Evolution Professor: Biological Designs Fall Into a Nested Hierarchy

I must have missed that class... Joe

Joe, a nested hierarchy is whatever evolution produces. You should know that. Mung

Evolve- what is a nested hierarchy? Please reference a valid source. Joe

Cornelius, This is so naive and silly. Even a high-school student can tell why your objections do not hold water. The conflict and incongruence you're trying to blow out of proportion still do not affect nested hierarchies at the broad level. For example, in the following paper you cite, they examined 2326 genes and found convergence in just 200 loci: http://www.nature.com/nature/journal/v502/n7470/full/nature12511.html Specifically, they found convergence between bats & dolphins in genes involved in echolocation. Now that doesn't mean we should dismantle the traditional tree and start regarding bats as the closest relative of dolphins. If you compare the remaining genes, you'll still see the broad nested hierarchy pattern consistent with the traditional tree. The convergence in some loci are due to similar evolutionary pressures experienced by the two species, which resulted in similar solutions. Distantly related species arrive at the same solution because nature works within constraints. There are only a limited number of solutions available for a problem. Such constraints are not expected if a supernatural designer was actually involved. You're claiming data are routinely filtered while drawing evolutionary relationships. But one cannot expect every base pair in the entire DNA to show the same effect. Several processes operate in nature that bring about variations in the genome. You're entirely missing the fact that nested hierarchy is present in many genes and loci even when some other loci show variations due to phenomena such as horizontal gene transfer and convergent evolution. Why is nested hierarchy present at all? Evolve

Summativity is the key to nested hierarchies. For example with Linnean classification all of the sets and levels under "Animalia" are all of the representative organisms of the Animal Kingdom. Animalia is the sum of its Phlyla, Classes, Orders, etc All of the Corps, Divisions, Brigades, Battalions, etc. are all under the Army- ie the Army is the sum of all of its Corps, Divisions, Brigades, Battalions, etc. Joe

OT: Discovery Institute has released a 'stunning' new three-minute video om the Kinesin molecular machine The Workhorse of the Cell: Kinesin - video https://www.youtube.com/watch?v=gbycQf1TbM0 article A Stunning New Illustration of Intelligent Design in the Cell: Video http://www.evolutionnews.org/2014/05/a_stunning_new085561.html bornagain77

Joe, thanks for the crisp definition. A keeper. I would add that the pattern observed in the fossil record is the exact 'top down' opposite of what Darwin predicted,,,

Challenging Fossil of a Little Fish "In Chen’s view, his evidence supports a history of life that runs opposite to the standard evolutionary tree diagrams, a progression he calls top-down evolution." Jun-Yuan Chen is professor at the Nanjing Institute of Paleontology and Geology http://www.fredheeren.com/boston.htm "The record of the first appearance of living phyla, classes, and orders can best be described in Wright's (1) term as 'from the top down'." (James W. Valentine, "Late Precambrian bilaterians: Grades and clades," Proceedings of the National Academy of Sciences USA, 91: 6751-6757 (July 1994).) The unscientific hegemony of uniformitarianism - David Tyler - May 2011 Excerpt: The pervasive pattern of natural history: disparity precedes diversity,,,, The summary of results for phyla is as follows. The pattern reinforces earlier research that concluded the Explosion is not an artefact of sampling. Much the same finding applies to the appearance of classes. These data are presented in Figures 1 and 2 in the paper. http://www.arn.org/blogs/index.php/literature/2011/05/16/the_unscientific_hegemony_of_uniformitar Disparity precedes diversity - graph http://www.veritas-ucsb.org/library/battson/images/G.gif Disparity preceding Diversity graphic on Cambrian Explosion from ‘Darwin’s Doubt’ http://www.evolutionnews.org/2013/07/its_darwins_dou074341.html Investigating Evolution: The Cambrian Explosion Part 1 – video http://www.youtube.com/watch?v=4DkbmuRhXRY Part 2 – video http://www.youtube.com/watch?v=iZFM48XIXnk “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas." James W. Valentine - as quoted from "On the Origin of Phyla: Interview

Disparity preceding diversity is not only found in the Cambrian Explosion but is found after it as well. In fact, in the following paper, some Darwinists tried to argue that since Disparity preceding Diversity is a consistent pattern in the fossil record after the Cambrian Explosion then, by their reasoning, that means the Cambrian Explosion wasn’t that special after all:

Cambrian Explosion Solved? - October 2010 Excerpt: Looking at the big picture, though, they argued that the Cambrian explosion was really not all that special; other parts of the fossil record show similar patterns: “the observation that disparity reaches its peak early in a group’s history seems to reflect a general phenomenon, also observed in plants (Boyce, 2005), the Ediacara biota (Shen et al., 2008), Precambrian microfossils (Huntley et al., 2006), and within many individual animal clades, such as crinoids (Foote, 1997), gastropods (Wagner, 1995), and ungulates (Jernvall et al., 1996). Although of significant interest, this high disparity soon after a group’s appearance is not unique to the Cambrian,” they said. http://www.creationsafaris.com/crev201010.htm#20101031a

Well, despite what the preceding researchers would like to believe, Disparity preceding Diversity is NOT what Darwinian Evolution predicts (But such a pattern is what ‘top down’ design predicts):

Scientific study turns understanding about evolution on its head - July 30, 2013 Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form. Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories. ,,,Dr Matthew Wills said: "This pattern, known as 'early high disparity', turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn't a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.",,, Author Martin Hughes, continued: "Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on. Co-author Dr Sylvain Gerber, added: "A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,, http://phys.org/news/2013-07-scientific-evolution.html “It is a feature of the known fossil record that most taxa appear abruptly. They are not, as a rule, led up to by a sequence of almost imperceptibly changing forerunners such as Darwin believed should be usual in evolution…This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large.” G.G.Simpson – one of the most influential American Paleontologist of the 20th century “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.” Fossils and Evolution, TS Kemp – Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

bornagain77

Linnean classification is the observed nested hierarchy and it doesn't have anything to do with common ancestry. Also gradual evolution would expect a smooth blending of defining characteristics which would ruin any objective nested hierarchy. The problem comes from evos not understanding nested hierarchies and thinking that any tree pattern is a nested hierarchy. Just because a nested hierarchy can be represented as a tree pattern does NOT mean all tree patterns are therefor nested hierarchies. Yet that is what evos think. Joe

