Denial of evolution IV

Discussion in 'Biology & Genetics' started by Hercules Rockefeller, Oct 27, 2009.

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  1. Skeptical Registered Senior Member

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    The evidence for feathers in a range of dinosaurs is overwhelming.
    http://en.wikipedia.org/wiki/Feathered_dinosaur

    I quote :

    "A number of non-avian dinosaurs are now known to have been feathered. Direct evidence of feathers exists for the following genera, listed in the order currently accepted evidence was first published. In all examples, the evidence described consists of feather impressions, except those genera inferred to have had feathers based on skeletal or chemical evidence, such as the presence of quill knobs (the anchor points for wing feathers on the forelimb) or a pygostyle (the fused vertebrae at the tail tip which often supports large feathers).

    Avimimus (inferred 1987: quill knobs)[8][9]
    Sinosauropteryx (1996)[10]
    Protarchaeopteryx (1997)[11]
    Caudipteryx (1998)[12]
    Rahonavis (inferred 1998: quill knobs)[13]
    Shuvuuia (1999)[1]
    Sinornithosaurus (1999)[14]
    Beipiaosaurus (1999)[15]
    Microraptor (2000)[16]
    Nomingia (inferred 2000: pygostyle)[17]
    NGMC 91 (2001)[18]
    Cryptovolans (2002)[19]
    Scansoriopteryx (2002)[20]
    Psittacosaurus? (2002)[21]
    Yixianosaurus (2003)[22]
    Dilong (2004)[23]
    Pedopenna (2005)[24]
    Jinfengopteryx (2005)[25][26]
    Juravenator (2006)[27][28]
    Sinocalliopteryx (2007)[29]
    Velociraptor (inferred 2007: quill knobs)[5]
    Similicaudipteryx (inferred 2008: pygostyle; confirmed 2010)[30][31]
    Epidexipteryx (2008)[32]
    Anchiornis (2009)[33]
    Tianyulong? (2009)[34]
    Concavenator"
     
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  3. Zenithar66 Registered Member

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    Believe me, joining this forum IS my further reserach! I am here to be rebutted so I can get a good fix on where my opinions are in terms of the evidence out there etc..

    My main point is, fossils dont prove evolutions MECHANISMS, they simply show us change over time
     
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  5. Zenithar66 Registered Member

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    Hmm, so it may be overwhelming to you but many scientists disagree, as I say, when it comes to this particualr issue there simply are no absolutes as yet becuase for every plausible peice of evidence there pops up an implausible route for anther part of the transition rears its head. some scientists even believe that it was the other way around or that they both evolve along totally separate lines from a common ancestor..this is far from a concensus(not that that means its worng of course) so i wouldnt say its overwhelming!

    and what is even more unlikely to me at this stage in my research(assumiing they did evolve into birds) is the mechanisms that are chellenged with producing such adaption and drastic reworking of an entire system.
     
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  7. Zenithar66 Registered Member

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    I dont think its so much if we define it as good or bad but rather if we define it as a direction at all. How can a blind process have direction?
    it doesnt move "towards organisms most likely to reproduce", becuase it dosent move towards anythign, they are simply the results of a blind process
     
  8. Zenithar66 Registered Member

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    The fact that fish in the past can resemelbe fish now, proves nothign about either ancestry or evolutions mechanisms, it simply means that there was an amphibious fish in the past.
     
  9. Skeptical Registered Senior Member

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    While that is true, they give some pretty strong hints.

    For example. the evolution of feathers is demonstrated by reptilian scales becoming long and tubular in some early fossils. Fossil evidence now permits a fair idea of how feathers evolved. Elongated scales becoming curved and then tubular, and then branching.

    These early structures, elongated scales, may have evolved for display, and later been coopted for thermal insulation by becoming tubular, and later branched. Final elongation for flight is another example of a pre-existing adaptation being further modified by evolution for a different purpose again.

