Friday, August 12, 2011

The Cod’s Unlikely Immune System and Evolutionary “Flexibility”

It’s being called “evolutionary flexibility.” Evolution’s effortless incorporation of the cod’s unusual immune system is yet another example of the near infinite plasticity of Darwin’s idea which, ultimately, could make unlikely alliances between everything from gradualism to saltationism, selection to drift, common descent to independent origin, bad designs to good designs, inefficiency to optimality, and so forth. Evolution is the ultimate big tent coalition where everything, save the truth of course, is allowed and flourishes.

Contrary to that quaint evolutionary expectation of similar designs in similar species, new research finds that the Atlantic cod (Gadus morhua) has an “unusual” immune architecture compared to other vertebrates whose genomes have been analyzed.

Unusual is right. In fact, G. morhua is missing the major histocompatibility complex (MHC) II. That’s right, the highly conserved and crucial MHC II is simply not present in the cod. Like the government which loses billions of dollars from time to time, evolution just happens to lose crucial molecular and cellular components now and then.

Needless to say, losing MHC II is not likely under evolution. Aside from the difficulty in simply losing all those genes (genes related to MHC II were also “lost”), such a loss would have left the cod with a crippled immune system—hardly the sort of adaptive change evolutionists are always talking about.

But true to form evolution can always find an explanation. First the hapless cod somehow lost its MHC II and related genes, but then cleverly compensated for the loss with massive additions to its MHC I. In the end all was well, and evolutionists have more puzzles to work on. As one explained, the finding could “challenge our understanding of the evolution and flexibility of the vertebrate immune system.” If only Ripley were alive today.

75 comments:

  1. Aah, there you are CH! Though maybe the Mall had lost power and you were trapped on the escalator for days.

    Glad to see you're back with your latest installment of "Golly here's something interesting in science, therefore all we know about evolution is false false false!!' theater. Also known as "Curly Howard explains biology".

    Your ongoing comedy act is one of the funniest things on the web. Moe and Larry would be proud!

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  2. Cornelius,

    Contrary to that quaint evolutionary expectation of similar designs in similar species...

    That's right, folks. Similar species should always be similar in all aspects according to evolution. Species are never to diverge from each other in any way at all. That's not expected what-so-ever in evolution. What a muddled mess is evolution.


    Evolution is the ultimate big tent coalition where everything, save the truth of course, is allowed and flourishes.

    Perhaps Cornelius could be so kind as to tell us what the truth is, then? He obviously knows.

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  3. I'm sorry, but I don't understand Dr Hunter's post. Is there a creationist prediction that was confirmed by the quoted research?

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  4. "Perhaps Cornelius could be so kind as to tell us what the truth is, then? He obviously knows."

    Yeah, what is the truth? Enquiring minds want to know. :)

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  5. HA HA HA HA HA, how lame!

    Cornelius, perhaps you could state exactly WHY the loss of MCH II is 'not likely under evolution'? The WHOLE POINT of the theory is that species branch and deviate genetically! New features are developed and lost all the time.

    You have failed to make any point at all in this post. How is this AT ALL problematic for ToE? You seem to think just insinuating it is will be sufficient.

    And the tragic thing is, for most of the knuckle-dragging, missing-link mouth-breathers in the ID movement, it probably is.

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  6. There are more things in earth, Cornelius,
    Than are dreamt of in your philosophy.

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  7. How wonderful to see the cabal of critics so thoroughly enjoying themselves!!! The cabal who couldn't acknowledge a point much less even see the point if it mutated on their noses! (Which it won't of course because even though such mutations occur all the time in their dreams, such mutations do not occur all the time in the real world. Oh well.) The point, clearly and coherently made in this and many other posts, is that evolution is NOT a real theory. A real theory can be falsified and NOTHING EVER seems to falsify evolution. Just like Ptolemaic Astronomy--there's nothing wrong with the theory that a few epicycles won't fix.

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  8. Red Reader said...

    The point, clearly and coherently made in this and many other posts, is that evolution is NOT a real theory. A real theory can be falsified and NOTHING EVER seems to falsify evolution.


    ToE is quite falsifiable. Finding multiple incompatible forms of DNA in different 'kinds' would do it. So would demonstrating the magic barrier that prevents micro-evolutionary changes from accumulating into macro-evolutionary ones.

    Sadly, you seem to be yet another clueless Creationist who doesn't understand the difference between not falsifiable and not falsified.

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  9. Last I looked, Einstein's Special Relativity hasn't been falsified yet either.

    Must not be a *real* theory.

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  10. Pedant said...

    Last I looked, Einstein's Special Relativity hasn't been falsified yet either.

    Must not be a *real* theory.


    Gravitational theory
    not falsified!

    Germ theory of disease
    not falsified!

