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Thread: Darwin Eclipsed & The Rise of Evo Devo

  1. #1 What if we're looking at the wrong things? 
    Forum Bachelors Degree x(x-y)'s Avatar
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    I've been thinking about alien life and wondering about whether they follow the same laws of biochemistry to life on our planet where the required elements for life are C, H, N, O, P (or As) and S. Astrobiologists may be looking the wrong way, they might be searching for signs of these elements and life on other planets according to these elements, yet other life may be completely different- they may follow completely different biochemistry laws to life on Earth. It could just be a case of laws of biochemistry being unique to each planet/moon- just as gravitational field strength is different for each.

    But, I'm no biologist so I wouldn't know if these elements are the ones required for life and that's that- but I doubt it. I'm just saying that we should keep a 'broad spectrum' about this kind of thing as life out there may be so weird and different to life on little old Earth that we may have seen it already- yet not recognised it to be life.

    Note: I think this is in the right sub-section, it was this or Astronomy and Cosmology- but I thought this section was more fitting.


    "Nature doesn't care what we call it, she just does it anyway" - R. Feynman
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    there are elements required for life as we know it. But what if we are like cells that constitute something of a bigger whole?


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    Indeed, that is essentially what I was implying...
    "Nature doesn't care what we call it, she just does it anyway" - R. Feynman
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    Let me ask you this: what makes you think that exobiologists have not considered alternative biochemistries?
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    Quote Originally Posted by Ophiolite
    Let me ask you this: what makes you think that exobiologists have not considered alternative biochemistries?
    Don't get me wrong, I'm not saying they haven't- it's just that whenever they mention anything about it on Newscientist for example, they always seem to be searching for life similar to the life on Earth; it just seems that they might not be focusing enough on investigating possible laws of biochemistry corresponding to different planets. But, then again, maybe I'm wrong/being unfair and that they do thoroughly investigate this kind of thing...
    "Nature doesn't care what we call it, she just does it anyway" - R. Feynman
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    We know that life based on carbon chemistry, using water as a solvent, can exist. We do not know if other forms may exist. It is therefore reasonable to focus our attention on the known unknowns, rather than the unknown unknowns. At least until we know more.
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    An interesting Wiki article HERE on possible alternatives.

    There is much to be learned from existing life on earth as far as alternatives go. Extremophiles and Archaea spring to mind.
    Disclaimer: I do not declare myself to be an expert on ANY subject. If I state something as fact that is obviously wrong, please don't hesitate to correct me. I welcome such corrections in an attempt to be as truthful and accurate as possible.

    "Gullibility kills" - Carl Sagan
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    It should be noted that Extremophiles/ Archaea/ Arsenic metabolising bacteria etc are all of course fundamentally similar however.

    What we find is vastly different variation of the same thing. Granted much of this is due to common ancestry of terrestrial life but the most alien yet familiar thing to life is virions/viroids and even they use the same (quasi)biochemistry.

    I'm personally inclined to believe that speculation of silicon-based life etc will not yield any success. After all, we look to silicon only for it being the most similar element to carbon, not for any independent reason.
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    Do we have to assume that life is limited to biochemistry? Couldn't a creature have a nuclear metabolism instead of a chemical one? If we meet a complicated system that develops through stages and is full of feedback loops and eventually dies, what criteria would we use to determine whether or not it was a living thing?
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    Surely looking for silicon based life could technically lead to success as previously we thought that phosphorous was required yet arsenic (in the same group) can replace it; so logic would tell us that other elements within the same groups as required ones for life on Earth are viable possibilities. However, I can see your point about carbon vs silicon- as carbon can form four covalent bonds making it able to form millions of different compounds, whereas silicon is different to this as far as I know...
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    @ Starlarvae:

    What do you mean by 'nuclear metabolism' instead of chemical? You don't mean to say that life could be based off of nuclear fission and fusion, do you?
    "Nature doesn't care what we call it, she just does it anyway" - R. Feynman
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    It should be noted that Extremophiles/ Archaea/ Arsenic metabolising bacteria etc are all of course fundamentally similar however.
    Agreed, I was specifically talking about alternative metabolic/energy chain reactions and structural chemistry that are often found and the possibility of expounding a hypothetical life form around that.
    Disclaimer: I do not declare myself to be an expert on ANY subject. If I state something as fact that is obviously wrong, please don't hesitate to correct me. I welcome such corrections in an attempt to be as truthful and accurate as possible.

    "Gullibility kills" - Carl Sagan
    "All people know the same truth. Our lives consist of how we chose to distort it." - Harry Block
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    Do we have to assume that life is limited to biochemistry?[/quote]

    Do we have to? no.

    Should we? a resounding yes.

    For a species to metabolise using nuclear fusion/fission is simply untenable.

    Why? There is currently a known self-sustaining nuclear entity in this very solar system. We don't refer to its self-sustaining as metabolism and despite being 2nd-3rd generation we don't call it reproduction.

    Life is definitively a chemical concoction. Other things that emulate attributes of life (Richard Dawkin's fire analogy from The Ancestors Tale for another example), is not life but something else.

    We defined life in the first place. Life is simply one of many manifestations prevalent in the universe. It is therefore safe to assert that we have a reasonably authoratative say regarding what we are looking for in regards to extraterrestrial life
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    The research on arsenic/phosphorus replacement life forms has been severely criticised by several scientists. The experimental methodology is thought to be sloppy and the conclusions are highly doubtful.
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    Quote Originally Posted by Ophiolite
    The research on arsenic/phosphorus replacement life forms has been severely criticised by several scientists. The experimental methodology is thought to be sloppy and the conclusions are highly doubtful.
    Do you mean this research?

    http://www.newscientist.com/article/...ife-forms.html
    "Nature doesn't care what we call it, she just does it anyway" - R. Feynman
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    The research into arsenic/phosphorous life has led to some pretty outlandish claims. I believe the most popular is that the life forms are the result of a seperate abiogenesis event.

    Ridiculous.
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    Quote Originally Posted by ProcInc
    For a species to metabolise using nuclear fusion/fission is simply untenable. [. . . .] There is currently a known self-sustaining nuclear entity in this very solar system. We don't refer to its self-sustaining as metabolism and despite being 2nd-3rd generation we don't call it reproduction.
    The sun's nuclear metabolism includes anabolic (fusion) and catabolic (fission) processes, just like the metabolisms of chemical organisms. Some stellar metabolisms are even catalytic (the CNO reaction). Stars are born, develop through definite stages, and die. They abide far from equilibrium thanks to feedback control. Stars share a striking number of attributes with chemical organisms. Only a chemocentric bias keeps us from recognizing stars as a genus of organism.
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  19. #18  
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    Quote Originally Posted by starlarvae
    They abide far from equilibrium thanks to feedback control.
    The entire point about star asatrophysics for the bulk of their 'lives' is that they are very much in an equilibrium condition. Demonstrate that this is false, if you can.
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    Quote Originally Posted by Ophiolite
    Quote Originally Posted by starlarvae
    They abide far from equilibrium thanks to feedback control.
    The entire point about star asatrophysics for the bulk of their 'lives' is that they are very much in an equilibrium condition. Demonstrate that this is false, if you can.
    If stars are in a state of equilibrium, why are they so dynamic?

    What's the difference, in terms of entropy, between a star when it first ignites and the same star at the end of its life, its protons fused? The latter state is one of equilibrium.
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    Do you mean this research?

    http://www.newscientist.com/article/...ife-forms.html[/quote]

    yes
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  22. #21 Darwin Eclipsed & The Rise of Evo Devo 
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    The development of any complex organism reveals a weave of relationships between the organism's phenotype and its genotype. I will focus on four of these relationships and argue for a new interpretation of the genetic data:

    First, although the skin, liver, muscle, brain and other cell types that compose a body are morphologically and functionally diverse, they are not genetically diverse. They all inherit the same genotype from their common ancestor, a zygote. That is, during the descent with modification from a zygote to its descendant cell types, DNA is conserved. Diverse phenotypes do not require diverse genotypes.

