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Taxonomic nested hierarchies don’t support Darwinism — transformed cladism rocks


Taxonomic nested hierarchies don’t support Darwinism or common descent, actually the opposite. Michael Denton convincingly argued that nested hierarchies can be used to argue against macro evolution. If the fish are always fish, then they will never be birds, reptiles, apes, or humans.

From a forgotten book called Catholics and the Theory of Evolution, there is a quote of Platnick and Nelson who were pioneers of transformed cladism:

‘Darwinism . . . is, in short, a theory that has been put to the test and found false’

Dawkins was clearly unhappy with the claims of Nelson and Platnick and the transformed cladists:

It isn’t that any transformed cladists are themselves fundamentalist creationists. My own interpretation is that they enjoy an exaggerated idea of the importance of taxonomy in biology. They have decided, perhaps rightly, that they can do taxonomy better if they forget about evolution

Richard Dawkins
Transformed Cladism

Indeed, we can see the nested hierarchy more clearly if we disregard evolution. Why? To illustrate, if we invoke Darwinian evolution we would have to say the nesting goes like this:

FISH are the common ancestors of humans, birds, and frogs. Ergo birds nest within fish, and so do humans, and so do frogs. That is what Theobald’s Markov chain would “predict” in terms of nesting. But the actual anatomical/taxonomic nesting tells a different story: fish are fish, humans are not fish, birds are not fish, frogs are not fish. Are you going to believe Theobald’s Markov chains that you are a fish or are you going to believe you’re a human and not a fish?

To try to nest humans with fish because we supposedly descended from them is at variance with the nested hierarchy we would build by simply looking and comparing traits instead of fabricating Darwinian stories.

One might argue that if Markov processes don’t support nested hierarchies at the anatomical level, Markov processes support nesting at the molecular level. But hierarchies at the molecular level create nasty problems of their own like having to invoke molecular clocks (which have been refuted). See: Zuck is out of luck

Nested hierarchies might be produced by Markov chains, but that is not the only reason nested hierarchies exist for functioning architectures. For example, in the world of man-made machines, there aren’t fully functioning vehicles with 2.3 wheels — there are 2-wheeled, 3-wheeled, 4-wheeled vehicles, etc… The notion of even a conceptual transitional (from 2-wheeled to 3-wheeled) via small steps makes little sense. There is no transition, but rather a leap, per saltum.

Further, intelligent agents create nested hierarchies, not only out of necessity but out of their sense of aesthetics. In the world of classical music there are somewhat well defined music forms: sonatas, minuets, concertos, symphonies, operas, variations, nocturnes, preludes, etudes, rhapsodies, etc. These forms create nested hierarchies and have little to do with Markov chains. So to claim that nesting is the result of common ancestry is only based on the presumption that mindless processes were at work — but that is no proof whatsoever, and worse, the nesting reinforces the notion transitionals never existed even in principle, and thus the missing links will remain missing, and thus the nesting in evidence today is actually anti-Darwinian.

One can, just by looking at traits, assemble creatures into nice nested hierarchies. They look at first like they descended conceptually from a common ancestor, but the problem is they all look like siblings with no real ancestor. In fact, many times a common ancestor doesn’t seem possible in principle.

For example, what is the common ancestor of vertebrates and invertebrates? Err, crash…hard to conceive of even in principle. It’s like looking for a square circle. Those gene sequence worshippers argue the genes show there was a common ancestor of vertebrates and invertebrates, but they seem to have problem describing anatomically what it would look like. Google “common ancestor of vertebrates and invertebrates” and try to find even a hypothetical description of what the common ancestor could look like even in principle. Maybe the lack of transitionals suggest there weren’t any.

In sum, the nested hierarchies in taxonomy don’t need Darwinism, in fact, Darwinism distorts the ability actually see the nested hierarchies, and finally nested hierachies based on taxonomy are evidence against Darwinism.


1. Paul Nelson and Marcus Ross have this article: PROBLEMS WITH CHARACTERIZING THE
This shows why the nesting resists a common anscestor.