After reading your article and seeing the problems with making hierarchies of species assuming common descent as true, I thought of the notion of species in the understanding of Vedic philosophy (especially in Samkhya and Vedanta schools) -- the species is classified in a totally different way, according to their conscious viewpoints. I hope it is interesting for you to see how some proponets of a new science based on Vedic insights, like Mr. Dalela, approaches the notions debated here. An excerpt from the book Vedic Creationism, by Ashish Dalela, Chapter 18: In a Semantic Universe "The distinction between various species of life is based in the Vedas upon the idea of semantic spaces. In particular, the notion of semantic spaces has interesting implications for the modern ideas about evolution and I will presently turn toward these. Darwinian evolution claims that different living beings have evolved from simpler life forms. Modern evolution extends this to suppose that the simpler living beings ultimately began with combinations of atoms and molecules. While there are a number of moral and religious concerns because of which evolution and Darwinism is debated today, I would not get into those debates. My concern here would primarily be questioning the conception of matter adopted by evolutionary theories in light of the concepts of matter that are allowed by quantum and relativity theories, when these theories are unified into a ToE. In any case, Vedic conceptions are not divorced from conceptions about matter, so it is prudent to limit the discussion within matter. Vedas support the fundamental theoretical tenet of Darwinism that living beings evolve in the world by adapting themselves to their environment. This evolution happens not just because of natural selection but also due to freewill and freedom (which are not accounted for in Darwinism), because of which we alter our inner views about ourselves and choose different models of life, even when they do not afford the highest survival value (one only has to look at the individuals who risk their lives for the sake of other ideals such as nationality, society, altruism, justice and liberty). The Vedas also support the idea that bodies are made up of atoms and the idea that a living being can adopt different kind of bodies. But Vedas don't support the evolutionary notion that evolution of bodies results in new kinds of species through natural selection. The reason for this is a semantic view of the world. In the semantic view, the world is possibilities of experience and the limits of experience have already been defined by the complete collection of logical distinctions that make up the universe. These distinctions are fundamental constituents of knowledge. New experiences involve a mutation of existing distinctions into newer distinctions; for example, the idea of a 'golden mountain" by combining the notion of 'gold' and 'mountain'. By such mutation, one would arrive at a new kind of experience that is within the domain of experience already prescribed by the complete set of distinctions that prescribe the universal space. A new experience is in this case quite literally like a new sentence arrived at by combining the letters, which are basic atomic distinctions. However, given that distinctions in nature are fixed, different domains of experience have also been fixed. So, all species with various experiences have already been defined a priori by the set of distinctions that make up the universe. Philosophers often call this a point-of-view or 'What it's like to be a bat?" problem. Basically, it is supposed -- correctly from the Vedic viewpoint -- that every species of life brings with it a unique kind of experience or viewpoint about the world. So, the creation of new species amounts to saying that evolution can create a new domain within the semantic phase space that did not exist earlier. But semantic phase space does not expand or contract, because it is given by the logical conditions of all possible distinctions, which are fixed [NOTE: these notions are discussed in detail in the previous chapters]. New knowledge can arise by combining existing distinctions and all such kinds of experiences already exist. Creation of a new distinctions must first be available in physics as new kinds of sub-atomic particles before we can use them as knowledge ingredients in the creation of new experiences. Such new particles will not only create new species but a whole new set of experiences across the universe. The evolutionary assumption that new kinds of knowledge can be created locally through natural selection is therefore unsustainable in a semantic universe. Distinctions are logical conditions of knowing by consciousness. Given that the distinctions by which a consciousness can know in the world are already fixed, the space of all possible distinctions has already been drawn [NOTE: by the Supreme Consciousness]. Indeed, the cosmos as a whole is the space of all possible distinctions that consciousness can experience; it is in a sense the limits to material knowledge. So, semantically speaking, a new species as the creation of a new possibility of experience cannot arise because all possibilities are already present in the universe as different semantic domains. One must however concede the possibility that certain rare possibilities in the cosmic semantic space were actualized in the past and don't exist currently or that they would be actualized in the future. The Vedic view would agree for such a claim, as the Vedas are full of narrations about creatures that existed at some point or other but don't anymore. When they existed, they inhabited a certain portion of the semantic space, and adopted a certain kind of view about the world. Indeed, all areas of cosmos can in principle be inhabited by a living being which define the point of view native to that location adopted by the living being. Living beings are said to be sarva-gatah or present everywhere in the Vedas (this 'everywhere' means space in a semantic sense). So, to say that living beings are everywhere means that all semantic viewpoints can be occupied. If some particular viewpoint is not presently occupied, then it may be occupied in the future, provided there is a consciousness that deserves and desires that viewpoint. The occupation of a viewpoint would however not occur at the cost of some other viewpoints, disappearing, because all viewpoints are simultaneously possible although they may not be simultaneously actualized. This means that when a new kind of species X emerges, this is not at the cost of some other species Y disappearing. Species X does not evolve from species Y, rather both species X and Y can, in principle, co-exist. The emergence of a species is therefore not an evolution, but the occupation of a viewpoint that already existed. The viewpoint that a living species adopts towards the world is a particular kind of psycho-socio-cultural bias taken in viewing the world. It may be likened to what continental philosopher Habermas called lebenswelt or life-world which is the pre-cognitive culturally-grounded set of understandings that every living being of a certain species share. One might now say 'But there are so many different cultures and viewpoints!' How do we classify or divide viewpoints? Also, since humans themselves belong to several distinct cultures, societies and life-worlds, why do we call them a single species? The Vedic answer to this dilemma is that humans are not a single species, although biologically they appear to be! In fact the Vedas describe that the various human cognitive stances number 400,000 out of a total possible species of 8,400,000. These species are not biological distinctions but semantic distinctions. Each of these species is different because it belongs to a different lebenswelt or life-world, carrying its own unique viewpoint about the world. These species must be distinguished not on the basis of physical characteristics (like for example we don't think of humans having differently colored skins as different species) but on the basis of their mental makeup. Together all species exhaust the possibilities of semantic space. Different locations in semantic space are either occupied now, or were occupied in the past, or will be occupied in the future by various possible world-views adopted by different beings. If there are portions of the semantic space that would be covered in the future, that does not imply the ceasing of currently existing viewpoints; the coming of a new species does not imply extinction of existing ones. If a semantic viewpoint can be adopted then species are not evolving. Rather, the co-existence of various viewpoints precludes any simple minded evolution. Different species can co-exist like different viewpoints can co-exist. Adaptation does not imply the creation of new species and elimination of old because all species are different locations in semantic space that can be occupied simultaneously. Evolution of a creature is its movement in a semantic space. This movement is not different than the movement of a physical object in quantum gravity [NOTE: subject treated in previous chapters]. When an object moves, it develops new relations with other objects and it is now a conceptually different object. This conceptual distinction through the act of senses leads to new experience. The fact that some viewpoints are inhabited and some are not, does not mean that one viewpoint arose from another because there can be instances when both viewpoints co-existed. The species being seen today are not beings that have evolvled from older species and left them behind to extinction. Rather, if some species are not seen, consciousness are not choosing to be in a particular mindset. If they did choose the mentalities, nature [NOTE: controlled by an aspect of God] would accord them bodies suited for those mindsets. The apparent extinction of species therefore is due to an evolution in mentalities because of which consciousness go through cycles of cultural, psychological and spiritual viewpoints rather than a physical or biological change in which a species is extinct because it cannot survive in a particular environment. In summary, consciousness evolves in two ways. One, it evolves within a species, whereby it adjusts physical and mental conditions governed by its own desires, freedom and of course as Darwinism suggests, because of the need to survive and selfishly thrive in the world. Two, consciousness also incarnates from one species to another, which is like jumping from one kind of life-world to another. Both these forms of evolution involve motion in physical and phase spaces. The science of this incarnation is not different from the science that applies to the motion of ordinary objects, or motion from one planet to another, since different regions in the universe are semantically distinct locations [NOTE: discussed in previous chapter]. The Vedas thus describe the processes by which one can alter his mind and body to travel to different places in the universe, adopt higher species of life and generally seek higher forms of experiences and pleasure. A better understanding of these sciences requires us to bring the theoretical discourse a newer conception of reality in which space is given not ontologically but epistemically through knowledge distinctions. Tenets of such a science were earlier described in this book. When consciousness undergoes different experiences, it is moving in the phase space. Motion in phase space is an evolution of consciousness and not the evolution of species. This is related to a distinct view of motion in the Vedas, where an ontologically fixed object does not take a new position but the old object disappears and a new one appears. The change from one location to another is not motion but a transformation of old into new by operators of choice. By having different experiences, consciousness has different contents, but a change to content does not change consciousness per se. Consciousness remains unaffected in terms of its capability to know and experience, even when it transmigrates through various species of life. The change to experience therefore does not imply a change to consciousness, because it is the possibility of experience and an experience actualizes possibility into content. When content evolves, it does affect consciousness as the possibility of experience. The Vedas describe that consciousness can stop its transmigration by changing its distinctions framework. The requires a kind of mental development by which one begins to see the active role God plays in the universe. A change to distinctions framework transports a consciousness into a new kind of body with different abilities suited to participating in God's activities. Though this is the domain of religiosity and mysticism, it is based upon principles identical to those by which a consciousness transmigrates through bodies or moves from one planet to another within the universe. These are also the principles by which we are manipulating the world and evolving our experiences as a consequence. The science of a semantic reality is the core principle around which all other principles rest in the Vedas. This science is within the reach of modern physics, and its gradual development into a better understanding of mind and intelligence and other subtler instruments can take us closer to a better appreciation of the principles on which a truly scientific conception of spirituality is based in the Vedas. In summary, the belief in the existence of God has scientific implications for the study of matter. These implications are evident at several levels. First, the causality in the universe is divided into six parts as final, efficient, existential, formal, instrumental and material causes and this stems from aspects of God's personality. The division into six cause has extremely important implications to the study of conscious experience, especially the study of pleasure, sensations, emotions and questions such as the meaning of life (the existential cause). Today, there are no scientific constructs by which these can be directly studied, because science is accustomed to studying objects and not experiences. Second, each of these levels of causes are further divided into five stages of creation through thinking, feeling, willing, knowing and acting which, even at the level of the material cause, results in a new conception of matter as a communicative device. It also leads us to a new view of order in nature which is not mathematical laws but mathematical operators. As choice, this construal of reality implies that change is governed not by blind force laws but by conscious state preparation and observation which are an outcome of abilities and their application in conscious beings. The Vedic view sets itself apart by answering the dilemmas posed by anti-religionists through a new conception of matter." tarmaras