    Second, Because all cells in a body (excluding parasites and symbionts) inherit the same genotype, they necessarily inherit many genes that they do not need. Skin cells don't express genes specific to the functioning of liver cells, for example. Neither do muscle cells express genes specific to the functioning of brain cells. And so on. The excess DNA in each cell type includes genes needed to create and operate all the other types. But from the point of view of a given type of cell, the DNA for the other types is junk.

    Third, the expression of genes in any particular cell type, and the timing of their expression, is controlled by other genes that act as on/off switches. This is how a single genotype expresses multiple phenotypes (skin, liver, muscle, etc.) in a single body -- by turning various genes on and off here and there at various times.

    Fourth, a zygote carries genes that will be required by its descendants. The zygote anticipates the needs of the skin, liver, muscle, and other descendant cell types and carries their genes, even if the zygote itself does not express them.
    These, then, are some of the characteristics of development. They include conservation of DNA, junk DNA, switches that conrol the expression of cellular phenotypes, and genes that anticipate the needs of descendants.

    Now, when we look at the genetics of evolution, we find all the same hallmarks. Since genetic sequencing and analysis have come online, the parallels between development and evolution--between ontogeny and phylogeny--have come sharply into focus. A new discipline within evolutionary biology, called evolutionary developmental biology, or Evo Devo, is trying to shoehorn the new genetic data into the old, Darwinian, paradigm. But comparative genomics is rewriting the book of evolution into something that readers of the first edition might not recognize as the same work.

    Consider:

    First, insects, fish, birds and primates are morphologically and behaviorally dissimilar, but not because their genotypes are to any comparable degree dissimilar. Genetic sequencing and analysis tell us that these creatures all inherited same basic genetic toolkit from a common ancestor. That is, despite all the phenotypic variation, DNA is conserved across species during evolutionary descent.

    Genes for limbs are pretty much the same from limbed species to limbed species, whether the wings are on a dragonfly, a bat, or a bald eagle. The underlying genes are about the same. Evolution, like development, conserves DNA. Researcher Sean Carroll, an architect of Evo Devo, comments, “Comparison of genomes tells us that not only do flies and humans share a large set of developmental genes, but that mice and humans have nearly identical sets of about 25,000 genes, and that chimps and humans are almost 99 percent identical at the DNA level. The common tool kit and the great similarities among different species genomes present an apparent paradox.” (All Carroll quotes are from his book, Endless Forms Most Beautiful, The New Science of Evo Devo.) Yes, the great similarities do present a paradox. Because they make evolution look like a large-scale development.

    Second, all species carry unexpressed "junk" DNA. Carroll calls this DNA "dark matter" because most of it "contains no instructions and is just space-filling 'junk' accumulated over the course of evolution. In humans, only about 2 to 3 percent of our dark matter contains genetic switches that control how genes are used."

    So, even if a small percentage of the "junk" is actually performing a function in a given organism, by switching genes on and off, the majority of it is truly junk (at least to those who carry it around unexpressed), which makes evolution look like development.

    Third, the control of phenotypic expression in any species is controlled by genetic "switches" that are themselves turned on and off by regulatory proteins. These switches provide a mechanism whereby conserved DNA can express dramatic phenotypic variation across species. This observation is foundational to Evo-Devo, which treats species as variants produced by the conbinatorics of genetic switching.

    Fourth, we notice that ancestral species carry genes required by remote descendants. Ancestral genomes anticipate the needs of phenotypes to come. An example is the Great Barrier Reef sponge Amphimedon queenslandica. A news article in Nature (The Amphimedon queenslandica Genome and the Evolution of Animal Complexity, Vol. 466, Pages 720–726, August 5, 2010) covering the sequencing of the sponge's genome reveals that the hoary creatures harbor a tool kit of metazoan genes:

    "The genome also includes analogues of genes that, in organisms with a neuromuscular system, code for muscle tissue and neurons."
    A curious finding. The article continues:

    "According to Douglas Erwin, a palaeobiologist at the Smithsonian Institution in Washington DC, such complexity indicates that sponges must have descended from a more advanced ancestor than previously suspected. 'This flies in the face of what we think of early metazoan evolution,' says Erwin."

    "Charles Marshall, director of the University of California Museum of Paleontology in Berkeley, agrees. 'It means there was an elaborate machinery in place that already had some function,' he says. 'What I want to know now is what were all these genes doing prior to the advent of sponges.'"
    The conundrum for normal evolution theory is clear. But, rather than propose that the genes needed by organisms with neuromuscular systems are in the sponge for the purpose of providing those genes to descendants, the scientists invent an imaginary ancestor of the sponge that needed the genes. But the ghostly ancestor would have had to have arisen within a very narrow window. Fossil evidence of sponges goes back 650 million years; it constitutes, the authors note, “the oldest evidence for metazoans (multicellular animals) on Earth.” So, what use would any species even more primitive than sponges have for the neuromuscular genes?

    Here's a longer quote from Sean Carroll that summarizes the unexpected findings that genetic research is yielding and the significance of Evo Devo in light of the preceeding observations:

    "The first and still perhaps the most stunning discovery of Evo Devo is the ancient origin of the genes for building all sorts of animals. The fact that such different forms of animals are shaped by very similar sets of tool kit proteins was entirely unanticipated. The ramifications of these revolutionary findings are powerful and manifold.

    "First of all, this is entirely new and profound evidence for one of Darwin’s most important ideas—the descent of all forms from one (or a few) common ancestor. The shared genetic tool kit for development reveals deep connections between animal groups that were not at all appreciated from their dramatically different morphologies.

    "Second, the discovery that organs and structures that were long viewed as independent analogous inventions of different animals, such as eyes, hearts, and limbs, have common genetic ingredients controlling their formation has forced a complete change in our picture of how complex structures arise. Rather than being invented repeatedly from scratch, each eye, limb, or heart has evolved by modification of some ancient regulatory networks under the command of the same master gene or genes. Parts of these networks trace back to the last common ancestor of bilaterians (Urbilateria), and earlier forms.

    "Third, the deep history of the toolkit reveals that the invention of these genes was not the trigger of evolution. The bilaterian tool kit predated the Cambrian, the mammalian tool kit predated the rapid diversification of mammals in the Teritary period, and the human tool kit long predated apes and other primates. It is clear that genes per se were not 'drivers' of evolution. The genetic tool kit represents possibility—realization of its potential is ecologically driven."
    This last comment begs the question, "How did all that potential get into the ancient genomes?" It's as if Earth's earliest life had zygote-like powers of anticipation. Researcher Michael Sherman argues for a similar conclusion in his paper, "Universal Genome in the Origin of Metazoa" (Cell Cycle 6:15 1873-1877, Aug 2007).

    So, do the genetic parallels between ontogeny and phylogeny add up to anything?

    They do. They suggest that ontogeny and phylogeny constitute two scales on which operates a common process of descent with modification. This suggestion implies that both the ontogenetic and the phylogenetic expression of phenotypes is susceptible to environmental contingencies. This is a mundane, noncontroversial observation. Environments are known to influence whether phenotypes become tall or twisted, atrophied or robust, as with vitamin deficiencies in animals and photo- and geotropisms in plants.

    But the counterpoint to that observation is inescapably controversial: The data that inform Evo Devo imply that both the phylogenetic and the ontogenetic expression of phenotypes unfolds according to a program. Phenotypic expression in both cases conforms to a process of development. It conforms to the unfolding of a life cycle.

    So, if species differentiate in an ecology and across a planet as cells do in and across an embryo, whose life cycle has been unfolding during the evolution of phenotypes on our planet?

    My candidate for the ontogeny underlying phylogeny is the stellar life cycle.