    Plate tectonics
    not falsified!

    Kinetic theory of gases
    not falsified!

    Cell theory of biology
    not falsified!

    Set theory of mathematics
    not falsified!

    Look at all those not *real* theories! Scientists must be a bunch of crooks!

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  11. This comment has been removed by a blog administrator.

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  12. Pedant said, "Last I looked, Einstein's Special Relativity hasn't been falsified yet either.

    Must not be a *real* theory."

    --

    Accurately stated, evolution is protected from falsification. The problem with evolution is that many of its predictions HAVE been falsified. However, evolution is just retrofitted to accomodate anything.

    IT easily accomodates contradictory findings. If you ask an evolutionists, "If such and such a prediction is shown to be false, then is evolution falsified?" I don't think you could get an evolutionist to seriously sign such a statement. This is proof that evolution is, at its heart, really not dependent on making accurate predictions. A theory that cannot make accurate predictions is worthless.

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  13. CH: It’s being called “evolutionary flexibility.”

    By whom? You? Creationists? The media, BTW one of which recently claimed that DNA was found in a meteorite?

    Given that the word "flexibility" wasn't found in the paper you referenced, perhaps you meant to say, "I'm interpreting it as 'evolutionary flexibility'"?

    CH: Needless to say, losing MHC II is not likely under evolution.

    Of course, to actually reach this conclusion you'd need a firm grasp of evolutionary theory and science in general. However, your posts here have continually demonstrated otherwise.

    The genome is a biological replicator. Specifically, it contains the knowledge of how to cause it's environment to replicate itself. Neo-Darwinian evolution represents a very specific theory of how this knowledge was, as still is, created.

    As such, predictions of evolutionary theory represent what we'd expect should this explanation be true, in reality, given our best understanding at the time.

    In contrast, if there was such a thing as Neo-Lamarckian inheritance, it would postulate that the knowledge present in the genome was created by use and disuse. A giraffe stretching it's neck to reach high leaves is creating the knowledge of how to build a longer neck. A blacksmith is creating the "knowledge"" of how to build stronger arms though his work. In both cases, this knowledge is "written" to the genome, which would be passed to their offspring.

    And, of course, there is ID, which tells us nothing about how the information in the genome was created. Rather it vaguely asserts the information was previously located in some sort of abstract "mind."

    As such, it's unclear how you can claim Neo-Darwinian evolution is not a well defined theory. Rather, it would seem your objections represent disengenous misrepresentations.

    Example? Let's take your earlier post suggested research indicated that "Larmark was correct and evolution is false".

    It's highly unlikely that you think knowledge was created at the time of the experiment. Rather you think the knowledge to adjust the plant's genome was already present. As such, it's unclear how this indicates that Larmark was correct, even if we took into account our current best explanation of how inheritance actually occurs.

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  14. Tedford's creationist logic:

    I don't think you could get an evolutionist to seriously sign such a statement. This is proof...

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  15. Another Tedford gem:

    A theory that cannot make accurate predictions is worthless.

    What predictions did creation science make besides "Junk DNA can't be junk, because Jesus wouldn't put junk in your DNA"?

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  16. Tedford the Idiot said...

    Accurately stated, evolution is protected from falsification.


    Except I just gave you some example of things that would easily falsify evolutionary theory, kill it 100% dead. Pity you're too much of an idiot to grasp anything beyond your own Bible-thumping.

    The problem with evolution is that many of its predictions HAVE been falsified. However, evolution is just retrofitted to accomodate anything.

    There's a huge difference between having a prediction about some small unexplored detail not be correct and having the overarching tenets of the theory be falsified. But you're an idiot, so that distinction is lost on you I'm sure.

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  17. Ahhhhhh...so saying "God did it" was religion...but saying 'evolution did it' and giving blind, random materialism the God-like qualities to do so, isn't. Well, I can see why they call neo-darwinism 'scientific' ;-)

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  18. National Velour said...

    Ahhhhhh...so saying "God did it" was religion...but saying 'evolution did it' and giving blind, random materialism the God-like qualities to do so, isn't. Well, I can see why they call neo-darwinism 'scientific' ;-)


    Er...the observed processes that lead to evolution happening aren't all blind and random. You really should learn at least a tiny bit about the subject before you attempt to criticize it.

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  19. Neal: The problem with evolution is that many of its predictions HAVE been falsified.

    Neal, as I've pointed out earlier, predictions of scientific theories are not prophecy. They do not predict what we will *experience* in the future.

    Rather predictions are the result of an assumption that an theories underlying explanation is true, in realty, in conduction with our best explanations at the time. However, our best explanations change over time. These changes impact what we would predict if the theory's underling explanation was true, in reality. Not to mention a near infinite number of unrelated possibilities that could effect what we actually experience in the future.