2. Or how about the transitionals between unicellular and multicellular. Denton pointed out Darwinists once hoped that we could demonstrate the notion of transitionals by finding living transitionals. The absence of living transitionals is also evidence that maybe they never existed, just like functioning 2.3-wheeled cars. It would appear functioning biological systems, like man-made machines, must make leaps per saltum rather than slow gradual steps. Biological systems tend to polarize and group, they don’t seem to like gradual transitions for certain major architectures or body plans. It’s not that the fossils can’t be found, they can’t exist even in principle.

The list is endless of problems of finding transitionals even in principle, the nesting and very distinct gaps in the nesting are evidence against Darwinian evolution and common ancestry.

Denton’s chapter: “Biochemical echo of typology” gives strong argument that humans aren’t descended from fish. At best one might argue humans and fish share a common ancestor, but well, where is that ancestor?

edvaessen- Darwinism is a big flaw. I suggest that you study science. Virgil Cain
I see some big flaws in thew attack on Darwinism. I suggest the writer should study science. edvaessen
It is inevitable that if one creates several themes and expands upon them in different directions, if you go backwards in time you see less distinction. This in itself has no significance for this debate. It is odd that innovation over time is associated so strongly with an unintelligent origin when we see this very process happening all the time in Human design. The only reason why it is foolishly imagined that if God did it, we won't see innovation over time is because there was an attempt to appease certain brands of Greek philosophy and their notions of perfection. Jul3s
The distinct sets in a phylogenetic tree are defined by their shared common ancestor.
Phylogenetic trees are not nested hierarchies. Read the paper I linked to in comment 52 Joe
Thank you. That is exactly why a nested hierarchy, which requires distinct sets, is not expected given gradual evolution and universal common descent The distinct sets in a phylogenetic tree are defined by their shared common ancestor. Tiktaalik is probably no a tetrapod, for instance. We shouldn't see "gradual blending" of characters in modern species from anciently-diverged groups, but the groups should become increasingly less distinct as we approach their origin. Just as you say, this is precisely the observed pattern. wd400
(a) what do with all the fossil that don’t fit in the boxes your creating. It Tiktaalik a fish or a tetrapod? What about Acanthostega? Is Archaeopteryx a bird or a reptile? Where do humans start and apes end (something creationists can’t agree on among themselves!)
Thank you. That is exactly why a nested hierarchy, which requires distinct sets, is not expected given gradual evolution and universal common descent. We would expect to see a gradual blending of defining characteristics.
(c) At what level common descent brakes down. Mammals descend from mammals you say, what about the so called mamma-like reptiles?
What about them? Can't really study them. It's funny how all the alleged transitional forms are gone but the base populations are still with us- ie reptiles and mammals. Joe
Common descent explains these patterns, special creation doesn’t.
Common descent can explain these patterns provided: 1. a transitional in pricniple is possible 2. a phylogenetic hypothesis is constructed which agrees with molecular data In various cases, for physiological reasons a transitional is not possible even in principle without invoking something close to a miracle The phylogenetic hypotheis that mammals descended from fish is refuted by the data (examples of which I provided above). At best one might suppose mammals and fish descended from some uber vertebrate, but that's just a hypothetical phylogenetic history with no conceivable historical reconstruction of the uber vertebrate from which mammals and fish descended. One can at best suppose common descent without a definite description of a phylogeny and thus avoiding the really tough question of how. One will thus invoke common descent without any sufficiently detailed description of the descent as a matter of faith. As I said, if I accepted common descent, I would say an uber vertebrate or uber chordate was the ancestor of fish and mammals, I wouldn't say mammals descended from fish. That's probably the closest we'll come to agreeing (which isn't vey close at all, but I'm saying if I supposed common descent, I would still lump mammals and fish under a vertebrate ancestor as you obviously do, but for different reasons). Thank you for your informative comments and criticisms. scordova