    Stars constitute a genus of organism. The stellar life cycle includes a larval phase. Biological life constitutes the larval phase of the stellar life cycle.
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    I'm not sure if the reply to me was an attempt at refuting me earlier or something but I will rephrase myself to ensure.

    "Nuclear life" would generate far more energy than it would require, could be able to maintain and, more importantly, reach.

    Evolution could not create such an organism nor would evolution preserve such an organism if it came about by "some other way".

    It is a solid guarentee that life elsewhere would be chemical, not just for the reasons in my earlier message but that life would still be chemical in form if not metabolism. Unless we want to take it a step further and assert that a life form could be an ethereal blob of pure energy.
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    Quote Originally Posted by ProcInc
    Unless we want to take it a step further and assert that a life form could be an ethereal blob of pure energy.
    I can see this in some fundamental chemical reactions ie. two compounds reacting together to give off energy or produce a new product, or oxi/redox rxn's. Although that is not considered ethereal, it can and does occur spontaneously. Its like; how do they know to transfer electrons from one place to another. Its just the way it is right?
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    A lot is to be said of the dubious nature of this article regarding a rather inappropriate 'begging the question' fallacy. For a cogent review of the evidence and information we currently have regarding the "Evolution of evolvability" (one of your primary "questions" begged) Gunther P Wagner and Jeremy Draghi's entry in "Evolution: The Extended Synthesis (2010)" is a good primer.

    However I take especial issue to your claim that stars are a Genus of life. Firstly, something that has certain analogues to phenomena we recognise in life does not constitute life (or else fire would be life too as would crystals and various types of mud as they each have reproduction and, in the former case, metabolistic capablities).

    This is a heavily pseudoscientific claim you charge preceded by non squiters. I am trying to sound as "kind" as I can in this response but there is little positive to say about its content. Even the "support" garnered in the form of quotes from various authorities (many of them dubious) are simply snippets of different variations of the authorities saying "we were surprised to find..." "we don't yet fully understand...". I would leave that to the creationists.
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    I'm not denying the production of light in chemical reactions (burning magnesium, glowsticks etc). I am talking about a life form that is made of energy, not chemical compounds.

    the example you give

    A. is not life
    B. Requires a chemical reaction.

    I don't think there is anything we disagree on in this context
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  27. #26 Re: Darwin Eclipsed & The Rise of Evo Devo 
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    Quote Originally Posted by starlarvae
    Fourth, we notice that ancestral species carry genes required by remote descendants. Ancestral genomes anticipate the needs of phenotypes to come. An example is the Great Barrier Reef sponge Amphimedon queenslandica. A news article in Nature (The Amphimedon queenslandica Genome and the Evolution of Animal Complexity, Vol. 466, Pages 720–726, August 5, 2010) covering the sequencing of the sponge's genome reveals that the hoary creatures harbor a tool kit of metazoan genes:

    "The genome also includes analogues of genes that, in organisms with a neuromuscular system, code for muscle tissue and neurons."
    omg - you cannot be serious

    please, please, please read up on exaptation, or the adoption of traits into new functions of structures that existed in ancestors for a totally different reason

    just like you, no organism "knows" what the future holds
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by ProcInc
    "Nuclear life" would generate far more energy than it would require, could be able to maintain and, more importantly, reach.
    I don't see how that's an objection to the idea. How can ANYTHING produce more energy than it can obtain? It would be a perpetual motion machine.

    Quote Originally Posted by ProcInc
    Evolution could not create such an organism nor would evolution preserve such an organism if it came about by "some other way".
    Who are you to declare the limits of evolution's possibilities? As for preserving such an organism, stars have been around for a long time.

    Quote Originally Posted by ProcInc
    It is a solid guarentee that life elsewhere would be chemical, not just for the reasons in my earlier message but that life would still be chemical in form if not metabolism. Unless we want to take it a step further and assert that a life form could be an ethereal blob of pure energy.
    The energetic "blob" is a common lay conception of stars. But the creatures are precisely structured, with discernible anatomy, physiology, and predictable life cycle.
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    Quote Originally Posted by ProcInc
    A lot is to be said of the dubious nature of this article regarding a rather inappropriate 'begging the question' fallacy. For a cogent review of the evidence and information we currently have regarding the "Evolution of evolvability" (one of your primary "questions" begged) Gunther P Wagner and Jeremy Draghi's entry in "Evolution: The Extended Synthesis (2010)" is a good primer.
    Thanks. I appreciate useful references.

    Quote Originally Posted by ProcInc
    However I take especial issue to your claim that stars are a Genus of life. Firstly, something that has certain analogues to phenomena we recognise in life does not constitute life (or else fire would be life too as would crystals and various types of mud as they each have reproduction and, in the former case, metabolistic capablities).
    If you're claiming to have the criteria by which admittance to the club of life is granted, please deliver. I think you'll find it's a contentious subject.

    Quote Originally Posted by ProcInc
    This is a heavily pseudoscientific claim you charge preceded by non squiters. I am trying to sound as "kind" as I can in this response but there is little positive to say about its content. Even the "support" garnered in the form of quotes from various authorities (many of them dubious) are simply snippets of different variations of the authorities saying "we were surprised to find..." "we don't yet fully understand...". I would leave that to the creationists.
    Are you suggesting that mine is a minority view? :wink: I come to these forums to defend my heterodoxy, and it's a letdown when people reply with, essentially, "You're disagreeing with the experts, and so you're wrong." If that's all people can muster, then how is orthodox science different from orthodox theology?

    Where does my logic break down? Which data have I presented inaccurately? Which references are "dubious"? You think Sean Carroll is a quack?

    And the many references to "surprise" and "unexpected" are significant. The weaker the theory (in this case, that of natural selection) the more surprises we can expect as new data (in this case, genomic data) come to light. Faultiness of theory and surprises in new data are positively correlated.
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    starlarvae, part of the problem is that half of what you have said is not controversial or even all that new. On the contrary, its rather mainstream modern evolutionary biology - I've been reading about this stuff for at least 20 years; the discipline of "evo devo" itself probably goes back a century and is built upon a solid a foundation of evolutionary biology. Somehow, at every corner you've managed to put a truly bizarre spin on things that makes it appear as if evolutionary biology is in crisis.

    A second problem is that you appear to have misunderstood "selection"; do you mean the source of variation that is exposed to selection? Or, perhaps, you do mean selection itself? I don't know.

    Another problem, as pointed out by others, is that in places you are leaving the world of science behind and entering a place you don't really want to go (pseudoscience). Ancestors do not anticipate the needs of remote descendants. As I'm sure you know, this is called teleological thinking. There is no plan. A redeployment of an entire gene network in a new developmental context sure can look that way to the unwary, I admit.
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    Quote Originally Posted by starlarvae
    The energetic "blob" is a common lay conception of stars. But the creatures are precisely structured, with discernible anatomy, physiology, and predictable life cycle.
    There's no descent with modification in start life cycles. Stars give birth to stars with no transfer of information between them. The new star is a product of it's constituents and environment. These things are influenced but not fully determined by the parent star.

    Stars are absolutely an example of persistence of the persistent, a sort of superset rule of survival of the fittest. But you seem to be implying that they're life, which would demand that they adhere to much more specific rules. They don't.
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  32. #31  
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    One reason to look for Carbon based lifeforms is that Carbon is much more abundant than other elements in the universe. It is only superseded by Hydrogen, Helium, and Oxygen. On earth it is the 15th most abundant element. Carbon is an highly stable element and forms the most compounds.

    http://en.m.wikipedia.org/wiki/Carbon
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  33. #32  
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    Quote Originally Posted by Darkhorse
    One reason to look for Carbon based lifeforms is that Carbon is much more abundant than other elements in the universe. It is only superseded by Hydrogen, Helium, and Oxygen. On earth it is the 15th most abundant element. Carbon is an highly stable element and forms the most compounds.

    http://en.m.wikipedia.org/wiki/Carbon
    Indeed, I understand that- but it still doesn't mean that we should dismiss all other possibilities of life to come from much different elements to Earth's biochemistry element laws.
    "Nature doesn't care what we call it, she just does it anyway" - R. Feynman
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    ProcInc wrote:
    "Nuclear life" would generate far more energy than it would require, could be able to maintain and, more importantly, reach.

