imperceptible change. There are modular genetic entities (Hox gene families, for example) which can via recombinatorial rearrangement bring about new devepmental pathways, and this is perfectly compatible with "greater leaps in evolution" of morphological features:

Even the use of Hox genes does not mean that the changes are incremental and accumlative. Nor does it say that it always goes at the same pace. You are not going to get an animal the size of the mouse into the size of an elephant in just 2 or 3 generations. That still does not stop the 'filter' of natural selection from increasing the beneficial mutations in the population and reducing detriemtnal mutations in the population (over time). It just means that the mechanism for creating the variations in the population is a bit more complicated.

[Rob]

The problem is it doesn't take a major, complex change to gain a huge benefit. A little stronger fins of a fish and you have something that can swim through muddier water, put the eyes a little closer together and that same creature can see bugs on the water surface easily....

That creature's fossiles were found by using the predictive ability of evolution. They tried to determine what characteristics of the environment would lead to a fish becoming able to travel on land. They considered that a major factor would be that it's water home would have to be going away, so they looked for locations that would have had something like that. They came upon the canadian north, where the ponds this guy lived in were drying up, so the creatures in the water that ended up able to survive were the ones able to travel from one dying pool to another, such as it.

Galphanore, I have read the text on the site and something is not adding up. Your interpretation appears to be implying a scenario that is not being claimed by the authors, unless I have missed the source you are basing this claim upon. If so, please cite it, otherwise, it appears you are reading incorrectly into this information a conclusion that is erroneous. According to their statements below, they never state that they found this "creature's fossils ... by using the predictive ability of evolution," or prior to their finding the fossil "tried to determine what characteristics the environment would to a fish becoming able to travel on land," and that they predicted "that a major factor would be that it's water home would have to be going away." In fact, they appear to be saying the exact opposite!

Before the discovery of Tiktaalik we knew that limbed animals (tetrapods) were well along their way to invading land by the Late Devonian (around 360 million years ago). We also knew that some fish in the Middle Devonian (375 million years ago) were experimenting with the internal structure of their fins in ways that would ultimately allow for the evolution of the weight bearing structure of tetrapod limbs. The thought was that as the habitat in the Devonian changed and became drier, fish with limb-like fins were able to survive and propagate because they were able to move from pond to pond over land in search of food and new habitats. ( http://tiktaalik.uchicago.edu/fossil.html )

First, they are stating that prior to finding the fossil their assumptions were the classical idea that as the environment became drier, those "fish with limb-like fins were able to survive ... because they were able to move from pond to pond over land in search of food and new habitats." Then they go on to say upon the discovery of the Tiktaalik fossil they "changed this thinking drastically."

The discovery of Tiktaalik changed this thinking drastically. It is clearly a fish because it has scales and fins, but it is also clearly living in shallow water environments. How do we know this? Unlike its fishy contemporaries, Tiktaalik's body is extremely flattened. Its eyes are on the top of its head, suggesting it spent a lot of time on the bottom[/i], looking up. Its shoulders are not connected to its skull, giving it a functional neck. And it has ribs exactly like those of its contemporary tetrapods which were used to support the body and aid in breathing. ( http://tiktaalik.uchicago.edu/fossil2.html )

Again, it appears that Galphanore has missed the essential point of the authors, which was that prior to the discovery of the fossil it was assumed that it was the change in environment (drying up of pools) that led to those fish with "limb-like" features surviving in greater numbers because their was an adaptive advantage to being able to move from pool to pool. But what they found, and what required them to "change this thinking drastically," was the fact that these fish with "limb-like structures" were not escaping dried up ponds but rather living in shallow water spending "a lot of time on the bottom," thereby suggesting that the "limb-like" structures were used for moving along the muddy bottom and not necessarily for moving "from pond to pond."

