The Sound of a Nested Hierarchy Shattering

_{Dave S.
November 28, 2006

Intelligent Design

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Intelligent Design}

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Chromosomal sex determination in the platypus discovered to be a combination of mammal and bird systems. The resemblance to birds is now more than just superficial.

http://www.newscientist.com/article.ns?id=dn6568

Comments

http://forums.christianity.com/m_2825724/mpage_5/key_/tm.htm#2872770 Here I go into great detail describing why UCD does not predict any alleged nested hierarchy. Namely, if you look at humans within its own specie we see violations all over the place. It's possible for someone to have a trait (or genetic sequence / gene), have a brother that doesn't have this trait, yet have a cousin that has this exact same trait (or genetic sequence). This produces a violation. It's possible for someone with a much more distant relationship to also have this trait that the two brothers don't share. Within a specie we see violations all over the place, nowhere do we see any such nested hierarchy. Evolution does not produce any such nested hierarchy within the human specie, likewise it would not produce any such hierarchy when they speciate. We see violations all over the place within a specie and those violations won't just disappear when the specie speciates. Despite the fact that UCD does not predict this alleged nested hierarchy, this alleged nested hierarchy resists horizontal gene transfer as being a significant factor in producing and spreading genetic variation (ie: new traits). It makes it much more difficult for evolutionists to explain away genetic diversity through horizontal gene transfer, which they would do if the data allowed it. The evidence was designed to resist naturalistic explanation. For more details, see the above link and read my posts (for this post is just very very general, I go into far more details within that link). Also note, much of this reasoning has been inspired by the book, "The Biotic Message" by Walter James ReMine, who, like I, believes the evidence was designed to resist naturalistic explanation.Bettawrekonize_{November 20, 2007
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Robin re front-loading http://telicthoughts.com/?cat=12DaveScot_{November 30, 2006
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Various posters here have refererd to "front-loading"; can anyone give a potted explanation of the term, together with references to some research papers for further reading?Robin Levett_{November 30, 2006
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OE needs more content so if you're a student (or a UD mod) feel free to jump into a related topic: http://www.overwhelmingevidence.com/oe/blog/scutus/does_id_accept_universal_common_descent#comment-193 http://www.overwhelmingevidence.com/oe/blog/troutmac/design_flaws_and_intelligent_design#comment-428 Oh, and personally I'd interpret that "Bushes in the Tree of Life" referenced in comment #3 by Jehu as possibly supporting multiple LUCAs.Patrick_{November 30, 2006
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It should be noted that the MYTH that nested hierarchy was evidence for Common Descent (meaning all extant living organisms owe their collective common ancestry to some unknown population(s) of single-celled organisms) was duly exposed in Chapter 6 of "Evolution: A Theory in Crisis". The botom-line is Common Descent can live with it or without it. Darwin was well aware of that.
Extinction, as we have seen in the fourth chapter, has played an important part in defining and widening the intervals between the several groups in each class. We may thus account for the distinctness of whole classes from each other- for instance, of birds from all other vertebrate classes from each other- by the belief that many ancient forms of life have been utterly lost, through which the early progenitors of birds were formerly connected with the early progenitors of the other and at that time less differentiated vertebrate classes.
IOW if all the alleged transitionals were still alive such distinct categories would not exist. What nested hierarchy does demonstrate is that the same evidence can be used for two opposite PoVs- both Mayr and Simpson recognozed that:
One would expect a priori that such a complete change of the philosophical bias of classification would result in a radical change of classification, but this was by no means the case. There was hardly and change in method before and after Darwin, except that "archetype" was replaced by the common ancestor.-- Ernst Mayr
("the hierarchy looked the same as before even if it meant something totally different." - Simpson)Joseph_{November 30, 2006
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Smidlee Well sir, an omnipotent creator could theoretically be creating a brand new universe, in place, with modifications, once every nanosecond or even more often. But if he is he's sure doing a good job in making it look like it's been here a long time and evolves according to a self-consistent set of natural laws - one of those laws being the law of biogenesis. How do you rationally determine when and how many special acts of creation there were? Occam's Razor would have us make those acts of special creation as few as possible. I count only one that was strictly required - the universe itself but I think life was created once too for a grand total of two separate acts of special creation.DaveScot_{November 30, 2006