    "I don't see how that's an objection to the idea. How can ANYTHING produce more energy than it can obtain? It would be a perpetual motion machine."

    Exactly my point, you have just refuted your own argument.

    "Who are you to declare the limits of evolution's possibilities?"

    Humanity has a collective has determined a very good idea of the limitations of evolution. A naturally evolving nuclear reactor organism is just such an example.

    Besides, if nuclear metabolism evolved then it would be from an originally chemical organism which also defeats your original assertion.

    "As for preserving such an organism, stars have been around for a long time. "

    Yes, it works for stars, objects 100 times wider than planets and with only superpressurised metal as available solids. The only way this could work for an organism is to imagine a creature growing so massive is collapses in on itself.

    In short your assertion is ridiculous.

    "The energetic "blob" is a common lay conception of stars. But the creatures are precisely structured, with discernible anatomy, physiology, and predictable life cycle."

    Again you're talking nonsense. Are you seriously attempting to suggest that stars count as living things?

    Or that a living thing might be a star?

    Yes, the world is full of phenomena and wonders etc etc but we can draw a line against the patently absurd when we see problems from every angle and have no good reason to overlook them.
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    "If you're claiming to have the criteria by which admittance to the club of life is granted, please deliver. I think you'll find it's a contentious subject."

    Whether or not we can determine what IS life the fact remains that you can not describe stars as life forms without extending the definition of life to fire and other miscellaneous things. We may not be able to fully determine what IS life (though the seven pillars is very effective and stars fail in it) but we can solidly disqualify known objects from the group.

    You want to group stars as life forms? you are effectively rendering the term useless.

    " Are you suggesting that mine is a minority view?"

    Not even that. It's a view held by nobody but yourself.

    You misunderstood your authorities you quote (so no, Sean Carroll is not a quack) and have as such riddled the article with inaccurate data. Others have beaten me to the specifics.

    I would let go of this silly preoccupation with attempting to label stars as life for a start
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    Hello friends.
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  37. #36  
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    Quote Originally Posted by Zwirko
    starlarvae, part of the problem is that half of what you have said is not controversial or even all that new. On the contrary, its rather mainstream modern evolutionary biology - I've been reading about this stuff for at least 20 years; the discipline of "evo devo" itself probably goes back a century and is built upon a solid a foundation of evolutionary biology. Somehow, at every corner you've managed to put a truly bizarre spin on things that makes it appear as if evolutionary biology is in crisis.
    Well, there's a disconnect somewhere. As I read up on evo devo, it's striking how often I encounter references to surprising and unexpected findings. If the Darwinian model really accounts for which genes get to be where, why all the surprises? Why does the Darwinian model have such feeble predictive powers?

    Quote Originally Posted by Zwirko
    A second problem is that you appear to have misunderstood "selection"; do you mean the source of variation that is exposed to selection? Or, perhaps, you do mean selection itself? I don't know.
    Selection is mostly bogus. Some creatures have more offspring than others. Big deal. They're the lucky ones. They were in the right place at the right time. They're the ones who didn't get caught in the forest fire. They're the ones that were outside the range of the epidemic. They're the ones that stumbled upon the more nutritious fruit.

    To paraphrase Fodor, To say that phenotypes are adapted to their environments is just to say that there are such phenotypes.

    As for the source of variation, what is the source of variation when a zygote gives rise to skin, muscle, nerve, etc., cell types? This is descent with modification -- but where's the modification come from? Natural selection?

    Quote Originally Posted by Zwirko
    Another problem, as pointed out by others, is that in places you are leaving the world of science behind and entering a place you don't really want to go (pseudoscience).
    Much of today's science was yesterday's pseudoscience: Continents that move? You must be kidding!
    Quote Originally Posted by Zwirko
    Ancestors do not anticipate the needs of remote descendants.
    Tell that to the specialized tissues that descend from a common zygote.
    Quote Originally Posted by Zwirko
    As I'm sure you know, this is called teleological thinking.
    Yes, I know that. Do you think that ontogeny is a teleological process?
    Quote Originally Posted by Zwirko
    There is no plan. A redeployment of an entire gene network in a new developmental context sure can look that way to the unwary, I admit.
    It looks that way because it is that way.
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  38. #37  
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    Quote Originally Posted by ProcInc
    Whether or not we can determine what IS life the fact remains that you can not describe stars as life forms without extending the definition of life to fire and other miscellaneous things.
    Not true, but I'd like to read your argument for disqualifying fire.

    Quote Originally Posted by ProcInc
    We may not be able to fully determine what IS life (though the seven pillars is very effective and stars fail in it) but we can solidly disqualify known objects from the group. You want to group stars as life forms? you are effectively rendering the term useless.
    Not at all. I'm liberating it from an arbitrary constraint.

    Quote Originally Posted by ProcInc
    You misunderstood your authorities you quote (so no, Sean Carroll is not a quack) and have as such riddled the article with inaccurate data. Others have beaten me to the specifics.
    No, I understand the quoted authorities just fine. My difference with them is that they want to protect their professional (and no doubt personal) investments in the Darwinian paradigm. I have no such investments to be concerned about. Admittedly, I have others.

    Quote Originally Posted by ProcInc
    I would let go of this silly preoccupation with attempting to label stars as life for a start
    Thank you for your concern.
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    Life is an arbitrary label we place on some things for our own convenience.
    I think it is most convenient to have this label not extend to such things as fire and stars.
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    There is no disconnect because "evo devo" is not something separate from evolutionary biology. One is an aspect of the other. Are these surprising findings you mention at odds with evolutionary theory or do they fit in neatly like another jigsaw-piece slotted into place? Does simple random mutation with minor selective advantage account for the diversity of life we see today? Of course not. What is the "Darwinian model" and what relevance does it have to today's biology? Evolution is really a whole bunch of theories and hypotheses sitting under the one umbrella with natural selection being only part of the story (how relevant is of much debate, granted).

    Quote Originally Posted by starlarvae
    Tell that to the specialized tissues that descend from a common zygote
    Development of a zygote into an adult multicellular organism is not an evolutionary process and is not an example of natural selection. It can only be described as "descent with modification" if you choose to bend the technical terminology needlessly and incorrectly. It is not an example of ancestors anticipating the needs of descendants - its an example of cellular differentiation; morphogenesis. Maybe you could provide a real example?

    Quote Originally Posted by starlarvae
    Do you think that ontogeny is a teleological process?
    No, I do not think that ontogeny is a teleological process. The scale and scope is entirely wrong.

    Most of today's science was certainly not pseudoscience in the past.
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  41. #40  
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    Quote Originally Posted by ProcInc
    ProcInc wrote:
    "Nuclear life" would generate far more energy than it would require, could be able to maintain and, more importantly, reach.

    "I don't see how that's an objection to the idea. How can ANYTHING produce more energy than it can obtain? It would be a perpetual motion machine."

    Exactly my point, you have just refuted your own argument.
    non sequitor. You mischaracterize stars as generating more energy than they obtain.

    Quote Originally Posted by ProcInc
    "The energetic "blob" is a common lay conception of stars. But the creatures are precisely structured, with discernible anatomy, physiology, and predictable life cycle."