    This theme of pre-adaptation is seen throughout the fossil record. The predecessors to amphibians were lobe finned fishes, like the extant coelacanth. Their fins were obviously not for support. However, their descendents, like Tiktaalik, living in stagnant fresh water, started to use those fins for support, to lift their heads to near the surface, for oxygen richer water. This, in turn led to the fins developing through evolution as stronger support, and the roof of the mouth becoming vascular for gas exchange, so those fishes could gain oxygen by mouthing surface water, including air bubbles. The vascular tissue became invaginated for more surface area, eventually evolving into lungs. The lobe fins became strong support, which served the animals just before the amphibians, and also the earliest amphibians themselves.

    The fossil record shows (from sediments) that these fish lived in shallow and low oxygen fresh water. They also show primitive leg-like lobe fins in true fishes. A pre-adaptation. The development of lungs is shown in embryology, but the fossil early amphibians support that picture.
     
  10. Zenithar66 Registered Member

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  11. Zenithar66 Registered Member

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    Bear in mind that this is a detective story - you're not likely to find definitive answers to things that happened billions of years ago, only ways that things might have happened that are consistent with what we can observe now. (Many creationists seem to hate that. They seem to hold 'science' to a different standard.)


    So what your saying is it definatly happened? we just dont know how?
    seems to me after reading your papers, that we dont have a clue!
    and I dont blame them. Although they make many guesses about the ancestry of this enzyme, they never adress the fact that it would simply HAVE to be there the very first time a double stranded dna replicated!
    At this moment in my reserach, i simply cannot take that on faith, that it coudl be "hit on" and coevolve with the dna duplex stretches credibilty to the very limit! Thanks for the papers.








    My understanding of molecular evolution in general is that new functions often evolve from older similar functions.

    It seems clear that supercoiled DNA would not be possible without mechanisms to split and join DNA.

    If so, then mechanisms to split and join DNA must have existed before supercoiling.

    Oh, simple as this eh? it "must have"... and go form there? wow



    If so, there must a use for those mechanisms before supercoiling - like DNA or RNA repair mechanisms?


    Im not talking about enzymes that purposflly supercoil the dna helix for an advangate, im talking about the natural(and drastic) supercoildign that occurs as the replication fork moves forward..this must be relieved, and to suggest that topo or its ancestres were "there on time" is ludacris to me at the moment!






    But I'm speculating. Here are some recent articles that look interesting and relevant (for the possible evolution pathways of the supercoiling mechanism, the possible selection pressures, and for the detective work involved), but that I haven't read. Let me know which ones you can't access the full text.
     
  12. Skeptical Registered Senior Member

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    It is more definitive than you realise. The chemistry of the keratin in reptile scales versus bird feathers is different. Some of the dinosaur fossils with feathers have actually left traces of that keratin in rock, which has been analysed. Guess what? The type of keratin is feather keratin, not scale keratin.
     
  13. Pete It's not rocket surgery Moderator

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    Not my papers.
    And no, I'm not saying anything definitely happened.
    And yes, we don't have and probably never will have any real clues into what happened. All we can do is guess, and consider the possibilities.

    What do you expect?

    Don't they? I find that surprising. Have you really read those papers? Could you access them all?

    Ok, so same applies - there must be a reason for those DNA modifying enzymes to have already existed.

    Nobody suggests that the enzymes for cutting and joining DNA simply appeared just as they were needed for replicating long double DNA strands. As you said, that would be ludicrous.

    Therefore, there must be some other reason for DNA cutting and joining enzymes to exist. We may never know what that reason was. Would you like to guess?


    Here's some questions for you to think about:

    How long a section of double stranded DNA can be replicated at least some of the time without a topoisomerase?

    What are the advantages of double-stranded over single stranded DNA

    What functions does topoisomerase have that would be useful for maintaining a single-stranded DNA genome?

    Did you know there is a quote button above this post?
     
    Last edited: Jun 29, 2011
  14. Zenithar66 Registered Member

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    wow


    well first off, I see you didnt deal with any of my other points.
    Second, if what you say is true then that is extremley intersting and would be the best evidecnce yet. got a link?
     