That’s very much the situation we have in biology. We have nested hiearchies where the differences are punctuated and where even conceptual transitionals seem absurd. Is your hangup the apparent gaps between groups? Evolution, because it's a branching process, makes gaps. That's why the difference between a fish and tetrapod is easy to spot when you look at modern species, deeply murky when you look at ancient ones. You admitted (tacitly) the last "absurd" transition wasn't that absurd, when you reeled of all the vertebrate-like traits the non-vertebrate hagfish has. You could do the same for lancelets, tunicates and even echinoderms if you looked a little deeper into it. wd400
scordova, The bits your story doesn't explain are (a) what do with all the fossil that don't fit in the boxes your creating. It Tiktaalik a fish or a tetrapod? What about Acanthostega? Is Archaeopteryx a bird or a reptile? Where do humans start and apes end (something creationists can't agree on among themselves!) (b) Why do some members of your naively difined groups share a whole suite of traits with animals from other groups. Lobe finned fishes and tetrapods. Or the skulls and teeth of birds, dinosaurs and crocodiles. Or why molecular phylogenetic studies unite those groups. (For that matter why do only fossil birds have teeth?) (c) At what level common descent brakes down. Mammals descend from mammals you say, what about the so called mamma-like reptiles? Common descent explains these patterns, special creation doesn't. That's why scientists don't take the second seriously. wd400
OT: Clam Fossils Divulge Secrets of Ecologic Stability - May 15, 2013 Excerpt: Clam fossils from the middle Devonian era -- some 380 million years ago -- now yield a better paleontological picture of the capacity of ecosystems to remain stable in the face of environmental change,,, The scientists took a new approach to testing ecological stability: In addition to counting numbers of clams, they examined repair scars on fossil clams that were left by the unsuccessful attacks from shell-crushing predators, and the body size of the clam assemblage as it yields biological information on the structure of food webs. "Surprisingly, predation pressure and the body size structure of the clams remained stable, even as abundance varied," ,,, "Our results thus raise serious doubt as to whether ecological stability can be tested meaningfully,,,, http://www.sciencedaily.com/releases/2013/05/130515174029.htm along that same line: Donald Prothero: In evolution, stasis was general, gradualism rare, and that’s the consensus 40 years on - February 2012 Excerpt: In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. Rather than answers, we have more questions— Donald Prothero - evolutionary biologist https://uncommondescent.com/darwinism/donald-prothero-in-evolution-stasis-was-the-general-pattern-gradualism-was-rare-and-that-is-still-the-consensus-40-years-later/ bornagain77
Doesn’t ID involve the intervention of God countless times over the course of history to make sure that evolution proceeded according to plan?
No. ID does not assert claims about chronology of when and how a design came about. ID is about recognizing design, special creation makes claims about how a design came about. By way of analogy, when you see a car you conclude it is designed without having to hypothesize a chronology or detailed mechanism of the cars manufacture. In principle, you could hypothesize a chronology and manufacturing process for the design, but that is a separate endeavor than simply recognizing something is designed. In biology ID is recognizing biological organisms are designed. Special creation is a claim about the steps of how something is designed, and special creation is a competing historical description of how biological forms came to be -- competing with the hypothesis of special creation are intelligent design through front-loaded evolution, extra terrestrials, intelligent universe, prescribed evolution, progressive creation, omega point theory, cognitive-theoretic-model-of-the-univers (CTMU), nomogenesis, platonic forms, etc. As far as God being involved, He's always involved, the question is when and how. He can operate through familiar predictable mechanisms (like nature) or miracles. The Bible says that he sends the rain and the sun. In those cases it is not blatantly obvious God is in operation, but He is still to be credited for the rain and sun. Whereas miracles are easily attributed to Him. So as far as God being involved, I'd say all the time He is involved whether it is obvious or not. As far as ID, the problem is that even if we assert ID is true, we cannot formally assert God was the proximal agent even though we might personally believe He is the ultimate agent. What do I mean? God could create angels that created space aliens that created all life on Earth. One ID proponent, Dave Scot, who was tossed from UD actually believed something not too far from that (minus the angels). Not that I believe that personally, but reconstruction of how God created life can't come from merely detecting and asserting design