    Again you're talking nonsense. Are you seriously attempting to suggest that stars count as living things?
    Yes. Not only are stars alive, but we are their larvae.
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  42. #41  
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    Quote Originally Posted by Zwirko
    There is no disconnect because "evo devo" is not something separate from evolutionary biology. One is an aspect of the other. Are these surprising findings you mention at odds with evolutionary theory or do they fit in neatly like another jigsaw-piece slotted into place?
    Sounds familiar. You remember epicycles? That, too, was a way to fit anomalous data into the accepted theory. But Ptolemy lost the debate.

    Quote Originally Posted by Zwirko
    Does simple random mutation with minor selective advantage account for the diversity of life we see today? Of course not. What is the "Darwinian model" and what relevance does it have to today's biology? Evolution is really a whole bunch of theories and hypotheses sitting under the one umbrella with natural selection being only part of the story (how relevant is of much debate, granted).
    Interesting. Reminds me of a quote about scientific progress. It goes something like this -- a new idea is first dismissed as preposterous, then admitted to be possible, and finally attains the status of "We knew it all along."

    Quote Originally Posted by Zwirko
    Quote Originally Posted by starlarvae
    Tell that to the specialized tissues that descend from a common zygote
    Development of a zygote into an adult multicellular organism is not an evolutionary process and is not an example of natural selection.
    I agree.

    Quote Originally Posted by Zwirko
    It can only be described as "descent with modification" if you choose to bend the technical terminology needlessly and incorrectly.
    The tissues descend from the zygote by way of modification. Plain and simple.

    Quote Originally Posted by Zwirko
    It is not an example of ancestors anticipating the needs of descendants - its an example of cellular differentiation; morphogenesis.
    Morphogenesis during ontogeny IS a case of descendant genes being present already in the common ancestor.

    Quote Originally Posted by Zwirko
    Maybe you could provide a real example?
    Of what?

    Quote Originally Posted by Zwirko
    Quote Originally Posted by starlarvae
    Do you think that ontogeny is a teleological process?
    No, I do not think that ontogeny is a teleological process. The scale and scope is entirely wrong.
    An acorn contains a program for an oak. A caterpillar contains a program for a butterfly. Ontogeny is a teleological process.

    Quote Originally Posted by Zwirko
    Most of today's science was certainly not pseudoscience in the past.
    Matter and energy are two forms of the same thing? Get serious. Gravity can bend light rays? Preposterous. Men descended from monkeys? Heresy! Or, read up on endosymbiosis. Lynn Margulis was ridiculed until the technology came along to prove her right.
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  43. #42  
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    Quote Originally Posted by starlarvae
    Quote Originally Posted by Zwirko
    Another problem, as pointed out by others, is that in places you are leaving the world of science behind and entering a place you don't really want to go (pseudoscience).
    Much of today's science was yesterday's pseudoscience: Continents that move? You must be kidding!
    Sure, but for every one idea that is ridiculed and later validated, there are millions that are ridiculed and then demonstrated to be unfounded, illogical or simply not in keeping with the evidence. It is not an argument in support of a ridiculed idea to point out that some previously vindicated ideas were also ridiculed. Indeed, that argument is a trope most notably used by peddlers of pseudoscientific ideas.

    Quote Originally Posted by Carl Sagan
    The fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright brothers. But they also laughed at Bozo the Clown.
    The Bozo the Clown defense serves as something of a warning sign to most people familiar with pseudoscientific arguments.

    Is it appropriate that so many new ideas be ridiculed? I don't know, but certainly all new ideas should be met with doubt, with skepticism proportionate to the implications of accepting that idea. Due to the implications in this case, your ideas are worthy of a most extreme skepticism, which would probably manifest itself as ridicule from some. It would be foolish to present that as some sort of vindication, for the reasons I have already stated.

    Due to the frankly baffling logical leap you have made (from re-interpreting the nature of ontogeny and phylogeny to considering stars to be life forms), combined with your use of the Bozo the Clown argument as a defense, this is looking to me like pseudoscience. I'll give it the benefit of the doubt for now, and move it to New Hypotheses. The Biology forum is not really the place for new research, though really a forum of any kind probably isn't.
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    StarLarvae, you appear to have more than one thread on this topic, so I have merged them. Please, unless you have a substantially different argument or point to make, don't start a new thread.
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    Sorry, starlarvae, but everything you say about evolution, development and philosophical concepts such teleology and pseudoscience seems hopelessly muddled to me; so much so that I'm unable to even know where to mount a reply.
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  46. #45 The Bozo Defense 
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    Quote Originally Posted by TheBiologista
    Sure, but for every one idea that is ridiculed and later validated, there are millions that are ridiculed and then demonstrated to be unfounded, illogical or simply not in keeping with the evidence.
    I was hoping that members of this forum would attack the logic of my argument and/or the evidence that I present. I am disappointed that that hasn't happened.

    Quote Originally Posted by TheBiologista
    Quote Originally Posted by Carl Sagan
    The fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright brothers. But they also laughed at Bozo the Clown.
    The Bozo the Clown defense serves as something of a warning sign to most people familiar with pseudoscientific arguments.
    The Sagan quote implies that whatever merits a new idea might have, they are not correlated with either laughter or lack of. I agree.

    Quote Originally Posted by TheBiologista
    Due to the implications in this case, your ideas are worthy of a most extreme skepticism, which would probably manifest itself as ridicule from some. It would be foolish to present that as some sort of vindication, for the reasons I have already stated.
    I agree. Ridicule has no place in a scientific forum. The merits of a new idea should be assessed in terms of empirical support, logic, and Occam's razor.

    Quote Originally Posted by TheBiologista
    Due to the frankly baffling logical leap you have made (from re-interpreting the nature of ontogeny and phylogeny to considering stars to be life forms), combined with your use of the Bozo the Clown argument as a defense, this is looking to me like pseudoscience. I'll give it the benefit of the doubt for now, and move it to New Hypotheses. The Biology forum is not really the place for new research, though really a forum of any kind probably isn't.
    I think the move to New Hypotheses is appropriate. But the accusation of pseudoscience is unwarranted.
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  47. #46  
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    Quote Originally Posted by Zwirko
    Sorry, starlarvae, but everything you say about evolution, development and philosophical concepts such teleology and pseudoscience seems hopelessly muddled to me; so much so that I'm unable to even know where to mount a reply.
    I can help you. Just point out a logical inconsistency or a misrepresentation of the empirical data that I present.
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  48. #47 Re: The Bozo Defense 
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    Quote Originally Posted by starlarvae
    Quote Originally Posted by TheBiologista
    Sure, but for every one idea that is ridiculed and later validated, there are millions that are ridiculed and then demonstrated to be unfounded, illogical or simply not in keeping with the evidence.
    I was hoping that members of this forum would attack the logic of my argument and/or the evidence that I present. I am disappointed that that hasn't happened.
    You state that ontogeny and phylogeny appear to follow programmed paths (this is not supported in evidence for the case of phylogeny but that is a side point). You then claim that this suggests that objects (stars) that display neither ontogeny or phylogeny, as we understand those concepts, are alive. You then suggest that we are in some manner descendant from stars (beyond merely being composed of matter formed within stars). If we assume for a moment that you're correct about the path followed by phylogeny, you still haven't argued sufficiently to connect stars to life in either sense.

    Part of that logical hole might be filled with evidence demonstrating 'biological' ontology and phylogeny in stars. Or indeed any evidence at all of descent (inheritance) with modification in stars. To suggest that we are star larvae implies that we in some manner become stars in a non-chaotic fashion (ie beyond the matter that composed us decaying into the Earth which itself will one day be a part of a collapsing nebula- a non patterned process).

    Quote Originally Posted by starlarvae
    Quote Originally Posted by TheBiologista
    Due to the implications in this case, your ideas are worthy of a most extreme skepticism, which would probably manifest itself as ridicule from some. It would be foolish to present that as some sort of vindication, for the reasons I have already stated.
    I agree. Ridicule has no place in a scientific forum. The merits of a new idea should be assessed in terms of empirical support, logic, and Occam's razor.
    You misunderstand me. I am saying that you should not use the argument that other good ideas have been ridiculed to suggest that your idea is a good idea. Ridicule is an expression of skepticism. I am ambivalent as to whether it is a good or valid expression, but I am not going to say it has no place in science, as it clearly serves a function.

