About Rationally Speaking


Rationally Speaking is a blog maintained by Prof. Massimo Pigliucci, a philosopher at the City University of New York. The blog reflects the Enlightenment figure Marquis de Condorcet's idea of what a public intellectual (yes, we know, that's such a bad word) ought to be: someone who devotes himself to "the tracking down of prejudices in the hiding places where priests, the schools, the government, and all long-established institutions had gathered and protected them." You're welcome. Please notice that the contents of this blog can be reprinted under the standard Creative Commons license.

Wednesday, April 05, 2006

Why cats don’t have a sweet tooth

Cats don’t care for chocolate and other sweets. Interestingly, neither do their wild cousins, like tigers and lions. That observation has prompted speculation among biologists that perhaps the ability to taste sweets was lost early on during the evolution of this group, probably as a byproduct of natural selection for carnivory. Since carnivors don’t seek sugar-laden foods, selection maintaining that ability would be relaxed, leading to the loss of both the taste for sweet and the gene(s) that make it possible (in reverse causal order, of course).

Now, contrary to creationist claims, evolutionary biology is a legitimate science because it makes testable predictions. If the above scenario is correct, one would expect to find in cats what is called a “pseudogene,” i.e. a segment of DNA that used to code for a functional protein (in particular, the protein that makes possible to taste sweets), but is no longer working because of a damaging mutation that was not eliminated by natural selection (since the gene wasn’t necessary any more anyway). Moreover, such pseudogene should also be present in all the closely related species to cats, such as tigers and lions.

Sure enough, recent work carried out by Xia Li and a host of collaborators has found exactly what evolutionary theory would predict (their paper was published in PLoS Genetics, July 2005). The ability to taste sweets in mammals depends on the action of two genes, Tas1r2 and Tas1r3. These produce two proteins – rather unimaginatively called T1R2 and T1R3 – which have to combine with each other in order to make a receptor for sweets in the taste buds. Li and coworkers found that cats, tigers, and lions have a functional version of Tas1r3, but also that Tas1r2 cannot make a functional protein because of mutations that stop the translation and transcription processes (from DNA to RNA, and eventually to protein) too early. Interestingly, the damaged gene exists in other mammals (such as ourselves), and works normally (allowing us not only to taste sugar, but artificial sweeteners as well). In other words, Tas1r2 is a pseudogene shared by domestic and wild cats, in accordance with the predictions of evolutionary theory.

Now, I ask you, would this piece of elegant detective work have been possible based on the “theory” of Intelligent Design? What would ID “scientists” have predicted, and why? Besides, what kind of intelligent designer would deprive cats of the taste of chocolate? I’d say that comes pretty close to animal cruelty.

85 comments:

  1. Speaking of predictions, Pharyngula has an account of scientists searching for an intermediate fossil form, and finding it!

    The link is here .

    I have sworn off trying to develop evolutionary scenarios, either real or imaginary, but the relevance to discussions on an earlier thread is pretty obvious.

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  2. Two really nice examples, thanks, guys.

    The fossil is already really famous, and no wonder. Such a(nother) beautiful example of real science in action for everybody to see: Theories make predictions. Scientists set out to test said predictions. Predictions confirmed.

    BTW, one more gap in the fossil record now. Let them gaps prosper and proliferate! :-)

    Cheers
    J

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  3. Wonder why my cat like Hershey Kisses, then...

    Great article,though.

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  4. Maybe Satan put those genes in those cats to trick us.

    Sorry...couldn't resist.

    noah

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  5. Well, cats ARE agents of Satan aren't they? ;)

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  6. I'm about 90% sure MY cats are.

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  7. My cat only does free lance work, by the way.

    Why your cat likes chocolate? My guess would be because of the fat chocolate contains (not little, BTW). I used to think of dogs as the great sniffers, and they might be the best really. But since I adopted my cat, I discovered they do have a very keen sense of smell too And since they require a high fat diet (just compare the labels on Fido's and Kitty's food), that might be doing the trick.

    But it might just be more probable that the Satan's theory is the right one...

    J

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  8. Getting back to the Fishapod (Tiktaaluk) for a second, there is a really fascinating article in Scientific American
    for December 2005 by Jennifer Clack, entitled "Getting a Leg Up On Land". Written before Tiktaaluk was announced it
    discusses the whole area of terapod Evolution, with reference to fossils that have been found in the last 15 years.

    Lots of interesting points: the number of recent fossil finds in this area, the apparent rapidity of Tetrapod evolution (10's
    of millions of years, use of forelimbs for breathing above water, the 5-digit vs. 8-digit foot,
    concurrent evolution of other parts of the anatomy (skull, neck, middle ear, etc.), the change of ecology around that time (vascular plants on both sea and land).
    She even touches on the role of hox genes in some of these developments.

    This article is well worth a trip to the library.