through observation of the irreducible complexity in biology. By way of analogy, I can use ID principles to recognize the design in a car, but I can't use ID principles to deduce the names of the engineers and workers in the manufacturing plant merely by looking at the design of the car unless I had some other set of knowledge. I focus more on ID because it is a relatively easier question to answer and defend than trying to defend the idea of God creating life on Earth. In fact many times, I don't even defend ID, simply bashing Darwinism is really easy because Darwinism is so bankrupt of substance, logic, and evidence. Bashing Darwinism is easy, asserting special creation by God according to a literal interpretation of Genesis? Pretty hard to reconcile with current scientific knowledge. I'm not saying it can't be done in the future, but we're no where close, especially in terms of physics. I have my personal beliefs, but I wouldn't promote those with the same vigor and conviction that I have when asserting Darwin was wrong. But anyway, we're diverging off topic with such questions. scordova
Hey Sal, For your reading enjoyment: The use of hierarchies as organizational models in systematics It explains the difference between nested, non-nested and semi-nested hierarchies. Joe
Not sure what you mean by "special creation." Do you think creationists believe that God created each species separately? Yes, I am aware of Dr. Wood's view that there is evidence for common descent. And I agree that some facts can be interpreted as evidence for common descent if one interprets the facts through an evolutionary mindset. However, like you, I believe there is also plenty of evidence that does not support common descent and this evidence has to be ignored or or explained away with ad hoc explanations. You mentioned that special creation needs a lot of miracles. I guess I'm unclear on the specifics of ID. Doesn't ID involve the intervention of God countless times over the course of history to make sure that evolution proceeded according to plan? How is this different? In fact, it seems that it would require even more intervention by God over a much longer period of time. In fact, I guess it could be said that His intervention is continuing today as well as things continue to change. For me, this violates the biblical principle of God's completion of creation and resting on Day 7 and thereafter, but I know that has little impact on this thread. Still I mention it for what it's worth. Can you explain to me your view of how God was involved in your ID view of creation? Thanks. tjguy
If the data doesn’t support common descent, why do some IDers support it?
Common Descent looks superficially resonable if one looks at the Linnaean Taxnomic hierarchy and the molecular data. It's only when you really scrutinize the data, as now being done, that problems with common descent begin to arise. Another reason is that special creation requires lots of miracles. Defending miracles as scientific is hard. I don't even try. Some who are sympathetic to ID hold out hope that there can be a scientific description to ID that doesn't invoke miracles, or at least fewer miracles. Even Todd Wood, a die-hard Young Earth Creationist gave a powerful argument for common descent, even though he doesn't believe in Common Descent. See: The Problem of Biological Similarity Sal scordova
A press release from Vanderbilt University summarizes a paper in Nature this week:
These days, phylogeneticists – experts who painstakingly map the complex branches of the tree of life – suffer from an embarrassment of riches. The genomics revolution has given them mountains of DNA data that they can sift through to reconstruct the evolutionary history that connects all living beings. But the unprecedented quantity has also caused a serious problem: The trees produced by a number of well-supported studies have come to contradictory conclusions.
What do you do when you have contradictory data? These guys recommend discarding the data that doesn't conform to theory - kinda like when dates for rocks that don't conform to theory are discarded or ignored. This is science? If the data doesn't support common descent, why do some IDers support it? tjguy