    Quote Originally Posted by starlarvae
    Quote Originally Posted by TheBiologista
    Due to the frankly baffling logical leap you have made (from re-interpreting the nature of ontogeny and phylogeny to considering stars to be life forms), combined with your use of the Bozo the Clown argument as a defense, this is looking to me like pseudoscience. I'll give it the benefit of the doubt for now, and move it to New Hypotheses. The Biology forum is not really the place for new research, though really a forum of any kind probably isn't.
    I think the move to New Hypotheses is appropriate. But the accusation of pseudoscience is unwarranted.
    Don't tell me that it is unwarranted. Show me.
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  49. #48  
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    Quote Originally Posted by ProcInc
    It should be noted that Extremophiles/ Archaea/ Arsenic metabolising bacteria etc are all of course fundamentally similar however.

    .
    http://www.slate.com/id/2276919/
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  50. #49  
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    Quote Originally Posted by starlarvae
    I can help you. Just point out a logical inconsistency or a misrepresentation of the empirical data that I present.
    Lets take the case of the Amphimedon queenslandica genome study as an example fo where I think you have made unnecessary leaps in the wrong direction. You suggest that this work reveals that this sponge has somehow anticipated the needs of its remote descendants.



    Amphimedon queenslandica (imaged above) is the ancestor of nothing except more examples of A. queenslandica. A. queenslandica itself is a remote descendant of a sponge-like ancestor. So are we, apparently. Now, although the phylogeny among the sponges themselves and their relationships to Ctenophora, Cnidaria and Placozoa are somewhat (even highly) contentious it's important to note that Porifera did not give rise to any other group; it's an early branching group on the Metazoan lineage. Whatever genes are present in this group can't be viewed as anticipating the needs of any other group, since there is no descendant group. Obviously these genes were present in the common ancestor of both A. queenslandica and of ourselves. Porifera are the simplest and probably the most ancient descendants of this ancient ancestor.

    This work implies that these genes initially evolved earlier than thought, further back in the Metazoan lineage. I don't see this as "inventing an imaginary ancestor of the sponge that needed the genes." That Porifera descend from a sponge-like ancestor was already known, so it's not a "ghost-like imaginary ancestor" invented ad hoc to accommodate a new finding. To repeat: all that has happened is that the so-called "toolkit" is now seen to have evolved earlier, somewhere along the lineage of the earliest Metazoans and after their divergence from their single-celled ancestors:



    The genes you mention are not sitting quietly biding their time, waiting for a time when they need to be called forth into action in a distant descendant. They are actively expressed in these organisms, presumably carrying out some other function*. Evolution can take components of this "toolkit" and use it in new ways; indeed evolution is a master at doing just that. It's far simpler to come up with a new use for a preexisting tool than to invent a new tool. That this developmental toolkit was present in some form in the ancestor of both Porifera and Eumetazoa isn't an unwarranted conclusion. Whereas suggesting that there is evolutionary foresight, with a long-term plan running is. Such a teleological conclusion, as presented by yourself, is not supported by the genome of A. queenslandica.

    * It's not a case of an entire set of genes for making muscle and neurons that is present in sponges. These genes code for DNA-binding proteins called transcription factors which are involved - in more complex organisms - in regulating differentiation of muscle tissue and nerves. Specifically, the authors mention PaxB, Lhx genes, SoxB, Msx, Mef2, Irx and bHLH neurogenic factors. Lots of studies have been done on the origins, expansion and diversification of these gene families in early Metazoans previously.
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  51. #50 Re: The Bozo Defense 
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    Quote Originally Posted by TheBiologista
    You state that ontogeny and phylogeny appear to follow programmed paths (this is not supported in evidence for the case of phylogeny but that is a side point).
    The support comes from the points in my original post: Conservation of DNA, junk DNA, genetic switches, and anticipatory genes. These are the genetic hallmarks of development. As we now have discovered, they also are the genetic hallmarks of evolution. So, we have a choice. We can figure that evolution is a developmental process, or we can suppose that natural selection among cells in an embryo produces the various specialized tissues (I've made this argument to goad people, and it can produce interesting results), or we can just call it coincidence. I think the first option is the most sensible.

    Quote Originally Posted by TheBiologista
    You then claim that this suggests that objects (stars) that display neither ontogeny or phylogeny, as we understand those concepts, are alive.
    For one thing, ontogeny is not necessary for life. What is the ontogeny of an amoeba?

    Nonetheless, stellar ontogeny is captured in the familiar Hertzsprung-Russell diagram. Stars live too long and change too slowly for us to study stellar ontogeny by watching a star mature.

    "The H-R diagram enables astronomers to do the equivalent of a botanist who studies a forest of trees that includes seedlings, saplings, and mature specimens and uses those studies to work out the life cycle of a tree."
    --John Gribbin, Blinded by the Light

    As for stellar phylogeny, I think it's too early to say. There have been only a few generations of stars since the universe began.

    Quote Originally Posted by TheBiologista
    To suggest that we are star larvae implies that we in some manner become stars in a non-chaotic fashion (ie beyond the matter that composed us decaying into the Earth which itself will one day be a part of a collapsing nebula- a non patterned process).
    Right. I think it will be a more or less orderly process. Which is not to say it won't be violent. Have you seen a live birth? Pain, blood, crying -- an uninformed person might think that's a chaotic process. I suspect that the religious association of divine/spiritual entities with the celestial and the "enlightened" is a premonition of the metamorphosis into stars.

    Quote Originally Posted by TheBiologista
    Quote Originally Posted by starlarvae
    Quote Originally Posted by TheBiologista
    Due to the frankly baffling logical leap you have made (from re-interpreting the nature of ontogeny and phylogeny to considering stars to be life forms), combined with your use of the Bozo the Clown argument as a defense, this is looking to me like pseudoscience. I'll give it the benefit of the doubt for now, and move it to New Hypotheses. The Biology forum is not really the place for new research, though really a forum of any kind probably isn't.
    I think the move to New Hypotheses is appropriate. But the accusation of pseudoscience is unwarranted.
    Quote Originally Posted by TheBiologista
    Don't tell me that it is unwarranted. Show me.
    I'm not sure what would do the trick. But consider that stars exhibit stable disequilibria, catalytic metabolisms, periodic physiological cycles, and homeostatic feedback controls. More details here: http://www.starlarvae.org/Star_Larva..._Organism.html

    If you think star are inanimate, can you name another inanimate object that has these attributes?
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  52. #51  
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    Quote Originally Posted by x(x-y)
    Quote Originally Posted by Ophiolite
    The research on arsenic/phosphorus replacement life forms has been severely criticised by several scientists. The experimental methodology is thought to be sloppy and the conclusions are highly doubtful.
    Do you mean this research?
    http://www.newscientist.com/article/...ife-forms.html
    Yes. that is the research that has been scathingly attacked by other experts in the field.

    Quote Originally Posted by starlarvae
    If stars are in a state of equilibrium, why are they so dynamic?
    You have heard of dynamic equilibrium? No? Stars exist in a state of equilibrum wherein pressure balances gravitational collapse. The balance is not perfect due to the nuclear reactions at the heart of the star, but even these are conditioned by that same balance. The point of balances changes over time, the exact path dependent upon the mass and initial composition of the star.

    In contrast, life as we know it exists far from equilibrium conditions, locally cockin a snook at the second law.
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    I think if there are any life forms living inside the Sun, or say the rocky core of Jupiter, or somewhere crazy/exotic like that, then probably it would be so exotic that we couldn't even interact with it.