    On the other hand, prophecy *is* a claim to know what we will experience because it supposedly *can* take into account an infinite number of possibilities. And it does so via supernatural means. I.e. it uses foreknowledge to take into all of the infinite possible that eventually did the outcome and/or a beings supposed ability to bring about its will regardless of any obstacles it faces. As such, if the outcome of a prophecy is not experienced, then yes - it must be false.

    However, Scientific theories make neither of these claims. As such, they clearly cannot make claims about what we will experience in the future. Nor should we expect them to.

    I'd suggest this sort of logic is ultimately based on the assumption we can use inductivism to justify theories in the first place. This is because inductivism assumes that we form theories by merely generalizing what we experience (observations).

    And, as Deutsch points out, there is little difference in believing in X and having an X shaped gap in one's scheme of things, which must be filed by something else. In either case, the assumption is that the problem of induction is a problem for science.

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  20. Pedant said, "What predictions did creation science make ..."?

    ---

    Here's a few:

    http://www.ideacenter.org/contentmgr/showdetails.php/id/1156

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  21. Scott said, "They do not predict what we will *experience* in the future. "

    Seriously? An important part of scientific methodology is the use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations. Then checking the performance of the experimental tests of the predictions by several independent experimenters and properly performed experiments.

    Evolution is protected from falsification. If the prediction is falsified then they say something like, "that's the way science works, we don't know everything about evolution yada yada yada...". The unknown is filled by "evolution of the gaps" or a new buzz word that actually has zero explanatory value.

    It's a scientific ponzi scheme that continues to offer its "investors" an ever-increasing flow of new buzz words and promises that the solutions are just over the next hill.

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  22. How did the Cod loose the MHC II? It would have to firatr gain the better MHC I, or it wouldn't survive the lose of the MHC II. But why would it gain a better MHC I if it doesn't need it because it still has the MHC II?

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  23. Neal -

    From your link:

    'Predictions' of ID:

    "1) that we will find specified complexity in biology. One special easily detectable form of specified complexity is irreducible complexity. We can test design by trying to reverse engineer biological structures to determine if there is an "irreducible core.""

    Why MUST a designed structure have irreducibly complex parts? I can see that if we DID find irreducibly complex parts, then that would be rather suggestive, but being designed doesn't NECESSITATE irreducibly complex parts, does it? If we took an organism apart and discovered no such parts, that wouldn't falsify ID, would it? So no, this prediction would not falsify ID.

    "2) rapid appearance of complexity in the fossil record,"

    Beyond the questions of 'How rapid is 'rapid'?' and 'How do we tell if we just haven't FOUND precursor fossils?', we have the same problem again as above. Who says a designed organism can't be the result of slow, arduous tinkering? Design doesn't NECESSITATE complexity appearing suddenly and immediately. So again, the discovery of the reverse does not falsify ID.

    "3) re-usage of similar parts in different organisms"

    Again, same problem. Design doesn't NECESSITATE the re-usage of similar parts in different organisms, to the discovery of the reverse does not falsify ID. Do the dis-similarities between a bat's wing and a bird's falsify ID?

    "4) function for biological structures"

    An odd one. What is the function of a blind cavefish's 'eyes'? What is the function of the human's 'broken' vitamin C gene?
    We can, of course, retreat into 'it has a function but we just haven't discovered what it is yet', but this could apply to any feature, thus ensuring this condition is never met. But again, WHY wouldn't a designer create a functionless feature? To declare so is to assume the intentions of the designer - a cardinal sin to listen to ID-ers such as Cornelius.

    In short, none of these can, in reality, serve to falsify ID.

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  24. Neal -

    "Evolution is protected from falsification. If the prediction is falsified then they say something like, "that's the way science works, we don't know everything about evolution yada yada yada...". The unknown is filled by "evolution of the gaps" or a new buzz word that actually has zero explanatory value."

    I'm afraid this just shows you do not understand biology in the slightest. This is categorically not how it works. ToE is highly falsifiable. The fact that it HASN'T been falsified is simply good testimony to the fact that it is likely true.

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  25. nat -

    "How did the Cod loose the MHC II? It would have to firatr gain the better MHC I, or it wouldn't survive the lose of the MHC II. But why would it gain a better MHC I if it doesn't need it because it still has the MHC II?"

    A reasonable question. But how are you going to address to it? Are you going to do some reading on the issue? Are you going to perform some scientific research yourself? Or are you going to not bother to do either, and if no-one here can explain it to you in a way which you cannot dream up any objections, merely conclude that because you don't know, it must be impossible?

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  26. "A theory that cannot make accurate predictions is worthless."

    And that's just one of the reasons why the so-called 'ID theory' will never be taken seriously by science.