We also now know that the deeply conserved genetic architecture for the evolutionary developmental pathway for fins-to-limbs, a fact not predicted by the classical neo-Darwinian Modern Synthesis, are controled by the Hox gene familiy, which provides the underlying genetic architecture and potential for limbs (via limb-like fins) in fish already existed. Fin, limb, and wing development are well undestood on the molecular level within evolutionary developmental biology:

The following article proposes that some other "macroevolutionary" (body plan) differences may be produced by genetic factors operating during embyological growth and development. The new field of "evo-devo" ... explores these and other subjects. The the review article by Hughes and Kaufman introduces some of these ideas as applied to the anthropod body plan....

Hox Genes and Evolution of the Anthropod Body Plan

Introduction

The evolution of different animal body plans is one of the great mysteries of biology. The phylum Anthropoda, for instance, includes millions of extinct and extant species with diverse morphology, including ticks and trilobites, crabs and centipedes, spiders, shrimps, and spittlebugs. From basic organization consisting of a series of segments encased in an exoskeleton, the various anthropod groups have developed a multitude of specialized forms. Such morphological diversity begs the question of how it arose. To answer this question in invoking natural selection is correct--but insufficient. The fangs of a centipede, the sucking proboscis of a bug, and the claws of a lobster indisputably accord these organisms a fitness advantage. However, the crux of the mystery is this: From what developmental genetic changes did these novelties arise in the first place? To begin to address this question, researchers have turned to the Hox genes. (Scott 2004: 191)

The Hox genes are a set of related genes encoding homeodain transcription factors. The genes are important developmental regulators, acting together to determine the identity of segments along the anterior-posterior axis of the embryo. Each Hox gene is thought to control the expression of a variety of target genes, which may number into the hundreds. Thus the activity of a single Hox gene can be sufficient to induce an entire "developmental module" of target genes, which act in concert to confer a particular identity upon a developing segment. Express a Hox gene in the wrong place, and a completely different kind of appendage will develop. For example, gain-of-function mutations in antennapedia cause legs instead of antennae to grow out of the head of the fruit fly. Because of their important role in determining segment identity, the Hox genes are closely associated with development of the regionalization of the body plan. (Scott 2004: 191)

In fact, it seems to be the expression profile of the Hox genes and their activity that are largely responsible for determining the body patterning of a species. Therefore, evolutionary changes in the expression of Hox genes or their activity might have caused evolutionary changes in body patterning. Why does the lobster have two pairs of specialized front legs (maxillipeds), whereas brine shrimp have none? It seems to be correlated with a shift in Hox gene expression. Why do insects have a thorax and abdomen, whereas centipedes have just one long homonomous trunk? Again, the difference may be due to the different expression of Hox genes. (Scott 2004: 191)

The Hox genes are typically found together in a single complex on the chromosome. The genes promote the identity of segments along the anterior-posterior axis of the embryo in the same order in which they lie on the chromosome…. In addition to conferring identity to segment(s) via target genes, most Hox genes interact with each other to maintain proper expression domain boundaries by both positive and negative regulation. For instance, in general a more posterior gene will suppress the expression or the function of the more anterior Hox gene, phenomena known as posterior prevalence, posterior dominance, or phenotypic suppression. Thus, Hox genes are not merely located together on the chromosome, but they also interact together in complex ways to collectively define segment identity along the anterior-posterior axis of the embryo…. (Scott 2004: 191-192)

Our goal in this review is to introduce the reader to the role of the Hox genes in the evolution of the anthropods. The cast of characters includes some genes that have changed their developmental roles wildly, some genes that have merely tweaked their expression patterns in different species, and some that have stubbornly remained expressed in a nearly invariant pattern. (Scott 2004: 192)

… Because of the high conservation of the Hox genes and their important role in specifying segment identity, they have been studied in many anthropod species. Unfortunately, this wealth of information is scattered among dozens of original data articles and thus is not easily compared. (Scott 2004: 192)

… After all, in general researchers are not obsessed with studying, say, a particular species of centipede purely for its own sake. Rather, each seemingly arcane study is meant to provide some enlightenment into general principles of evolution that may apply to all animal life. But have we actually achieved this quixotic goal? To some degree the answer is yes. In fact, the study of changes in anthropod Hox genes might well be called one of the first success stories of the nascent field of evo-devo. In addition to a greater understanding of the development of particular anthropod species, emerging themes have led to some provocative general models for how Hox genes may have been involved in evolution…. The comparative work in anthropod hox genes has been truly revolutionary because it has succeeded in providing some of the first concrete models of the mechanistic basis of morphological evolution (pp. 459-462). (Scott 2004: 192)