    Maybe it's whole life cycle is 5 seconds long. Suppose it's as intelligent as you and I, but it's born, attends school, attends college, gets married, has kids, and then dies of old age ..... all in 5 seconds. How would we interact with that? Or in the alternative: what if it's life cycle is a million years? How would it interact with us?

    I think if you allow yourself to get too fixated on it then sooner or later you'll start looking for intelligent life forms in your coffee, think you've found some, and then refuse to drink your coffee for fear of committing genocide. It would be like Dr. Seuz's book Horton Hears a Who. But it's fun in moderation.
    Some clocks are only right twice a day, but they are still right when they are right.
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  54. #53  
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    Quote Originally Posted by Zwirko
    Quote Originally Posted by starlarvae
    I can help you. Just point out a logical inconsistency or a misrepresentation of the empirical data that I present.
    Lets take the case of the Amphimedon queenslandica genome study as an example fo where I think you have made unnecessary leaps in the wrong direction. You suggest that this work reveals that this sponge has somehow anticipated the needs of its remote descendants.
    You are right. The genes in question are not those of the sponge but of the common ancestor.

    The report states,
    The A. queenslandica genome harbours an extensive repertoire of developmental signalling and transcription factor genes, indicating that the metazoan ancestor had a developmental 'toolkit' similar to that of modern complex bilaterians. The origins of many of these and other genes specific to animal processes such as cell adhesion, and social control of cell proliferation, death and differentiation can be traced to genomic events (gene birth, subfamily expansions, intron gain/loss, and so on) that occurred in the lineage that led to the metazoan ancestor, after animals diverged from their unicellular 'cousins'.
    Brig Klyce comments (link to his site is at bottom of this post), "The actual "events" to which these "origins" can be "traced" are not at all clear in darwinan theory. What is "gene birth"? The genes, whole or in a few pieces, are simply there, ready for assembly and deployment."

    Quote Originally Posted by Charles Marshall,director of the University of California Museum of Paleontology in Berkeley
    "What I want to know now is what were all these genes doing prior to the advent of sponge."
    I would like to know that, too. Wouldn't you?

    But there are other examples of anticipation: See http://www.pnas.org/content/early/20...15107.abstract

    The researchers sequenced a newly discovered giant marine virus designated Cafeteria roenbergensis virus (CroV). It has a double-stranded DNA genome of ~730 kb, with 544 predicted protein-coding genes. Half of these have no match among sequenced genomes, but many others have various apparent functions among higher life forms.

    "We're finding suites of genes that you would really never expect to find in viral life, but would expect to find in cellular organisms." — marine virologist Curtis Suttle of the University of British Columbia

    If HGT is significant in evolution, it begs the question: What are the genes doing in the viruses in the first place?

    And take a look at
    http://www.landesbioscience.com/jour...rmanCC6-15.pdf Observations here include:
    +...One does not expect to find genes responsible for development of bilateral organisms in primitive Metazoa with radial symmetry. Surprisingly, such genes, e.g., orthologs of hox genes, were found in Cnidaria....
    + Though sea urchin lacks eyes and, of course, brain, it has six opsins, belonging to several families found in humans, Drosophila, Scallops and other groups. While the presence of the opsins could be explained by their possible function in a simple light sensing, sea urchin has the entire set of orthologs of major genes involved in the eye development....
    + Another surprise came from a complexity of components of the immune system in sea urchin.... Genes that are seemingly useless in sea urchin but are very useful in higher taxons exemplify excessive genetic information in lower taxons.

    These and many more refs to similar findings are compiled at http://www.panspermia.org/oldgenes.htm
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  55. #54  
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    Quote Originally Posted by starlarvae
    [If HGT is significant in evolution, it begs the question: What are the genes doing in the viruses in the first place?
    Viruses are acquisitional by nature. Where is the surprise? I don't see it.
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    Quote Originally Posted by kojax
    I think if there are any life forms living inside the Sun, ...
    Sorta gives new meaning to "hot babe".
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    Quote Originally Posted by starlarvae
    You are right. The genes in question are not those of the sponge but of the common ancestor.
    No, they are orthologous genes common to the sponge AND more complex animals. That they can be found in both sponges and organisms such as humans indicates that these particular genes arose in a common ancestor of both, further back on the Metazoan lineage. Ironically, this doesn't change much about the general thrust of your anticipatory hypothesis at all; all it really means is that you can't use A. queenslandica, or any sponge for that matter, as evidence to support it in the manner that you did. Brig Klyce's comments on the topic don't really make much sense to me. I'm not sure that they make sense at all.

    Quote Originally Posted by starlarvae
    If HGT is significant in evolution, it begs the question: What are the genes doing in the viruses in the first place?
    CroV is not an example of "anticipation" either. It's an example of a complex virus. Genes moving from one genome to another doesn't support your hypothesis. The genes are in the virus because it's a system that works. It evolved that way.

    Michael Sherman's idea of a universal ancestral genome doesn't impress me. While I admit that I didn't read every last word of the paper (you might want to fix the broken link that you provided), from what I did read I can honestly say that I didn't see anything that can't be explained by standard theory. It also gave me a headache - there are too many errors of basic biology in there for me take the piece seriously. I'd love to know why he thinks some sea urchin genes related to those of the adaptive immune response of vertebrates are "seemingly useless". He seems to base a great deal of his hypothesis on the simple fact that we haven't yet had the time to work out all the inner workings of organisms at the molecular level - "God of the Gaps" stuff, basically.

    Nothing presented in your last post supports the hypothesis of ancestral genomes anticipating the needs of descendant genomes. It all supports modern evolutionary theory, without exception. Surprises and unexpected findings are just that - cool discoveries. That they increase our understanding of the evolutionary history of metazoans rather than threaten to overturn evolutionary theory itself is something rather profound that you should perhaps consider taking note of.
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    Quote Originally Posted by Zwirko
    Quote Originally Posted by starlarvae
    You are right. The genes in question are not those of the sponge but of the common ancestor.
    No, they are orthologous genes common to the sponge AND more complex animals. That they can be found in both sponges and organisms such as humans indicates that these particular genes arose in a common ancestor of both, further back on the Metazoan lineage
    Okay, so genes related to neuromuscular functioning "arose" in an animal more primitive than a sponge, and that doesn't strike you as strange?

    Quote Originally Posted by Zwirko
    Quote Originally Posted by starlarvae
    If HGT is significant in evolution, it begs the question: What are the genes doing in the viruses in the first place?
    CroV is not an example of "anticipation" either. It's an example of a complex virus. Genes moving from one genome to another doesn't support your hypothesis. The genes are in the virus because it's a system that works. It evolved that way.
    It's the existence of the genes in the first place, in a virus no less, that is the point. What are they doing in a virus?

    There's a line about a theory that explains everything explaining nothing.
    Evolution is a case in point. ANY finding in the organic world can be rolled into the neoDarwinian model, just by invoking the mystical concepts of "adaptation" and "fitness". It's WHATEVER way it is in the organic world, because that was more adaptive than the alternative.

    Is the theory of evolution falsifiable? Short of finding rabbit fossils in precambrian strata, what finding would falsify the theory?

    Quote Originally Posted by Zwirko
    Michael Sherman's idea of a universal ancestral genome doesn't impress me. [. . . .] He seems to base a great deal of his hypothesis on the simple fact that we haven't yet had the time to work out all the inner workings of organisms at the molecular level - "God of the Gaps" stuff, basically.
    I eagerly anticipate the working out of the inner workings. I suspect that anomalous data will accumulate until the Darwinian edifice crumbles. But only time will tell.