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  27. Ritchie:

    I read the artilce. I didn't find any explanation for how it happened. Dariwinists calim that everything happens via naturalistic mechanisms. If I see something that, at present, is difficult to explain via naturalistic mechanisms, I add it to the pile of evidence against evolution. Its a preponderance of evidence thing.

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  28. box of rocks schuster said...

    Ritchie:

    I read the artilce. I didn't find any explanation for how it happened. Dariwinists calim that everything happens via naturalistic mechanisms. If I see something that, at present, is difficult to explain via naturalistic mechanisms, I add it to the pile of evidence against evolution. Its a preponderance of evidence thing.


    So once again you are too lazy to do the slightest bit of reading or research on your own. Did you read the Nature paper? There are dozens of cross-references in there for you to look up. Or did you just skim the abstract again and decide you're now an expert? No surprises there, as you seem to revel in your comfortable willful ignorance.

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  29. Ritchie commenting on Tedford's linked "predictions" of creation science:

    In short, none of these can, in reality, serve to falsify ID.

    What's more, nothing in that list is a prediction. They're all claims made long after discoveries in biology were made by real scientists.

    Shameful cheap creationist lies.

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  30. If I see something that, at present, is difficult to explain via naturalistic mechanisms, I add it to the pile of evidence against evolution. Its a preponderance of evidence thing."

    You must be joking. Just because something is difficult to explain, especially to you, doesn't mean it's evidence against evolution.

    You godbots expect absolute perfection from science RIGHT NOW. Otherwise, you dismiss and denigrate science. At the same time, you don't expect any sort of evidence or reasonable explanations from your religious programming.

    If you were to actually apply the standards you expect from science to your religious beliefs, you would have to see your religious beliefs as ridiculous fairy tales.

    What you really need to ask yourselves is why do you believe in ridiculous fairy tales, and what is it inside you that makes you so determined to do so? It can't be a preponderance of the evidence. Evidence is something real and testable, and there is nothing real or testable in religious fairy tales.

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  31. TWT:

    Why isn't it evidence against evolution? And why is it anti science. Evolutionists claim that everything can be explained via the mechanisms or RN and NS. If there is something that probably can't be explained by those mechanisms, then it means that those mechanisms are inadequate.

    And I don't consider myself an expert. I'm asking a question.

    Another thing I don't understand is why my religious beliefs are relevant to this topic. I'm asking whether a proposed scientific method is adequate. Can't we just stick to the science?

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  32. Neal: Seriously?

    Yes, seriously. Why do you suppose one of Cornelius reoccurring objections an inability to account for a near infinite number of un-conceived possibilities?

    As a confessed Christian, Cornelius may *think* he can appear neutral by refusing to publicly disclose where he puts divine revelation on the traditional hierarchy of deduction induction and philosophy, however there is little difference in believing in X and having an X shaped gap in one's scheme of things, which must be filled by something else.

    Only prophecy could supposedly claim to know what we'll experience.

    For example, some have suggested "finding a single fossilized rabbit in the cambrian" would falsify evolution. However, this isn't necessarily the case. This is because there could be some yet undiscovered geological process that could have moved this fossil into from one strata to another.

    This is why I keep pointing out that we must take into account our current best explanations when evaluating a theories predictions.

    If, during this same discovery of the fossil, we also discovered some new geological process which explains why it would appear in an unpredicted strata, this observation wouldn't falsify evolutionary theory.

    Furthermore, should only one fossil be found, we would ask the questions, "what would better explain only one fossil?" and "why this particular fossil?" This is because the underlying explanation presented by neo-darwinisnm is concerned with how knowledge found in biological replicators is created. A mere claim that this knowledge previously existed in a mind doesn't explain either of these things better than some other explanation, such Lamarkian inheritance, etc. They both fail to explain how the knowledge found in the genome is created.

    In other words, the assumption that neo-darwinisnm would be falsified by "finding a single fossilized rabbit in the cambrian" confuses neo-darwinisnm (a theory of how knowledge in the genome is created ) with a specific history of how life evolved on our planet. However, we regularly make discoveries that alter our specific placement of species in regards to their common ancestry, which doesn't falsify neo-darwinisnm either.

    Again, I'd suggest this line of thinking is the flip side of assuming we generalize observations to create theories.

    This is not to say that observations do not come in to play at all. For example, new observations may lead us to conclude one of our current explanations seem lacking. And we us observations to test the empirical content of theories themselves for errors. However, we do not justify theories via observations. We justify them via the quality of their explanations.

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  33. I'm asking whether a proposed scientific method is adequate.

    After all of this time, and your entire life experience, you still don't know? Maybe you should go back to school?

    That is, if you really want to know...

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  34. box of rocks schuster said...

    Why isn't it evidence against evolution?


    Because "we don't know all the details" doesn't equal "ToE is falsified".