… Although our understanding of genetic events that occurred million of years ago can never be totally conclusive, the ability to simulate evolutionary events in the laboratory environment by manipulation of a critical gene would be convincing evidence to support a theoretical model. With the increased power of expanding functional techniques, the field of anthropod evo-devo is coming to the stage of its development in which some of the beautiful theories described here are bound to be shattered by some ugly facts. But as developmental biologists know, although the coming-of-age process may be awkward at times, it is a necessary step to full maturity. Finally, in further studies we must avoid Hox snobbery. Although Hox genes are important developmental regulatory genes and have been extremely practical to begin studying the evolution of the anthropod, analysis of the Drosophilia genome suggests that there are approximately 13,590 other genes in the genome, which we have barely begun to explore in other species (p. 494). (Scott 2004: 192)

[References omitted.]

Selection excerpted from:

Hughes, Cynthia L., and Thomas G. Kaufman. 2002. Hox Genes and the Evolution of the Anthropod Body Plan. Evolution and Development 4 (6): 459-499.

-- Scott, Eugenie C. Evolution vs. Creationism: And Introdution. California: University of California Press; 2004; pp. 191-192.

[Galphanore]

From here :

Our team has been looking for this fish for past six years. We made four trips up to the Arctic to find this particular kind of fish. The first year we struck out almost completely. The second year we found bits and pieces of some things that suggested that something might be there. The third year we found a locality and larger bits of fish that suggested we might be on to something important. And it wasn't until the fourth year, July 2004, when we discovered whole skeletons of this creature.

I think that fairly well justifies my use of the phrase "using the predictive ability of evolution" and from the very part you highlighted :

The thought was that as the habitat in the Devonian changed and became drier, fish with limb-like fins were able to survive and propagate because they were able to move from pond to pond over land in search of food and new habitats.

Shows exactly what I claimed. They did go to that region because they thought the land would require it to move from pond to pond. Whether or not that was accurate in the end is irrelevant.
Also, from here :

When you take all these features together--from a fin with a shoulder, an elbow, and a wrist, to a neck, to ribs--what you have is an animal that can prop up and support itself in gravity. It has a very strong arm-like fin. It has a head that can move independently of the body. It has eyes that are on top, not on the side, so that it is able to look up. You have an animal that is able to support itself in gravity, either in the shallow waters, or on land.

Which very directly shows they have not discounted the idea of it moving from pond to pond, only that they have discovered that it's primary habitat, when it is able to remain in it, is shallow water. Which makes since in my interpretation because the drying pools would be shallow, and getting shallower. Perhaps you should read more of the linked page before assuming someone is completely wrong in their understanding of it.

They even have video's for each of those quotes.

[Rob]

The problem is it doesn't take a major, complex change to gain a huge benefit. A little stronger fins of a fish and you have something that can swim through muddier water, put the eyes a little closer together and that same creature can see bugs on the water surface easily....

That creature's fossiles were found by using the predictive ability of evolution. They tried to determine what characteristics of the environment would lead to a fish becoming able to travel on land. They considered that a major factor would be that it's water home would have to be going away, so they looked for locations that would have had something like that. They came upon the canadian north, where the ponds this guy lived in were drying up, so the creatures in the water that ended up able to survive were the ones able to travel from one dying pool to another, such as it.

Before the discovery of Tiktaalik we knew that limbed animals (tetrapods) were well along their way to invading land by the Late Devonian (around 360 million years ago). We also knew that some fish in the Middle Devonian (375 million years ago) were experimenting with the internal structure of their fins in ways that would ultimately allow for the evolution of the weight bearing structure of tetrapod limbs. The thought was that as the habitat in the Devonian changed and became drier, fish with limb-like fins were able to survive and propagate because they were able to move from pond to pond over land in search of food and new habitats. ( http://tiktaalik.uchicago.edu/fossil.html )

First, they are stating that prior to finding the fossil their assumptions were the classical idea that as the environment became drier, those "fish with limb-like fins were able to survive ... because they were able to move from pond to pond over land in search of food and new habitats." Then they go on to say upon the discovery of the Tiktaalik fossil they "changed this thinking drastically."