I use to have this 'perfect' view of science:

“Science seeks the truth. And it does not discriminate. For better or worse it finds things out. Science is humble. It knows what it knows and it knows what it doesn’t know. It bases its conclusions and beliefs on hard evidence -­- evidence that is constantly updated and upgraded. It doesn’t get offended when new facts come along. It embraces the body of knowledge. It doesn’t hold on to medieval practices because they are tradition.” Ricky Gervais - British comedian - Why I’m an Atheist," WSJ, 2010 http://blogs.wsj.com/speakeasy/2010/12/19/a-holiday-message-from-ricky-gervais-why-im-an-atheist/

And I would hold that science itself, in the long run, is like that. But scientists, as hard core Darwinists have made abundantly clear to me, are very different than science itself:

"Scientists have thick skins. They do not abandon a theory [merely] because facts contradict it. They normally either invent some rescue hypothesis to explain what they then call a mere anomaly and if they cannot explain the anomaly, they ignore it, and direct their attention to other problems. Note that scientists talk about anomalies, [recalcitrant instances,] and not refutations. History of science, of course, is full of accounts of how crucial experiments allegedly killed theories. But all such accounts are fabricated long after the theory has been abandoned." Imre Lakatos, Science and Pseudoscience

Indeed, because of Darwinists, I'm now more inclined to take Planck's pessimistic view, i.e. science 'advances one grave at a time' :

"A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it." Max Planck

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