I'm reposting a comment I made at VJ Torley's thread because it bears repeating. The main point is Theobald is correct to assert a markov process will create a phylogenetic nested hierarchy, but over time it will preclude the emergence of a taxonomic nested hierarchy. Consider that if we played the game of telephone except with music. I could take a piece of music written by a human and then subject it to random revision of notes via some random generator. We can repeat the process so as to make a phylogenetic nested hierachy of compositions that were randomly generated from a parent. You can trace the nested phylogentic hierachy rather easily if all you had were the final product of awful sounding music. Hypothetically we could create say 128 of these randomly generated pieces whereby we began with the ancestor which had 2 children, then 4, then 8....128. It would have a nested hierarchy consistent with phylogeny, and in principle we might be able to even reconstruct the original composition from which all 128 "composition" descended. By way of contrast, I could create 128 pieces that would have such radically diffent architectures that you would know the only way to classify them is via taxonomy, not phylogeny. For example I could make half of the pieces in one key and the other in another key. And with each half I could further subdivide them with different melodies, and then further with harmonies, etc. Thus you'd have a taxonomic nested hierarchy that resists interpretation as a phylogenetic nested hierachy. (By the way, that is an implicit prediction of a forgotten ID theory by name of Biotic Message). That's very much the situation we have in biology. We have nested hiearchies where the differences are punctuated and where even conceptual transitionals seem absurd. This is the comment I provided in another thread that I repeat here:
gpuccio, I respect the reasons people accept common descent, and to my mind, I’m glad a large segment of those in the ID community are not creationists. But I had to take issue with KeithS claim:
that this subset just happens to be the subset that creates a recoverable, objective, nested hierarchy of the kind that is predicted by unguided evolution
KeithS equivocates the notion of nested hierarchy. We have a nested hierarchy that is phylogenetic (like a family tree) and another that is taxonomic (like the way we perceive biology in terms of platonic types). The taxonomic platonic nested hierachy is not predicted by evolution, and actually a naturalistic mindless process will not create a platonic nested hierarchy even though it can generate a phylogenetic nested hierarchy. Like most Darwinists, KeithS, equivocates and conflates taxonomic nested hierarchies with phylogenetic nested hierarchies to prove a claim, but equivocations are no proof whatsoever! You might look at some of the later comments I posted in the separate thread on how it is empiricallly evident the taxonimic nested hierarchy that is constructed by looking at taxonomic traits is at complete variance with the phylogenetic nested hierarchy constructed by the prevailing notions of how mammals evolved from fish. One can provisionally accept Common Descent and conclude that the taxonomic nested hierachy is at complete variance with the predicted phylogenetic hierarchy. Denton was correct to point out that the persistence of certain diagnostic characters that define things like mammals is actually the antithesis of Darwinisn and supports strongly the PRE-Darwinian conception of platonic forms in biology versus mindless accidents. Platonic forms expressed in biology implies Intelligent Design. Darwinists have successfully equivocated phylogenetic nested hierarchies with taxonomic nested hierarchies in public and scientific circles and thus through a process of distortion furthered their undeserved domination of the origins controversy. By the way, Theobald is making the same equivocations KeithS makes. I don’t think they even realize it! By the way, Theobald though correct that evolution will create a nested phylogenetic hierarchy via a Markov process is completely incorrect to imply that a Markov process will create a nested taxonomic hierarchy. The fact he doesn’t even realize the distinction only shows how lacking in insight the Darwinists are, and it pains me to say it because Theobald is a good guy and accomplished scientist.
Does anyone besides me find it extremely bizarre that a neo-Darwinist would list the Coelacanth of all creatures in defense of Darwinism?
Picture - The coelacanth, a 400-million-year-old fish, represents an impasse for the theory of evolution. This fish has not undergone any changes in 400 million years. The fact that it has preserved its earliest physiological structures over this length of time—despite continental shifts, climate changes and changes in environmental conditions—baffles evolutionists.,,, http://thefactofcreation.blogspot.com.au/2012/09/living-fossils-sf0024-25-coelacanth.html
wd400, in all seriousness, do you really believe that a creature that appeared suddenly in the fossil record and shows 400 million years of stasis supports evolution? ,,, And that pattern, sudden appearance and relative stasis, is what we find over and over,,,
Living Fossils Interview with Dr. Carl Werner - video http://www.youtube.com/watch?v=Y6LmWznY4Ys
supplemental note
Coelacanth Fish Genome Undermines Evolution Industry - 2013 http://www.darwinthenandnow.com/2013/04/coelacanth-fish-genome-undermines-evolution-industry/
For tetrapods to nest within fish they need to have all of the defining characteristics of fish plus the defining characteristics that makes them tetrapods. For example in the nested hierarchy of living organisms we have the animal kingdom. To be placed in the animal kingdom an organism must have all of the criteria of an animal. For example:
All members of the Animalia are multicellular (eukaryotes), and all are heterotrophs (that is, they rely directly or indirectly on other organisms for their nourishment). Most ingest food and digest it in an internal cavity. Animal cells lack the rigid cell walls that characterize plant cells. The bodies of most animals (all except sponges) are made up of cells organized into tissues, each tissue specialized to some degree to perform specific functions.
The next level (after kingdom) contain the phyla. Phyla have all the characteristics of the kingdom PLUS other criteria. For example one phylum under the Kingdom Animalia, is Chordata. Chordates have all the characteristics of the Kingdom PLUS the following:
Chordates are defined as organisms that possess a structure called a notochord, at least during some part of their development. The notochord is a rod that extends most of the length of the body when it is fully developed. Lying dorsal to the gut but ventral to the central nervous system, it stiffens the body and acts as support during locomotion. Other characteristics shared by chordates include the following (from Hickman and Roberts, 1994): bilateral symmetry segmented body, including segmented muscles three germ layers and a well-developed coelom. single, dorsal, hollow nerve cord, usually with an enlarged anterior end (brain) tail projecting beyond (posterior to) the anus at some stage of development pharyngeal pouches present at some stage of development ventral heart, with dorsal and ventral blood vessels and a closed blood system complete digestive system bony or cartilaginous endoskeleton usually present.
The next level is the class. All classes have the criteria of the kingdom, plus all the criteria of its phylum PLUS the criteria of its class. This is important because it shows there is a direction- one of additive characteristics. Yet evolution does NOT have a direction. Characteristics can be lost as well as gained. And characteristics can remain stable. Joe
Salvador: “For example, what is the common ancestor of vertebrates and invertebrates?”, WD40: Hard to imagine non-vertebrates that have vertebrate-like features? Like Hagfish?
Hagfish still have a nervous system consistent with vertebrates plus a cranium consistent with vertebrates. One issue is the rewiring necessary to create a working nervous system. A non-functioning transitional nervous system is lethal. Here is one invertebrate nervous system: http://media-1.web.britannica.com/eb-media/38/73338-004-D4AE19AA.jpg Notice the the central nerves are on the "bottom" versus the way we would see the nerves in a vertebrate like a fish where its "above" the digestive system: http://www.infovisual.info/02/img_en/033%20Internal%20anatomy%20of%20a%20bony%20fish.jpg What's the transitional or common ancestor of the arthropod (invertebrate) and the fish (vertebrate) layout of nerves? A nervous system that's wired right through the middle of the digestive tract? If anyone finds one, feel free to post. scordova
This is because the coelacanth’s DNA is similar to other types of fish and not land animals,
I just showed that with the Indian Coelacanth. Frankly that would hold pretty much true for all fish save a few outlier sequences. But the majority sequences ought to show fish are fish and mammals are not fish. Humans nest nicely in primates (like 99%-100% identity on some sequences), but they (like other tetrapods), do not nest within fish. The sequence data I provided above is just the tip of the iceberg, and not only that, you can see with your own eyes : mammals are not fish. At best we might argue, if one accepts common descent, that mammals and fish descended from an ancestral chordate or vertebrate, but you can't argue ( except with some of the most tortured distortions of molecular data) that mammals nest within fish. That is not in evidence by the molecular data, excerpts of which I provided above.... The reader may wonder thenm given the taxonomic nested hierarchy, why it is favorable to creation? Well the argument would go like this: Chordates descend only from other chordates Vetebrates descend only from other vertebrates Tetrapods descend only from other tetrapods Mammals descend only from other mammals Primates descend only from other primates Humans descend only from other humans The nested hierachy is preserved beautifully if one is willing to suppose special creation of species. The strength of the hierarchy is empirical evidence that transitionals between diagnostically defined groups does not happen. If you accept the taxonomic nested hierarchy as a picture of how evolution works, then only micro evolution is in evidence, not macro evolution between major diagnostically defined groups. But if one doesn't accept special creation, on the assumption of common descent, it is evident humans don't nest within fish. That flies in the face of empirical data. scordova