  15. Zenithar66 Registered Member

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    topoismimerase, the molecular magician!

    And no, I'm not saying anything definitely happened.
    And yes, we don't have and probably never will have any real clues into what happened. All we can do is guess, and consider the possibilities.

    What do you expect?


    okay, first off(I don't join many forums!) i actully dont know how to use the quote function...sorry about that(any directions on the site?)..
    anywho...




    okay i didnt actually mean they were your papers...just the ones you sent me. Yes, but you see, just beucase you dont know and admit that, that doesnt stop these guys writing the paper from already deciding what happened and going from there!
    you see, before they write up the paper, the should(maybe they did who knows eh) reevaluate the mechanisms they are charging with "bringing about" the enzyme, along with its initiator at the same time, along with its binding site for atp and all at just the right time. They even come to teh conclusion that it originated multiple times in many forms separatly and ALL of these "origination events" occured extremly early in the FIRST ancestor!
    Not only is this guesswork but its absolutly stretching the boundaries of specualtion to their limit. This enzyme is mind blowing and i cannot simply ascribe the blind mechanisms of evolution to its "creation"..(not yet anyway!)





    Don't they? I find that surprising. Have you really read those papers? Could you access them all?


    Well, of course there were 1 or 2 i think i couldnt acess but i am activly downloading as many papers as i can from google scholar which is great.
    But of course I am also reading alberts molecular biology of the cell and watching youtube lectures and not even those two sources addressed it. They certainly addreseed its importance in maintaning DNA's fidelity at replication and repair but nothign about its co evolution of parts and its "timely arrivel" on the scene....



    Ok, so same applies - there must be a reason for those DNA modifying enzymes to have already existed.


    Infact, there is NO reason for anythign to have existed unless you already think you know how it came about. And of course, saying there must have been a reason just brings the same question backwards in tme, becuase as soon as it was needed, it was there! we have to ask ourselves, before we consider how it originated through evolutions proceses, rather could it!
    and could it "on time"...its like the evolution of the sexes or the anchor fish mating ritual or girrafes neck etc, co evolution on such a scale as to be basically impossible!(opinion subject to change )




    Nobody suggests that the enzymes for cutting and joining DNA simply appeared just as they were needed for replicating long double DNA strands. As you said, that would be ludicrous.



    Well infact i have heard that they did indeed "appear" and have heard that same term in reference to the origin of many cellular parts. So if, as you say, its is ludacris(which i wholeheartedly agree with), then what did DNA do the first time it replicated, or repaired itself and needed to releive super coiling..(this is forgetting about the gobsmackngly complex replication and repair holoenzymes!)....what did it do? did it "recruit" other proteins at just the right time? now that would be a miracle...



    Therefore, there must be some other reason for DNA cutting and joining enzymes to exist. We may never know what that reason was. Would you like to guess?




    We may never no what the reason was.....but ther WAS a reason right?
    there....MUST have been.....BECAUSE its here now? personally i wouldnt make any claims to know ANYthign about its origin, so i wont even speculate.(sorry bout the caps, just obviiosly need to emphazise some parts of the text)





    Here's some questions for you to think about:

    How long a section of double stranded DNA can be replicated at least some of the time without a topoisomerase?


    To my knowledge, none, because as soon as you have 2 strands with 2 full turns of about 20 base pairs, coling insues...but anyway im not saying such a state of DNA couldnt have existed, i am referign to the tiem when it did need to be negativley supercoilded to relieve,well, positive suepercoiling!




    What are the advantages of double-stranded over single stranded DNA

    what releveance does this have to the topoisimerase?



    What functions does topoisomerase have that would be useful for maintaining a single-stranded DNA genome?


    mayve its cleavage function? or its ligase like function for sealing breaks..




    Did you know there is a quote button above this post?[/QUOTE]
     
  16. Fraggle Rocker Staff Member

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    No, but you're certainly justified in judging it by the ones who are chosen to be its leaders. Integrity is simply not a major concern for these people.
     