The discovery of Tiktaalik changed this thinking drastically. It is clearly a fish because it has scales and fins, but it is also clearly living in shallow water environments. How do we know this? Unlike its fishy contemporaries, Tiktaalik's body is extremely flattened. Its eyes are on the top of its head, suggesting it spent a lot of time on the bottom[/i], looking up. Its shoulders are not connected to its skull, giving it a functional neck. And it has ribs exactly like those of its contemporary tetrapods which were used to support the body and aid in breathing. ( http://tiktaalik.uchicago.edu/fossil2.html )

Again, it appears that Galphanore has missed the essential point of the authors, which was that prior to the discovery of the fossil it was assumed that it was the change in environment (drying up of pools) that led to those fish with "limb-like" features surviving in greater numbers because their was an adaptive advantage to being able to move from pool to pool. But what they found, and what required them to "change this thinking drastically," was the fact that these fish with "limb-like structures" were not escaping dried up ponds but rather living in shallow water spending "a lot of time on the bottom," thereby suggesting that the "limb-like" structures were used for moving along the muddy bottom and not necessarily for moving "from pond to pond."

Our team has been looking for this fish for past six years. We made four trips up to the Arctic to find this particular kind of fish. The first year we struck out almost completely. The second year we found bits and pieces of some things that suggested that something might be there. The third year we found a locality and larger bits of fish that suggested we might be on to something important. And it wasn't until the fourth year, July 2004, when we discovered whole skeletons of this creature.

They say absolutely nothing about prior predictions based upon evolutionary theory. There is nothing unusual in using our understanding of different epochs, such as the knowledge noted above that "we knew that limbed animals (tetrapods) were well along their way to invading land by the Late Devonian." This was information already known from previous fossil finds, and they only applied this knowledge in determining where the best likelihood of finding similar fossils might be.

And it does not change the distortion of the fact that they entered the hunt under the assumption "as the habitat in the Devonian changed and became drier, fish with limb-like fins were able to survive and propagate because they were able to move from pond to pond over land in search of food and new habitats." And that after finding the fossil their assumption was proven incorrect in that they "changed this thinking drastically," a point you ignore evidently, and which was the point of the shift in assumptions which they describe as drastic. Clearly, that is your interpretation of what they are saying, and not their argument. They could "predict" where to look based upon past fossil finds and extrapolate what environments would most likely have these conditions, but has nothing to do with the assumption regarding the reasons for the adaptation of fins-to-limbs, which was that the first assumption was that such features evolved as an adaptation to the drying up of the habitat, so they could move from pond to pond, and then found that they were actually used to function within the pond to move along the muddy bottom (and it is only common sense this would equally well work in moving from pond to pond in another drier environment), implying that the fin-to-limb transition was present prior to the drying up of the ponds. Of course, you seem to miss this point, which they make clear, too. Why is that I wonder?

Your confusion also doesn't change the fact that we also now know that the deeply conserved genetic architecture for the evolutionary developmental pathway for fins-to-limbs are controlled by the Hox gene familiy, which provides the underlying genetic architecture and potential for limbs (via limb-like fins) in fish already existed. Fin, limb, and wing development are well undestood on the molecular level within evolutionary developmental biology.

The evolution of the morphological change entailed in a fin-to-limb-like-fin were conditions that existed in these creatures living in the shallow waters. It was then also useful for moving to land. But the original adaptation had nothing to do with "adapting" to the dried up ponds. The change in form was due to a change in the Hox gene family controlling fin and limb development. Science knows this now conclusively. And it was the change in thinking regarding the "adaptive" story that they highlighted in their comments.

Paleontological inferences about where to look for fossils based upon past paleontolgical fossil finds has little to do with evolutionary theory: what are the causal mechanisms underlying those morphological changes from one form to another. That is the qustion and the reason we try to find fossils which will shed light on the underlying mechanisms of evolution.