    And why is it anti science.

    Because "we don't know all the details" doesn't equal "ID wins by default".

    Evolutionists claim that everything can be explained via the mechanisms or RN and NS. If there is something that probably can't be explained by those mechanisms, then it means that those mechanisms are inadequate.

    How did you determine natural mechanisms are probably inadequate? Do you have perfect knowledge of every naturalistic process in the universe?

    And I don't consider myself an expert. I'm asking a question.

    No you're not. You're trolling.

    Another thing I don't understand is why my religious beliefs are relevant to this topic.

    They're relevant because they're the sole motivating reason for you constant attacks on science.

    I'm asking whether a proposed scientific method is adequate.

    To the best of our knowledge, yes.

    Can't we just stick to the science?

    We have been. It's you ignorant Creationists who keep trying to force your Deity into the equation.

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  35. Thorton:

    Can you explain to me how RM and NS is an adequate exlanation for the Cod's immune system?
    Evolutionists say that they are adequate to explain all biology. I would like to know how they are adequate here. I'm not asking about every single mechanism in the Universe, just the Darwinian ones. I couldn't find any answers in the articles linked. And if they aren't adequate, why isn't that a problem for evolution? And I didn't say it falsifies evolution, but it is a problem. Again, it is a preponderance of evidence thing. And I don't see God anywhere in my post. I asked a question based on the fact that I don't see how a Darwinian process could account for the Cod's immune system for the reasons I mentioned. No religion at all. Demonstrate how it coulkd happen to me, and I'll say you answered my question. I personally find the "we hope to have an answer for you someday" I get so often to be intellectually unsatisfiying. But that is just me.

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  36. Nat: Can you explain to me how RM and NS is an adequate exlanation for the Cod's immune system?

    Nat, care to clarify what you mean by "adequate"?

    For example, would you say it's "adequate" to explain solid objects as being composed mostly empty space? Do you add this to a pile of evidence against quantum mechanics? Is it "adequate" to explain how the angles of a triangle could add up to more than 180 degrees via the warping of space-time? Do you add this to a pile of evidence against general relativity?

    In other words, should we point you to papers which elaborate on the theories behind these observations, it's unclear how YOU'D find them any more of an "adequate."

    Solid objects do not appear to be mostly empty space. Nor do we directly observe atoms, quarks or the warping of space-time.

    So, it seems that your objections are NOT based on the ease by which observations are explained, but whether the particular underlying explanation happens to conflict with your particular theology.

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  37. box of rocks schuster said...

    Thorton:

    Can you explain to me how RM and NS is an adequate exlanation for the Cod's immune system?


    Yes, I can. But I won't, since you're just a disingenuous troll who ignored the last dozen times people explained things to you.

    I couldn't find any answers in the articles linked.

    And you didn't bother to do any research or reading on your own because 1) you're a disgustingly lazy turd 2) you don't want to find an answer.

    I don't see how a Darwinian process could account for the Cod's immune system

    That settles it then. Nat schuster, the laziest most willfully ignorant Creationist on the web can't conceptualization something, so therefore it must be impossible.

    Demonstrate how it coulkd happen to me

    Go pound sand.

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  38. box of rocks schuster said...

    Again, it is a preponderance of evidence thing. And I don't see God anywhere in my post.


    OK then, give us your scientific explanation for the observed evidence. But no GAWD or other supernatural designers.

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  39. Scott:

    Empty space isn't the explanation for mass. It has something to do with virtual particels. And I'm not sure what explanations have to do with triangles in non-euclidean space. I said above that I don't see how RM and NS can lead to the Cod's immune system. And I explained why. If yuo could provide me with a scenario that addresses the problems I mentioned, then I will consider it adequate.

    And I don't have any scientific explanation for the Cod's immune system. I'm asking a question, not making an assertion.

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  40. box of rocks schuster said...

    And I don't have any scientific explanation for the Cod's immune system. I'm asking a question, not making an assertion.


    "God helps those who help themselves"

    Have you read the Nature paper yet? Have you read or researched any of the other references in the paper?

    Come back when you have.

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  41. I've been Googling and Googling and I couldn't find anything else on the evolution of the Cod's immune system. I guess I'll have to settle for "we have faith that we'll have an answer for you someday." I guess I just don't have enough faith.

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  42. I read the article linked and didn't see anything on evolution. I might have missed it. I do that sometimes.

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  43. natschuster said...

    I read the article linked and didn't see anything on evolution. I might have missed it. I do that sometimes.


    Try reading more than just the abstract this time.

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  44. I read the whole article, Didn't see anything on how it evolved.

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  45. Nat: Empty space isn't the explanation for mass. It has something to do with virtual particels. And I'm not sure what explanations have to do with triangles in non-euclidean space.