    Quote Originally Posted by Zwirko
    Surprises and unexpected findings are just that - cool discoveries. That they increase our understanding of the evolutionary history of metazoans rather than threaten to overturn evolutionary theory itself is something rather profound that you should perhaps consider taking note of.
    Advice noted. "threaten to overturn evolutionary theory" is a revealing phrase. Is that what you think I'm trying to do? No, I just want to amend the theory with mechanisms to explain descent with modification that are in better agreement with the data than is the (incoherent) mechanism of Natural Selection.
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    Okay, so genes related to neuromuscular functioning "arose" in an animal more primitive than a sponge, and that doesn't strike you as strange?
    It's not strange at all since these orthologs are not neuromuscular genes. They are transcription factors that are involved in the expression of neuromuscular genes in some groups. In the sponges and ancestral metazoans they are not involved in regulating expression of genes involved in muscle or neural tissue development. They have other functions. Just because in all cases these functions have not been investigated fully needn't set off any alarm bells. Why would a re-tooling of preexisting genes appear strange? Does the process of exaptation not adequately account for these sorts of things? Ancestral genes expand into families over evolutionary timescales; all members of the family don't have to be doing the same thing in all organisms. If these genes were non-functional they would have decayed into random noise long before they were needed. The only slightly odd thing on show here is the idea that perhaps the most fascinating and innovative period in evolutionary history occurred at such a remote point in time. That's the surprise. It doesn't change anything about the theory from a mechanistic standpoint.

    It's the existence of the genes in the first place, in a virus no less, that is the point. What are they doing in a virus?
    Large DNA viruses such as CroV and Mimivirus are full of eukaryotic genes. I'm not too sure where you see something problematical that needs a different sort of explanation. In direct response to your question, the genes are there because that is how the system evolved - the genes are needed to complete its rather unusual life cycle. The real question here is 1) did the virus pick these genes up through serial horizontal gene transfers or 2) is the virus itself some kind of degenerate life form that was previously cellular in nature?

    Granted these viruses raise all sorts of challenging and interesting questions, but they are of a different nature to the ones you are asking. We already have the conceptual toolkit to explore these viruses; there is nothing about them that requires new mechanisms. I don't really see the connection these viruses have to the hypothesis that ancestral genomes anticipate the needs of descendant genomes.

    "threaten to overturn evolutionary theory" is a revealing phrase. Is that what you think I'm trying to do? No, I just want to amend the theory with mechanisms to explain descent with modification that are in better agreement with the data than is the (incoherent) mechanism of Natural Selection..
    Well, you did refer to the "Darwinian edifice" crumbling and you've previously described aspects of the theory as "bogus". Current theory is neither incoherent nor in disagreement with any data. You've not pointed out any incoherence and you've certainly not provided any evidence that would support such claims. Everything you've shown so far falls squarely within the domain of standard theory. Again, to repeat: that new and surprising findings fit so comfortably within the framework of evolutionary theory is very revealing. If ancestral genomes really can somehow anticipate the needs of descendant genomes then there must be some evidence for it. You'd need to find examples of genomes building unselected suites of genes that are completely non-functional to even begin to raise a "huh?" type question.
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    I don't know why we are giving this "starlarvae" the time of day. He thinks that we are the larvae of stars!

    Its difficult to compete with creationism for unadulterated ineptitude beyond a cosmic scale but somehow this person took total ignorance of evolutionary biology with an equally incompetent level of understanding regarding cosmology and combined them into a mutant hybrid of seemingly inexhaustable crankery

    Why hasn't this been oved to pseudoscience? The only reason I can think of is it does the term "pseudoscience" a disservice.
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    Quote Originally Posted by starlarvae
    Quote Originally Posted by Zwirko
    Quote Originally Posted by starlarvae
    You are right. The genes in question are not those of the sponge but of the common ancestor.
    No, they are orthologous genes common to the sponge AND more complex animals. That they can be found in both sponges and organisms such as humans indicates that these particular genes arose in a common ancestor of both, further back on the Metazoan lineage
    Okay, so genes related to neuromuscular functioning "arose" in an animal more primitive than a sponge, and that doesn't strike you as strange?
    I think we have a cart and horse problem here, which is similar to the problem experienced by monotheists when they talk about how amazing it is that the prophets recorded in the bible were able to give accurate predictions.

    Many of them did give accurate predictions. The reason it seems so phenomenal is because the one's who's predictions failed were simply erased from the records. Only the ones who were right are present in the bible. So we've got thousands of "prophets" all making predictions, and randomly a few of them luck out and aren't wrong... you see where I'm going with this? The junk in our genome is similarly full of false predictions that go unexpressed.




    Quote Originally Posted by Zwirko
    Quote Originally Posted by starlarvae
    If HGT is significant in evolution, it begs the question: What are the genes doing in the viruses in the first place?
    CroV is not an example of "anticipation" either. It's an example of a complex virus. Genes moving from one genome to another doesn't support your hypothesis. The genes are in the virus because it's a system that works. It evolved that way.
    It's the existence of the genes in the first place, in a virus no less, that is the point. What are they doing in a virus?
    The virus might similarly wonder what virus genes are doing in a human's genome. It's the same answer as before: because there's a lot of junk in there.



    There's a line about a theory that explains everything explaining nothing.
    Evolution is a case in point. ANY finding in the organic world can be rolled into the neoDarwinian model, just by invoking the mystical concepts of "adaptation" and "fitness". It's WHATEVER way it is in the organic world, because that was more adaptive than the alternative.

    Is the theory of evolution falsifiable? Short of finding rabbit fossils in precambrian strata, what finding would falsify the theory?
    That is a good question to ask. Stochastically determined theories are difficult to falsify because they are not susceptible to any kind of "smoking gun". Any single weird event would show up as a fluke or out lier in the data, not proof of anything. A large amount of data has to accumulate over time and form a recognizable pattern in order to overturn the patterns that have previously been recognized.

    It's like if I told you that there was a statistical correlation between drivers who get tickets for speeding and those same drivers getting into an accident. You couldn't disprove that just by showing me a single driver who had lots of tickets on their record and no accidents. Clearly such examples exist, but the correlation is still valid.
    Some clocks are only right twice a day, but they are still right when they are right.
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    Quote Originally Posted by ProcInc
    Why hasn't this been oved to pseudoscience? The only reason I can think of is it does the term "pseudoscience" a disservice.
    Actually, I meant to make the move some time ago and it slipped my mind. Done.
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    Wait a minute... I didn't make this thread, well I didn't come up with the title actually. My original post isn't pseudoscience is it?
    "Nature doesn't care what we call it, she just does it anyway" - R. Feynman
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    You can relax x(x-y), this thread is a bunch of similar topics that got merged together. It had me foxed for a while too.
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    I'm not sure it's necessary for the ancestral genes to be completely inactive in the ancestor for my interpretation to work. Certainly SOME genes in the zygote continue to work in at least some of the descendant tissues. I suppose the question is whether they perform always exactly the same function in every descendent, or whether they sometimes function in descendants in a variant or modified manner. If you know, let me know. It's an area for research. If the latter, then the parallelism between ontogeny and phylogeny remains.

    I'm trying to lay out the parallels to make the case that onto and phylo represent two scales on which the same process operates. This model implies that the notion of life cycle, and whatever teleology that brings to the table, needs to be factored into descriptions of phylogeny, just as it implies that environmental contingencies, and whatever stochastic dimension they bring to the table, need to be factored into descriptions of ontogeny.

    As for the edifice of darwinism, you have to distinguish between descent with modification from a common ancestor, with which I'm on board, and the mechanisms proposed to account for the particular modifications that we see. Natural selection is not a plausible primary mechanism. I'll defer to Jerry Fodor for the detailed critique, but just add that adaptive advantage and fitness are always, and can only be, attributed a posteriori. They consitute an alternative vocabulary for saying that some genes/organisms leave more copies/descendants than others. That's not a theory it's just an observation.

    I can come at the overall onto-phylo issue from the opposite side. I'll put together a new topic, just asking questions and posing hypotheticals, not proposing answers, and maybe the moderator will tolerate me.
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