[Galphanore]

The problem is it doesn't take a major, complex change to gain a huge benefit. A little stronger fins of a fish and you have something that can swim through muddier water, put the eyes a little closer together and that same creature can see bugs on the water surface easily....

That creature's fossiles were found by using the predictive ability of evolution. They tried to determine what characteristics of the environment would lead to a fish becoming able to travel on land. They considered that a major factor would be that it's water home would have to be going away, so they looked for locations that would have had something like that. They came upon the canadian north, where the ponds this guy lived in were drying up, so the creatures in the water that ended up able to survive were the ones able to travel from one dying pool to another, such as it.

Before the discovery of Tiktaalik we knew that limbed animals (tetrapods) were well along their way to invading land by the Late Devonian (around 360 million years ago). We also knew that some fish in the Middle Devonian (375 million years ago) were experimenting with the internal structure of their fins in ways that would ultimately allow for the evolution of the weight bearing structure of tetrapod limbs. The thought was that as the habitat in the Devonian changed and became drier, fish with limb-like fins were able to survive and propagate because they were able to move from pond to pond over land in search of food and new habitats. ( http://tiktaalik.uchicago.edu/fossil.html )

First, they are stating that prior to finding the fossil their assumptions were the classical idea that as the environment became drier, those "fish with limb-like fins were able to survive ... because they were able to move from pond to pond over land in search of food and new habitats." Then they go on to say upon the discovery of the Tiktaalik fossil they "changed this thinking drastically."

The discovery of Tiktaalik changed this thinking drastically. It is clearly a fish because it has scales and fins, but it is also clearly living in shallow water environments. How do we know this? Unlike its fishy contemporaries, Tiktaalik's body is extremely flattened. Its eyes are on the top of its head, suggesting it spent a lot of time on the bottom[/i], looking up. Its shoulders are not connected to its skull, giving it a functional neck. And it has ribs exactly like those of its contemporary tetrapods which were used to support the body and aid in breathing. ( http://tiktaalik.uchicago.edu/fossil2.html )

Again, it appears that Galphanore has missed the essential point of the authors, which was that prior to the discovery of the fossil it was assumed that it was the change in environment (drying up of pools) that led to those fish with "limb-like" features surviving in greater numbers because their was an adaptive advantage to being able to move from pool to pool. But what they found, and what required them to "change this thinking drastically," was the fact that these fish with "limb-like structures" were not escaping dried up ponds but rather living in shallow water spending "a lot of time on the bottom," thereby suggesting that the "limb-like" structures were used for moving along the muddy bottom and not necessarily for moving "from pond to pond."

Our team has been looking for this fish for past six years. We made four trips up to the Arctic to find this particular kind of fish. The first year we struck out almost completely. The second year we found bits and pieces of some things that suggested that something might be there. The third year we found a locality and larger bits of fish that suggested we might be on to something important. And it wasn't until the fourth year, July 2004, when we discovered whole skeletons of this creature.

They say absolutely nothing about prior predictions based upon evolutionary theory. There is nothing unusual in using our understanding of different epochs, such as the knowledge noted above that "we knew that limbed animals (tetrapods) were well along their way to invading land by the Late Devonian." This was information already known from previous fossil finds, and they only applied this knowledge in determining where the best likelihood of finding similar fossils might be.

Nor did I ever claim there was anything unusual about it. You're the one who singled out parts of my sentences to try and refute the whole. The point is that they determined that the region would have creatures like the one they found based on information they know about fossils and about the region, and then found creatures like it. As for your insistance that they did not use the word evolution in their discription of what lead them to the region, what, exactly, do you think looking for a missing link is based on? Voodoo?