    Nat, your response indicates you do not understand these things either. So, how can something you do not understand be "adequate"? Why do we not observe you complaining as to how inadequate they are?

    Nat: I said above that I don't see how RM and NS can lead to the Cod's immune system. And I explained why.

    Are you referring to this? If I see something that, at present, is difficult to explain via naturalistic mechanisms, I add it to the pile of evidence against evolution.

    Again, it's not clear what you mean by difficult to explain.

    If you're willfully ignorant about RM and NS, then such explanations will be difficult and you will put them into a pile of what you consider evidence against evolution. However, this appears to be by design (no pun intended)

    Cornelius appears to do this regularly.

    We bring up instances of this in comments, at which time someone change the subject to some other misrepresentation which was also brought up earlier, as if this never occurred. And the cycle repeats itself. Its as if everyone here is bound and determined to remain ignorant, as it suits their agenda of attacking evolution.

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  46. natschuster said...

    I read the whole article, Didn't see anything on how it evolved.


    I don't believe you. Why don't you summarize in your own words the key points presented in the paper. If you can't, I'll know you were lying about having read it.

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  47. Scott:

    I wrote in my post that the mechanisms of RM and NS don't seem adequate n the case of the Cod's immune system, for specific reasons, not that I don't understand.

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  48. Thorton:

    Okay.

    Paragraph 1 - methodology

    Paragraph 2 - compares the genome of the Cod to other fish such as the stickleback

    Paragraph 3 - discusses hemoglobin and temperature regulation

    Paragraph 4 - discusses how there is no MHC II in the Cod, but more MHC I.

    Paragraph 5 - something about an unusual TLR

    Paragraph 6 - said that the Cod fish is similar to the axolotl

    How'd I do?

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  49. natschuster said...

    How'd I do?


    LOL! Now that I've shamed you into at least glancing at the paper it's going to be really hard for you to keep claiming there is nothing in there about the cod's evolution.

    What is the significance of the phylogenies of the various TLR proteins shown in fig.4?

    What is the significance of the supplemental data tables 18,19 for the evolutionary history of the Gadidae?

    In your owns words please.

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  50. Nat: I wrote in my post that the mechanisms of RM and NS don't seem adequate n the case of the Cod's immune system, for specific reasons, not that I don't understand.

    Nat,

    In the interest of clarity, please restate these specific reasons, so we have a clear understanding of them.

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  51. Thornton:

    "ToE is quite falsifiable. Finding multiple incompatible forms of DNA in different 'kinds' would do it."

    http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

    Why do you think this falsifies ToE?

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  52. Thorton:

    Table four talks about the Cod's interesting TLR sequence.

    Tables 18 talks about the genes sequenced in different fish. Table 19 talks about which genes are found in different fish.

    I don't see where the paper addresses the problem I mentioned. That is the Cod couldn't loose the MHC II until it got the turbo charged MHC I. But if it has a MHC II why would it evolve a super MHC I. It is superfluous.

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  54. natschuster said...

    Thorton:

    Table four talks about the Cod's interesting TLR sequence.

    Tables 18 talks about the genes sequenced in different fish. Table 19 talks about which genes are found in different fish.


    I didn't ask you to to parrot back the table captions. I asked you to explain the significance of the data as it pertains to the cod's evolutionary history. You can't do that if you didn't read and understand the paper.

    Can you explain the significance of the data or not?

    I don't see where the paper addresses the problem I mentioned. That is the Cod couldn't loose the MHC II until it got the turbo charged MHC I. But if it has a MHC II why would it evolve a super MHC I. It is superfluous.

    Why is it a problem? One plausible scenario is that the distant ancestral lineage that gave rise to the present cod family lived for a time in an environment where degradation of the MHC II complex wasn't deleterious but neutral. Through genetic drift, the degraded version of MHC II spread through the population. An analogy would be the broken GULO gene in humans, and how it is not deleterious because in our environment we have alternate ways to get vitaminn C. Then later the Cods' environment changed and there was once again selection pressure for an improved immune system. This time around evolution hit on the solution of increasing variation in in the MHC I loci that provided the same immunity effects instead of reactivating the MCH II.

    So where's the problem?

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  55. I not sure what the significance of the data in the tables is other than if the fish are closer genetically, then they must be more closly related. And some of the TLR seems to be conserved since it is kind of like TLR is some other vertebrates, some of it isn't. So some of it is from deep homology. I don't know how this addresses the problem I brought up.

    And does there exist anywhere an ennvironment where a strong immune system isn't necessary? Aren't there bacteria everywhere? So it could loose it's MHC II and survive. It's a little different than vitamin C becuase there are some environments where there is a lot of vitamin c available.

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  56. natschuster said...