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So Dave what you mentioned in #27 sounds a lot like Plato's idea theorem: "He asserted that there is realm of Forms or Ideas, which exist independently of anyone who may have thought of these ideas. Material things are then imperfect and transient reflections or instantiations of the perfect and unchanging ideas." (source: wikipedia)tb_{November 30, 2006
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Thanks for the clarification, Dave!tb_{November 30, 2006
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"Every living thing thus far examined uses virtually the same genetic code. Couple this with the law of biogenesis and you have an exceedingly strong case for common (blank) IMO." you can just about fill in the blank with anything ; descent.creator, language,etc. IMO all life has a lot in common period. That about as far as you can go with science.Smidlee_{November 29, 2006
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Jehu Every living thing thus far examined uses virtually the same genetic code. Couple this with the law of biogenesis and you have an exceedingly strong case for common descent IMO. If gradualism were indeed true in all cases a nice, neat phylogenetic tree with no ambiguity should be easy to construct today with molecular homology serving as a twin nested hierarchy confirming phenotype homology. In point of fact it isn't easy and ambiguities are common. Convergent evolution, horizontal gene flow, epigenetic factors, and very limited understanding of what all contributes to phenotype expression at the molecular level mucks it up. Furthermore, the fossil record is not a record of gradulism, it's a record of saltation. This raises the question of how saltation can occur. I suspect the answer to that lies in a nested hierarchy of phenotype control mechanisms. Regulatory regions in individual genes are the lowest level. These are capable of fine tuning of a species but not saltation. A higher level of control would be genes that regulate the expression of groups of genes but I don't believe those are capable of saltation in a general case as it doesn't provide a mechanism for reproductive isolation. Gould recognized these problems and came up with a spatial theory of reproductive isolation - small populations get cut off by physical boundaries, genetic drift takes over, and you can get a new species in geologically short amount of time with little evidence of it in the fossil record because the population was so small. I find that rather contrived to preserve a dogmatic belief in gradualism. More likely, IMO, is the existence of an even higher level control mechanism. Consider coding genes as components in a Lego set. You can build all kinds of different structures by changing their relative number and arrangement. While it's true you can gradually remove and add components to change a bridge into an igloo it's a lot easier if there's a master plan for an igloo, a master plan for a bridge, and you set out to build one instead of the other from the ground up. I suspect the master plan, the highest level in the control heirarchy, lies in the structure of chromosomes. Chromosomal rearrangements typically cause reproductive isolation in one fell swoop through reduced or zero hybrid fertility. Large chunks of genetic material can be rearranged instantly without change in lower level hierarchies through chromosome reorganization. Position effect is well enough established. Moving a gene from one spot to another on a chromosome causing phenotype change has been amply demonstrated. Chromosome organization varies widely among different species while the basic building blocks remain more or less a constant set. Is that wide variance in chromosome organization a meaningless thing brought about by random events? A higher level hierarchy of junk DNA? I dont' think so. So in the case of the platypus, if all or most of the basic building blocks are shared between mammals and birds, and all the building blocks were present in their common ancestor, then each is distinguished by a master plan describing how to arrange the blocks. Thus mixing and matching large phenotype characteristics is possible in saltational events. For instance you could mix things up to get an egg bearing animal that produces milk, has webbed feet like a duck, has limbs positioned at the sides like a lizard, has leg spurs like a rooster tipped with snake-like venom, has electroreception in its snout like a shark, thermoregulates body temperature much lower than birds or mammals, has a cloaca like a reptile, and (drum roll please) has sex determination chromosomes part bird and part mammal.DaveScot_{November 29, 2006