And it does not change the distortion of the fact that they entered the hunt under the assumption "as the habitat in the Devonian changed and became drier, fish with limb-like fins were able to survive and propagate because they were able to move from pond to pond over land in search of food and new habitats." And that after finding the fossil their assumption was proven incorrect in that they "changed this thinking drastically," a point you ignore evidently, and which was the point of the shift in assumptions which they describe as drastic. Clearly, that is your interpretation of what they are saying, and not their argument. They could "predict" where to look based upon past fossil finds and extrapolate what environments would most likely have these conditions, but has nothing to do with the assumption regarding the reasons for the adaptation of fins-to-limbs, which was that the first assumption was that such features evolved as an adaptation to the drying up of the habitat, so they could move from pond to pond, and then found that they were actually used to function within the pond to move along the muddy bottom (and it is only common sense this would equally well work in moving from pond to pond in another drier environment), implying that the fin-to-limb transition was present prior to the drying up of the ponds. Of course, you seem to miss this point, which they make clear, too. Why is that I wonder?

I did not miss the point, I just didn't make it in my two paragraph summery. I was not trying to explain the entire history of the creature or what it means about it's past, the claim you are making is common sense. Of course the transition was present before the environment dried up to the point that moving from pond to pond would be necessary, were it not it would not have time to develop. Evolution doesn't move fast enough for that. Nor does that one creature prevent their being others in the area further along to the point that it was necessary for them to move pond to pond.

Your confusion also doesn't change the fact that we also now know that the deeply conserved genetic architecture for the evolutionary developmental pathway for fins-to-limbs are controlled by the Hox gene familiy, which provides the underlying genetic architecture and potential for limbs (via limb-like fins) in fish already existed. Fin, limb, and wing development are well undestood on the molecular level within evolutionary developmental biology.

The evolution of the morphological change entailed in a fin-to-limb-like-fin were conditions that existed in these creatures living in the shallow waters. It was then also useful for moving to land. But the original adaptation had nothing to do with "adapting" to the dried up ponds. The change in form was due to a change in the Hox gene family controlling fin and limb development. Science knows this now conclusively. And it was the change in thinking regarding the "adaptive" story that they highlighted in their comments.

Paleontological inferences about where to look for fossils based upon past paleontolgical fossil finds has little to do with evolutionary theory: what are the causal mechanisms underlying those morphological changes from one form to another. That is the qustion and the reason we try to find fossils which will shed light on the underlying mechanisms of evolution.

I never denied any of that. I made the claims I made because otseng stated this :

If evolution is true, shouldn't it be a simple matter to demonstrate it in the biological world? Why only show it by principle through human devices?

And from what I gather, it is because it is not demonstratable through biological examples. When I read through Dawkins' The Blind Watchmaker, this was also the same situation. The explanations he gave of evolution were all hypothetical scenarios rather than demonstrating any evidence from biology.

Using principles are fine, but if it cannot be shown to have correlation to the subject matter, then it is of little use.

Insisting that he wanted more then just information about how we know the "underlying genetic architecture and potential for limbs".

[Rob]

Even the use of Hox genes does not mean that the changes are incremental and accumlative. Nor does it say that it always goes at the same pace. You are not going to get an animal the size of the mouse into the size of an elephant in just 2 or 3 generations. That still does not stop the 'filter' of natural selection from increasing the beneficial mutations in the population and reducing detriemtnal mutations in the population (over time). It just means that the mechanism for creating the variations in the population is a bit more complicated.

Yes, in general I agree with what you are saying. Natural selection is certainly the 'filter', although I would qualify this statement that there are limits to this filter, hence such theories as "neutral molecular evolution," which does not discount the role of natural selection, but only suggests a more complex relationship between mechanism for creating variation and natural selection. In addition, there may be mechanisms of variation that could create sudden change in morphology compared to the classical idea of incremental gradualism, (a relative concept, which requires explanation) and it is this area of research within the fields of evo-devo and comparative genomics and evolutionary genomics which is raising some interesting questions of whether or not their needs to be a re-synthesis of the so-called Modern Synthesis which the historian of biology Peter Bowler pointed out was more of a "constriction" rather than "synthesis" in that it excluded the findings in the field of developmental biology of its day.

It is fascinating, and none of the findings of evo-devo or developmental genetics or comparative genomics in the least refutes the fact of evolution; in fact, they all indisputably point to descent with modification is a reality.