    I not sure what the significance of the data in the tables is other than if the fish are closer genetically, then they must be more closly related. And some of the TLR seems to be conserved since it is kind of like TLR is some other vertebrates, some of it isn't. So some of it is from deep homology. I don't know how this addresses the problem I brought up


    Exactly as I suspected, you didn't read (not skim) or understand the paper.

    And does there exist anywhere an ennvironment where a strong immune system isn't necessary? Aren't there bacteria everywhere? So it could loose it's MHC II and survive.

    How do you know MCH II is required for a strong immune system in every possible environment? Especially one that existed hundreds of millions of years ago?

    Did you forget you wrote this above?:

    natschuster: "If you could provide me with a scenario that addresses the problems I mentioned, then I will consider it adequate."

    You got your scenario, why are you still trolling?

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  57. I must have some reading comprehension problems. I still don't know why it is relevant.

    Now, if must vertebrates have a strong MHC II, that would seem to indicate that it is necessary, and was necessary all the way back in vertebrate history. That's why it is so strongly conserved. The only way around this is for something like a strong MHC I to be present. And your scenario, while it is a scenario, yes, has the further weakness of relying on the very unlikely possibility that there was some pristine, pure, bacteria free environment.

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  58. natschuster said...

    I must have some reading comprehension problems.


    What you really have is a refusal to read problem, also known as willful ignorance. Can't help you with that one.

    Now, if must vertebrates have a strong MHC II, that would seem to indicate that it is necessary,

    Not all vertebrates have a strong MHC II, so it's obviously not necessary in all cases.

    The only way around this is for something like a strong MHC I to be present.

    Or to have an environment where MHC II wasn't necessary.

    And your scenario, while it is a scenario, yes, has the further weakness of relying on the very unlikely possibility that there was some pristine, pure, bacteria free environment.

    How do you know it was unlikely? How do you know it was bacteria free and not an environment where the local bacteria didn't provide a threat to the cod?

    You discount my scenario but won't provide one of your own to explain the evidence. Simple fact is, you won't accept any explanation besides GAWDDIDIT. And you agreed to keep GAWDDIDIT out of this discussion.

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  59. If they have a weak MHC II, don't they have to have something to compensate. And are there any natural environments where there are no harmful pathogens? Or where there are no bacteria harmful to one organism. To the best of my knowledge, germs are everywhere. This is why I say it is unlikely.

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  60. natschuster said...

    If they have a weak MHC II, don't they have to have something to compensate.


    Not if having a weak MHC II doesn't hurt evolutionary fitness in their particular environment.

    And are there any natural environments where there are no harmful pathogens? Or where there are no bacteria harmful to one organism.

    The environment wouldn't have to have no harmful pathogens, just few ones that required MHC II to fight off.

    To the best of my knowledge, germs are everywhere. This is why I say it is unlikely.

    But not all germs are harmful to all other living creatures under all circumstances. Good old 'box of rocks' schuster and his 'to best of my knowledge' whine. There's the willfully ignorant dummy we all know and love.

    BTW, I never said my scenario is what actually happened. I offered it as a hypothesis of how a strictly naturalistic series of events could explain the data. You're the guy who claims there aren't any possible naturalistic scenarios, remember?

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  61. Thornton:

    "ToE is quite falsifiable. Finding multiple incompatible forms of DNA in different 'kinds' would do it."

    http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

    Why do you think this falsifies ToE?

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  62. John said...

    Thornton:

    "ToE is quite falsifiable. Finding multiple incompatible forms of DNA in different 'kinds' would do it."

    http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

    Why do you think this falsifies ToE?


    Those aren't mutually incompatible, they're just small variations in the most common form. They also don't exist in different 'kinds'. Ask a creationist to define 'kind' for you.

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  63. Thorton: "Those aren't mutually incompatible, they're just small variations in the most common form."

    So if you just go through the genome and replace UAA and UAG stop codons with glutamine, you consider that compatible? Just a little more dice rolling, eh?

    Thorton: "They also don't exist in different 'kinds'."

    Now you are putting algae and humans in the same 'kind'?

    Thorton: "Ask a creationist to define 'kind' for you."

    Why? I'll be generous and let you define it as I'm very curious to find out how algae and humans are not different kinds. It sounds that your demarcation criteria will turn out to be very interesting.

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  64. John said...

    Thorton: "Ask a creationist to define 'kind' for you."

    Why? I'll be generous and let you define it as I'm very curious to find out how algae and humans are not different kinds.


    They're both biological life. To science the term 'kind' has no meaning. It's something only five year olds and Creationists use - the doggy kind, the horsie kind, the fishie kind, etc. If you think otherwise, provide your definition, and a subjective way to tell what 'kind' an animal belongs to.

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  65. Thorton: "To science the term 'kind' has no meaning."