Of note: Coelacanths: Evolutionists Still Fishing in Shallow Water by Timothy L. Clarey, Ph.D., and Jeffrey Tomkins, Ph.D. * - April 2013 Excerpt: A recent report, published in Nature,1 on the genome sequence of the so-called living fish fossil, the African coelacanth, has some evolutionists scrambling to defend their story. This is because the coelacanth's DNA is similar to other types of fish and not land animals, thus forcing the evolutionists to postulate that the coelacanth evolved slowly.1,, http://www.icr.org/article/7412/ supplemental note: Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% – by Jeffrey P. Tomkins – February 20, 2013 Excerpt: For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor. http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome No evolution for 300 million years and horrendously fast evolution within 6 million years? No matter, Darwinism must be the answer because Darwinists told us to think otherwise is not science! :) The Fate of Darwinism: Evolution After the Modern Synthesis - David J. Depew and Bruce H. Weber - 2011 Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.,,, http://www.springerlink.com/content/845x02v03g3t7002/ With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory - November 2011 Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,, http://www.evolutionnews.org/2011/11/with_a_startling_candor_oxford052821.html The next evolutionary synthesis: Jonathan BL Bard (2011) Excerpt: We now know that there are at least 50 possible functions that DNA sequences can fulfill [8], that the networks for traits require many proteins and that they allow for considerable redundancy [9]. The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate – it is really only half a theory! http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf bornagain77
Wd40, Thank you again for your civil tone and your informative criticisms, they are helpful and where I feel you are right, I will revise in future writings. But with respect to nested hierarchies if we make an organization purely with respect to diagnostic characters, tetrapods lump diaganostically into one group as they all share common diagnostic characteristics which fish do not have. In like manner bony fish share diagnostic characterstics that set them apart from other groups. One things is true, both fish and mammals share diagnostic characters common to all chordates. Superficially, if we presume common descent we might presume bony fish and tetrapods have an uber chordate ancestor since both fish and tetrapods are chordates. Thus from diagnostic characters alone fish and tetrapods would look more like siblings or cousins or some other arrangement wherby some uber chordate was ancestor. I'm not stating anything that other non-Creationists have not been aware of like the transformed "cladists". You pose an interesting question about molecular data, and a cursory look at the data suggest something parallel to the anatomical typology, namely fish and tetrapods nest within chordates. For tetrapods to nest within fish, frequent (not just sporadic) identity of say 92-100% on sequences might begin to possibly qualify tetrapods as fish. How can we test this claim? Take any random fish, take a protein, run BLAST, just list the hits that are within say 10%, do they echo the morphological nesting created by taxonomy? If they do, then on the assumption of common descent, it suggests fish and tetrapods descended from an uber chordate, it does not suggest tetrapods descended from fish. The preliminary blast sequence I ran is consistent with this. It would be an interesting bioinformatic project to conduct on large scale. It may something I might study for my own personal edification if I choose that line of study, but that would mean returning to grad school. It's a worthy scientific question, and one that cannot be done sufficient justice in the short lifetime of our present discussion. There are two-conflicting nested hierarchies today, one created by pure taxonomy and another by the phylogenists of the present day. For small phylogentic trees, the taxonomic tree ought to agree with the phylogenetic tree. For example, if we take human males, the phylogenetic family tree will tend to agree with the taxonomic tree (i.e. Jewish males traced by the Y-chromosome will have some anatomic features that presumably match a taxonomic nested hierarchy assuming we can find physical traits goverened soley by the Y-chromosome). So it would seem the concordance between phylogeny and taxonomy should agree. Let's say for the sake of argument that they will agree if we have found the right phylogeny, it then suggests if the taxonomic tree and the synthesized phylogenetic tree do not agree, then the phylogenetic tree is likely wrong. I'm not the only one to point out there is an incongruity between the taxonomic and presumed phylogentic trees. I provided an references to that effect above. I ran the following BLAST on Cytochrome c oxisdase subuint 1 for the Coelacanth. I chose Coelacanth since some say a Coelacanth could be the ancestor of tetrapods. What did I find as the most closely related? Other fish, not tetrapods:
>tr|Q9PSF7|Q9PSF7_LATCH Cytochrome c oxidase subunit 1 OS=Latimeria chalumnae PE=3 SV=1 MITRWLFSTNHKDIGTLYMIFGAWAGMVGTALSLLIRAELSQPGALLGDDQIYNVVVTAH AFVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSFWLLPPSLLLLLACSGVYAG AGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTVINIKPPTMTQYQT PLFIWSVLVTAVLLLLSLPVLAAGITMLLTDRNLNTTFFVPVGGGDPILYQHLFWFFGHL EVYILILPGFGMISHIVAYYSGKKEPFGYMGMVWAMMATGLLGFIVWAHHMFTVGMDVDT RVYFTSATMIIAIPTGVKVFSWLATLHGGVTKWDTPLLWALGFIFLFTVGGLTGIVLANS SLDIILHDTYYVVAHFHYVLSMGAVFAIMGGLVHWFPLMTGYTLHNTWTKIHFGVMFTGV NLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSLISLIAVIMFMFILWEAFLAKRE VLIVEMTTTNVEWLHGCPPPHHTY Latimeria chalumnae (West Indian ocean coelacanth) 100.0% Latimeria chalumnae (West Indian ocean coelacanth) 98.0% Latimeria chalumnae (West Indian ocean coelacanth) 98.0% Latimeria menadoensis (Indonesian coelacanth) 98.0% Triacanthodes anomalus (red spikefish) 93.0% Megalops cyprinoides (Indo-Pacific tarpon) 93.0% Elops saurus (Ladyfish) 93.0% Carapus bermudensis 93.0% Pantodon buchholzi (Freshwater butterflyfish) 93.0% Capros aper (boarfish) 92.0% Elops hawaiensis (Hawaiian ladyfish) 93.0% Neoceratodus forsteri (Australian lungfish) (Ceratodus forsteri) 92.0% Gasterosteus wheatlandi (blackspotted stickleback) 92.0% Pungitius sinensis (Amur stickleback) 92.0% Megalops atlanticus (Tarpon) (Clupea gigantea) 92.0% Mola mola (ocean sunfish) 92.0% Masturus lanceolatus (sharptail mola) 92.0% Phractolaemus ansorgii (hingemouth) 92.0% Neoceratodus forsteri (Australian lungfish) (Ceratodus forsteri) 92.0% Rondeletia loricata (redmouth whalefish) 92.0% Psephurus gladius (Chinese swordfish) 93.0% Salmo salar (Atlantic salmon) 92.0% Sargocentron rubrum (redcoat) 92.0% Dactyloptena tiltoni 92.0% Esox lucius (Northern pike) 92.0% Retropinna retropinna (cucumberfish) 92.0% .....
That went on for 10 pages. Then I cranked BLAST up to look for 1000 hits, and the taxonomy table look up showed ZERO tetrapods. It is true that the Coalecanth might have more identity in some sequences to humans than to to TUNA, but a cursory look at the data suggest we could synthesize a fish outgroup on which fish would cluster. The conculsion, taxonomically speaking and even from molecular evidence: "fish are fish, mammals are not fish. The typology holds even at the molecular level." You are free of course to hypothesize mammals descended from fish, whereas, if I believed in common descent, it would seem to me mammals and fish descended from an uber chordate and are siblings or cousins rather grand daughter (mammals) and grand mother (fish). A Markov process acting on a common ancestor would create a nested hierarchy (as we find in tracing human family trees to ancestors several generations back), but on that presumption, it would seem the data argue that mammals had chordate ancestor that wasn't a fish. Theobald's claim is more consistent with that sort of nested hierarchy, but then, that would go against the prevailing Darwinian story that mammals descended from fish. scordova
Exactly wd400- you are denying the obvious. Tetrapods are nested within Vertebrata- Linnean taxonomy is the observed nested hierarchy, even Theobald uses it. How is a tree structure a nested hierarchy? Why don't YOU start there. Joe
Joe - I really don't see the point in talking with someone who denies the obvious. Unless you can tell me why a tree-structure isn't an example of nested heirachy, or how you can find a a set in Fig. 1 that contains all the fish and no tetrapods, then I'll go back to ignoring you. wd400
Figure 1 doesn't show tetrapods are nested within fish.... Joe
Umm trees are not nested hierarchies. Joe
Joe. I'll indulge you this one. Check out the tree in this paper on the coelacanth genome. Now - try and find a complete group that includes all the fish and no tetrapods... wd400
Please make your case as opposed to just baldly declaring it. Demonstrate how tetrapods a nested within fish. YOU are the attention seeker here wd400. YOU are saying totally ridiculous things. And your position cannot account for neither fish nor tetrapods. I take it that bothers you. Joe
Tetrapods do not nest within fish. Is the some kind attention seeking behaviour? By saying increasingly ridiculous things you hope someone might reply to you? wd400
wd400: Think for a second about the fact tetrapods nest within “fish” (and bony fish+tetrapods nest within fish for that matter, for that matter). You just made that up. Tetrapods do not nest within fish. And unfortunately you cannot demonstre that fish can evolve into something other than fish. You lose. Joe
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