  17. Zenithar66 Registered Member

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    tsk tsk


    so then do you judge america by its leaders? do you judge science by its leading scientists, to you judge a town by its mayor?
    you have to stop worrying about the persons involved and worry about the information presented, which is unfortuntly not all rubbish, though most probably is. You see, though these people are dangerous becuase of a prior commitment to a particaulr text, they are not the only ones questioning evolution, and the fact that they are so driven by there theism means they go to great lenghts to dig out some very interestign facts...

    For instance, i recently found on a creationist sight a very intersting article on the apparent problem of chirality in terms of an natural cause for abiogeneiss. I have since done the reserach and have yet to see a senseible argumetn to account for the chirality of boht dna and amino acids. Its quite a predicamnet for any abiogenesis model...
     
  18. Mr MacGillivray Banned Banned

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    There is actually an amphibious fish in the current time. That is what extant means.

    Sorry if I use difficult words.

    And actually the current amphibious fish doesn't resemble the predecessor of amphibians at all.
     
  19. Skeptical Registered Senior Member

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    http://en.wikipedia.org/wiki/Feathered_dinosaur

    I quote :


    "more than twenty genera of dinosaurs, mostly theropods, have been discovered to have been feathered. Most fossils are from the Yixian formation in China. The fossil feathers of one specimen, Shuvuuia deserti, have tested positive for beta-keratin, the main protein in bird feathers, in immunological tests."

    The other points you raised seem to be the claim that there is too much and too complex a change to be explainable by the mechanisms I posted.

    Perhaps true, but you have to start somewhere. If that is your argument, it is starting to get ominously like a creationist argument. These have been fought out in enormous detail by others, and I am not sure I want to go down that road. We might still be at it next decade!

    As MacGillivray points out, the coelacanth is a currently living species of lobe finned fishes. it is not, of course, an ancestor to the amphibians, and still lives in the sea like its ancient forebears.

    However, other, and very ancient lobe finned fishes have left fossils in sediment characteristic of shallow fresh water environments. There appears to be a transition towards limb development for support. This is not Lamarckism. The individuals without reasonable support would not have reproduced, and Darwinian evolution has caused changes resulting in stronger supporting fins.
     
  20. Zenithar66 Registered Member

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    i dont really get what this replys to?
     
  21. Zenithar66 Registered Member

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    I quote :


    "more than twenty genera of dinosaurs, mostly theropods, have been discovered to have been feathered. Most fossils are from the Yixian formation in China. The fossil feathers of one specimen, Shuvuuia deserti, have tested positive for beta-keratin, the main protein in bird feathers, in immunological tests."


    unfortuantly, now that i look at it(i actually read this wiki page earlier but missed this part) i really dont see this as great evidence and the reasons are

    A. it was found in a structure that is hotly contested to even be a feather!
    other scientists are convinced it is collegen, found in bones, which brings me to my next point

    B. Bones have beta keratin in them, and can be incorporated into the strcuture for better bone mass! so its not at all unusual to find bones with beta keratin in them. Using it as evidence becuase it is "the main protein in birds feathers" is kind of odd sinece its also the main protein in many other structures.

    Im not saing its not evidence, and I'm not even saying I have a problem with common ancestry or one speices evolving into another, only that i am as of yet unconvined.




    The other points you raised seem to be the claim that there is too much and too complex a change to be explainable by the mechanisms I posted.

    Perhaps true, but you have to start somewhere. If that is your argument, it is starting to get ominously like a creationist argument. These have been fought out in enormous detail by others, and I am not sure I want to go down that road. We might still be at it next decade!


    So it is perhaps true? doesnt that mean those "creationist arguments" have not truly been rebutted as you sugest?
    If one takes a logical look at what is required of mutations and selection in this case, especially with the coevolution of parts, it becomes very obvious how unlikely it is to have occured. And of course, somethign can be so implausible that, though technically possible, will never actaully happen!

    we cant look at the fossils and say, oh the mechanisms did it!
    we must say, hmm, these fossils look like evidence that these organisms are somehow related through time, and thats intersting, but the mechanissm are a totally different kettle of amphibious fish!!