    Then how high have you set the bar for the falsifiability of evolution when you say it can be falsified by, "Finding multiple incompatible forms of DNA in different 'kinds'..."

    I guess were back to evolution not being falsifiable and it's the creationists fault because they can't define the terms for me!

    Heads you win, tales I lose.

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  66. John said...

    Thorton: "To science the term 'kind' has no meaning."

    Then how high have you set the bar for the falsifiability of evolution when you say it can be falsified by, "Finding multiple incompatible forms of DNA in different 'kinds'..."

    I guess were back to evolution not being falsifiable and it's the creationists fault because they can't define the terms for me!

    Heads you win, tales I lose.


    Feel free to keep using the term 'kind' in scientific discussions - the kitty cat kind, the moo cow kind, etc. It will earn you the exact level of respect from the scientific community you deserve, guaranteed.

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  67. Thorton, you used the term 'kind' first, so are you a 'five year old or a Creationist'?

    If you think the term 'kind' is incoherent, then you will have to explain what you mean by "ToE is quite falsifiable. Finding multiple incompatible forms of DNA in different 'kinds' would do it."

    As you see, you have apparently by your own definition become a five year old or a Creationist at the same time that you falsified the ToE. Uncanny!

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  68. John said...

    Thorton, you used the term 'kind' first, so are you a 'five year old or a Creationist'?


    Scare quotes: (n): Either of a pair of quotation marks used to emphasize a word or phrase or to indicate its special status, especially to express doubt about its validity or to criticize its use.

    'kind'

    Is English your first language?

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  69. Oh, here's another way for you to falsify ToE.

    Define and positively identify the mechanisms of that Creationist claimed magic barrier that makes it impossible for one 'kind' to evolve over time into another 'kind'.

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  70. Thorton: "ToE is quite falsifiable. Finding multiple incompatible forms of DNA in different 'kinds' would do it."

    Why do I care what 'kinds' means to Creationists? I care what it means to you so I can decipher your original statement. It is your exercise to explain what you originally mean by 'kind'. Have you falsified ToE or was your original criteria to strict and in need of goalpost moving? No fair blaming creationist for forcing you to use their icky gooey words.

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  71. I beg your pardon for butting in to this squabble, but it seems to me that the issue is not what 'kinds' refers to. The issue is what 'multiple incompatible forms of DNA' refers to.

    The reference quoted by John cites minor differences in codon assignments. Do those differences fit the meaning of 'multiple incompatible forms of DNA'?

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  72. Pedant said...

    The reference quoted by John cites minor differences in codon assignments. Do those differences fit the meaning of 'multiple incompatible forms of DNA'?


    Of course they don't, as was already pointed out. That's why John-boy here decided to shift gears and try an equally stupid attack over the semantics of 'kind' (in scare quotes there John!). Our latest Creationist is just out on a troll since he can't possible admit - EGAD!- that ToE is indeed falsifiable.

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  73. I'll refer you to post August 18, 2011 11:45 AM

    As you can see, any gear shifting was done by you.

    John: "So if you just go through the genome and replace UAA and UAG stop codons with glutamine, you consider that compatible? Just a little more dice rolling, eh?"

    You are free to answer this at any time.

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  74. John the liar for Jesus said...

    John the liar: "So if you just go through the genome and replace UAA and UAG stop codons with glutamine, you consider that compatible? Just a little more dice rolling, eh?"

    You are free to answer this at any time.


    Well John the liar, while you were busy boasting on the other thread how you showed ToE to be unfalsifiable you completely forgot to demonstrate that the minor variations in codons represent multiple incompatible forms of DNA, and you forgot to give your objective definition of 'kind'.

    It doesn't surprise me in the least that you'd try and lie your way out of the corner you painted yourself into. You're a Creationist, lying is a way of life.

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  75. Thorton: "Well John the liar, while you were busy boasting on the other thread how you showed ToE to be unfalsifiable..."

    No I said YOU did. Does this make you henceforth "Thorton, the liar for Jesus" or were you just being hasty?

    Thorton: "you completely forgot to demonstrate that the minor variations in codons represent multiple incompatible forms of DNA,"

    not true, I'll refer you to post August 18, 2011 11:45 AM again. Is it possible that you don't even understand the significance of your own criteria? Did someone else tell you to make this argument?

    Thorton: "and you forgot to give your objective definition of 'kind'."

    Your lack of being objective in your criteria is not my fault. This has been covered in post August 18, 2011 6:27 PM.

    Thorton: "It doesn't surprise me in the least that you'd try and lie your way out of the corner you painted yourself into. You're a Creationist, lying is a way of life."

    I was wondering if you felt you were a little cornered. Funny how you also change the subject at August 18, 2011 6:54 PM then accuse me of "shifting gears" in your very next post. You are starting to exhibit a trend have you noticed?

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