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A tad off-topic: Jehu wrote: Ã¢â‚¬Å“Talk.Origins is looking stupid:Ã¢â‚¬Â You know I never visited Talk.Origins until last night. I saw it mentioned here so I gave it a look-see. IÃ¢â‚¬â„¢m actually a little disturbed after reading their FAQÃ¢â‚¬â„¢s Ã¢â‚¬â€œ pure Darwinist propaganda. Their Ã¢â‚¬Å“tree of lifeÃ¢â‚¬Â makes it look as though the only dispute is over how long it took evolution to work its unguided, physics-defying miracles. I was particularly taken aback by their Ã¢â‚¬Å“observed instances of speciationÃ¢â‚¬Â It seems to be written for the sole purpose of confusing the would-be truth seekerÃ¢â‚¬Â¦scary stuff. I could see how someone (say, an impressionable high school student) would have a very difficult time discerning fact from fiction.shaner74_{November 29, 2006
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I thought I'd clarify my personal position real quick. I have my personal preferences but I also have no problems with multiple LUCAs and other narratives. Directed panspermia (front-loading with no further design interaction), intelligent evolution, progressive creation, separate creation (possibly combined with more limited front-loading), it doesn't matter. As long as intelligence is involved as the data shows and the evidence is compatible with a scenario. The evidence might be interpreted using logical reasoning in a particular framework (a prior commitments, assumptions, etc). The reasoning might be correct but unfortunately the framework might not represent reality. In short, a framework is being imposed on the evidence but the interpretation is only valid within that framework. It's sometimes fully possible to have 2 or more parties looking at the same exact data points and come to mutually exclusive conclusions until more evidence is gathered. Emotional reasoning or personal beliefs are usually the only reason a particular conclusion is given preference. I figure we'll narrow it down over time. Yes, I'll fully admit to being lenient on ID proponents since I don't want to create a schism. I don't mind if someone supports a position as long they're honest about their preferred scenario being tentative...I just have a tendency to attack when a Darwinist gets dogmatic. :) Oh, and no snarky comments about my position being one giant "I don't know". :PPatrick_{November 29, 2006
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jpark320, Thanks for the link. From the article.
Spindle neurons probably first appeared in the common ancestor of hominids, humans and great apes about 15 million years ago, the researchers said -- they are not seen in lesser apes or monkeys. In cetaceans they would have evolved earlier, possibly as early as 30 million years ago, the researchers said. Either the spindle neurons were only kept in the animals with the largest brains or they evolved several times independently, the researchers said.
This is a good example of a mosiac pattern of features in life. Whenever such features cannot be explained by common descent the convergence card is played. But are we really seeing common descent or are we imposing our own pattern upon a mosiac of life.Jehu_{November 29, 2006
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I donÃ¢â‚¬â„¢t think anyone is going to put a dent in common descent.
My understanding is that there is no evidence for common descent among single cell organisms at the base of the tree of life. Rather than a tree there is a mosiac "wheel" like pattern. After the base, there is the cambrian explosion in which more phyla appear than currently exist - without any fossil record of common descent. Since the cambrian explosion common descent has been inferred from morphological homology. However, morphological homology is contradicted by molecular homology. And then different molecules tell different stories concerning relationships. So it is not clear when homology is really homoplasy. I wonder if we are really finding phylogenic tree or if we are just selecting features from what is really a mosiac pattern of life to fit a preconcieved notion of common descent.Jehu_{November 29, 2006
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Patrick Exactly.DaveScot_{November 29, 2006
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I donÃ¢â‚¬â„¢t think anyone is going to put a dent in common descent.
I'd agree. Common descent from a single LUCA may be true itself but the historical narratives we have now may not be true themselves. Some ideas like land mammals to whales may have never existed (or persisted to this day) if the bearded buddha had never posited his bear story. If front-loading and universal common descent are both true then why couldn't the whale have evolved entirely in the ocean and received the mammal-like features from internal information?Patrick_{November 29, 2006
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jpark320: "I also read an article where they apparently find spindle cell neurons in whales..." And the eyeless, earless sea urchin has genes that in humans are involved in detecting sight and sound:and sound: (for some reason the link isn't copying: it's to www.nature.com/news/2006/061106/full/06116-15.html)dacook_{November 29, 2006
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jpark320: "I also read an article where they apparently find spindle cell neurons in whales, which are only found in primates apparently, and now all of sudden there is a ancestral link or it evolved independently." And sight and sound sensory genes in sea urchins (which are blind and deaf): http://www.nature.com/news/2006/061106/full/061106-15.htmldacook_{November 29, 2006