    As MacGillivray points out, the coelacanth is a currently living species of lobe finned fishes. it is not, of course, an ancestor to the amphibians, and still lives in the sea like its ancient forebears.

    However, other, and very ancient lobe finned fishes have left fossils in sediment characteristic of shallow fresh water environments. There appears to be a transition towards limb development for support. This is not Lamarckism. The individuals without reasonable support would not have reproduced, and Darwinian evolution has caused changes resulting in stronger supporting fins.[/QUOTE]


    The same argument i made above goes here.
    Those fossils suggest that forms of fossils may well be linked through time, on the other hand, they may simply look alike.
    Just becuase they look like they are going towards somethign, i could say that about anything alive today, yet evolution has no "towards" anything so its a strange one!

    thanks for the reply!
     
  22. Pete It's not rocket surgery Moderator

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    No problem. Try this page: BB Code List
    Briefly, a bbcode 'tag' is a keyword in square brackets. Tags usually come in pairs (the second one has a slash before the keyword), and apply some formatting to the text between them.
    For example, anything that's surrounded by quote tags, like this:
    [noparse]
    [/noparse]
    Appears like this:
    Clicking the 'quote' button above a post automatically quotes the entire post and puts your cursor at the bottom, but you can go up into the post and type your own tags to cut the quote into sections for a piecewise reply.
    You can also use the toolbar in the advanced editor to put tags in for you.

    The piecewise reply thing works reasonably well as a discussion technique, although it can get a bit unwieldy when replies get longer and sidetracks develop. You can find yourself carrying on several different conversations with one person!
     
  23. Pete It's not rocket surgery Moderator

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    Are you sure they're not suggesting a possibility and exploring the potential consequences?
    Perhaps you could give an example?
    Who do you mean, specifically?
    Who has said that a particular enzyme and associated machinery appeared at exactly the same time as it was required?

    Yes. That part isn't guesswork, but detective work.
    No, that's doesn't match what I've read. Who came to that conclusion?
    Probably because you've mislearned the supposed evolutionary origins from creationist sources.

    Which ones? I'll email them to you if you like.

    A molecular biology text is chiefly concerned with molecular biology as it is *now*, not as it was 4 billion years ago. And Youtube? Needles and haystacks spring to mind.
    And once again, you're looking for knowledge that we don't have. We don't know and perhaps can't know the details of what happened. All we can do is speculate, and examine whether those speculations are consistent with what we see now.

    I don't know what you're thinking. We can look at something and see the reason for its existence in it's apparent purpose, its function. No origin theories required.
    No, it doesn't work that way. That's a typical creationist caricature of evolution.
    Actual evolution is about combinations and subtle changes in existing machinery or its environment, that sometimes results in new useful functions.

    The idea that some amazing biological functions seen today sprang into existence fully formed is creationism. It is no part of evolution.


    Where did you hear it? In what context?
    Like I said, the required machinery must have been there already, and performing some pre-existing function. Why is that miraculous?

    Absolutely correct.

    Then why are we having this discussion?
    I think you do very much want to speculate on origins.
    Isn't that what creationism is?

    Are you confusing coiling with supercoiling? Or are you only thinking of circular DNA?
    Many full turns of non-circular DS DNA can be replicated before supercoiling becomes a problem, because the tension in the double helix can be relieved by twisting the whole molecule. It would have to be pretty long before that twisting results in a supercoiled tangle.

    The relevance is that there would have been a reason for DNA manipulation before long DS DNA existed.

    Right, so the functions of DNA topoisomerase might have been performed less efficiently by other enzymes, at least for short DNA segments.

    Can you see the potential for gradual change? As DNA maintenance machinery gradually becomes more efficient, it can gradually maintain longer and longer DNA strands.

    There is no point at which development is halted unless several things appear at once.
     
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