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Dave, Are you arguing for a new Classification based on these findings? A Mammaves? Ahmmm... half-joking, half-serious. ;-)Michaels7_{November 29, 2006
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Dave, Thanks for the clarification. I was surprised to see the headline "The Sound of a Nested Hierarchy Shattering," because I had gotten the impression before that you didn't have a problem with common descent per se. In fact, the evidence for common descent (the nested hierarchy itself, but especially the nested hierarchy with respect to endogenous retroviruses) seems to me to be almost airtight. That said, I'd be more than happy to look at evidence to the contrary, which I was hoping someone might have found.Reed Orak_{November 29, 2006
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tb Close enough. Reed I don't think anyone is going to put a dent in common descent. I pointed out this anomaly because I'd blogged about the platypus before and was criticized for linking certain features to birds instead of reptiles. I didn't intend this article to be an attack on common descent only an attack on monotreme classification as a mammal branch.DaveScot_{November 29, 2006
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I think attacking the nested hierarchy at the genetic level is the most promising means of falsifying the Common Descent hypothesis. Does anyone have any references of other violations of the nested hierarchy?Reed Orak_{November 29, 2006
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hi UC, I would like to know what is meant by front loading? I have read it so many times here but I am not quite understanding the concept! Can anybody explain? From Patrick: "My predication would be that weÃ¢â‚¬â„¢d find evidence for front-loading, other scenarios, and information re-use in general" I assume it is a concept referring to a (single) bio structure (DNA) that may be used to assemble the variation of species according to a build algorithm, yet has all information about all species from the start. Like a Construction kit. Something like that? Thanks for an answer! tbtb_{November 29, 2006
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I am curious what happens if they knock out a few x/y chromosomes in the xxxxx or yyyyy what will happen. What a peculiar duck....Michaels7_{November 28, 2006
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#4 Salvador, Just a note of thanks for your response last week re: Wnt and hypotheticals regarding conservation of information.Michaels7_{November 28, 2006
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I also read an article where they apparently find spindle cell neurons in whales, which are only found in primates apparently, and now all of sudden there is a ancestral link or it evolved independently. http://www.cnn.com/2006/TECH/science/11/27/humpback.whales.brains.reut/index.htmljpark320_{November 28, 2006
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The other day I was musing what might happen if the genomes for animals not considered to be related were compared. My predication would be that we'd find evidence for front-loading, other scenarios, and information re-use in general. I was thinking of North American squirrels and Australian sugar gliders but a platypus will do. ;)Patrick_{November 28, 2006
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Very interesting post! However, it is not nearly as cool as Pegasoferae!johnnyb_{November 28, 2006
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What? Ernst Mayr doesn't believe birds evolved from dinosaurs? Obviously Ernst Mayr needs to spend more time reading the propoganda over at Talk.Origins.Jehu_{November 28, 2006
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(FYI) Re: "Anyone who reads any evolutionary literature, even at a basic level, will quickly find out that birds are thought to have evolved from dinosaurs in the Jurassic about 150 million years ago"
Refutation of the Dinosaurian Origin of Birds 1. Age -- The dinosaurs structurally most similar to birds are very recent (80-110 million years ago), whereas Archaeopteryx is a great deal older (145 mya) and no birdlike dinosaurs are known from the Jurassic or Triassic that could qualify as ancestors of birds. 2. The three digits of the hand of the dinosaurs are 1,2,3, those of a bird are 2,3,4. It is quite impossible to derive the avian digits from those of dinosaurs. 3. Teeth -- Theropods have recurved, flattened, serrated teeth, quite different from the peglike, waisted, nonserrated teeth of Archaeopteryx and other early birds. 4. The pectoral girdle and anterior extremities of the late theropod dinosaurs are much too small and weak to have served as the foundation of a powerful wing to lift an incipient bird from the ground. No factors are known that could have caused a sudden drastic growth of anterior extremities. 5. The leading aerodynamic experts of bird flight claim that an origin of flight from the ground up is a near impossibility. (Ernst Mayr, What Evolution Is: Now Everyone Please Stop With This Dinosaurs-Became-Birds Nonsense. (2001), p. 68.)
j_{November 28, 2006
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