    Actually I managed to bring it up on line this morning by going to sciam.com, and clicking on


    Print Edition-Past Issues (2005-december)

    Or just try this (it worked for me a minute ago, but I haven't had much luck with liks lately.

    http://sciam.com/article.cfm?chanID=sa006&colID=1&articleID=000DC8B8-EA15-137C-AA1583414B7F0000

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  9. "...But the details of this seminal shift remained hidden from view. Furthermore, estimates of when this event transpired varied wildly, ranging from 400 million to 350 million years ago, during the Devonian period. The problem was that the pertinent fossil record was sparse, consisting of essentially a single fish of this type, Eusthenopteron, and a single Devonian tetrapod, Ichthyostega, which was too advanced to elucidate tetrapod roots.
    With such scant clues to work from, scientists could only speculate about the nature of the transition..." SA

    At least the article is quite honest about missing data. But whether three days or three million years, the odds of any of these events occurring naturally or miraculously is not necessarily helped by the addition of time.

    As a matter of fact, the addition of time actually adds increased levels of difficulty to overcome. One runs into the problem, for instance, of erosion. Current estimates of erosion rates suggest that 10 million years of erosion would bring the entire earth roughly at sea level. So either the "early" earth has reached some awfully high altitudes in the past, (which means untold layers of the fossil record are all but missing, making our interpretations of what’s left completely inept) OR one cannot trust all the ways we measure erosion.

    Something has to give here.

    Nonetheless, the hippopotamus makes all those transitions (existing here and today) that were supposed to take untold millions of years to emerge in different forms of in different creatures.

    The Hippo and Rino are wonderful creatures, some even think prehistoric in appearance. One has to wonder where they would be placed in a fossil record today, if they were extinct.

    cal

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  10. "scientists could only speculate"

    Well, well, well!

    the next paragraph begins "Since then, however, many more fossils..."

    After that comes the rest of the article!

    Is this what they call quote mining?

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  11. Cal

    Just a thought. The SciAm article is in 7 "pages" or parts. You can click on Printer-Friendly version to get the whole thing in one window.

    Not sure if you realized that. No offense if you did.

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  12. Lily,

    maybe I was mining for something or another. And yes, I do have an agenda. But the matter of 'how many' fossils actually do exist wasn't the emphasis of my argument anyway.

    Placing fossils in their proper order should require more than assuming a pre-understood, agreed upon, order of things. If I don't FIRST recognize the understood and accepted role of geology and physics before I set forth to make a statement about a fossil, the fossil will determine what is true about geology and physics.

    That would make the fossil something akin to a philosophical icon.

    In the end, a reasonable sort of organization of tools and technique is more important than what order fossils happen to fall into.

    Now, back to the matter of erosion...

    cal

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  13. The fossil is evidence. It probably should have a role in determining the truth of biology, at least.

    Placing fossils in their proper order should require careful comparison and analysis, using proper dating techniques.

    Now back to plate tectonics, volcanic action, variable rates of erosion, etc.

    No actually, back to work! Gotta go.

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  14. Back to Massimos origional post. How is loss of ability (sense of taste)proof of evoltution? Because it makes a prediction? this is not evolving, it is devolving. Many Id-ers predict the same for all species. That there is a natural process of decay, biologically for all species. I don't know if I agree, but it is out there. If sweets are not nutricious or even harmful to the cat, then the ability to taste sweets should be an advantage to allow the species to defer from sweets. Perhaps the cat lost the ability to utilize sweets as a fallback food as other species do? How could this ever be an advantage in times of enviormental strains (which bring on evoltionary change in the first place). Proof of loss of ability in my opinion does not strengthen evolution any more than it helps I.D.

    Lilly, I will spare you the same debate we already had, since your link is extreemly similar to examples we already discussed.

    God Bless

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  15. btw, lily.

    I placed my comment to you and your last comment in the wrong topic heading under:

    "One more non-difference between humans and animals"

    cal

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  16. Cal

    I have been going back and forth between my home town and my present domicile, because of my mother who is ill. So I'm not sure I've given your link the attention it deserves. It seems that they are batting some opinions back and forth, and this is what scientists do. I mentioned earlier "careful comparison and analysis, using proper dating techniques", which I hope would cover it, with all the uncertainties that that implies. It seems to me that scientists generally do a conscientious job trying to arrive at a consensus in these matters. All that I would like to insist on in this discussion is that facts (or artifacts), such as fossils have a certain resistance to manipulation by our thought processes, basic empiricism (garden-variety empiricism) if you like; or the idea that there is no view of fossils that a "right-thinking man" must take. [I am quoting from a Muslim creationist film].

    Here is the kind of thing I like. I hope you don't think I'm being flippant by referring you to something that is 140 years old, but this essay by T. H. Huxley really seems to embody the spirit of scientific
    reasoning- and is an excellent example of practical agnosticism to boot. He is fair-minded, and eager to distinguish what we really know from what we assume we know. His take on fossils is pretty interesting, he is writing when the impact of new fossil discoveries was fresh. Keep in mind that he was writing before radioactive dating techniques were available. I don't think you would need to read to the end if you found it tedious. Hope the link works.

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  17. Well, the Earth isn't flat by now because it is geologically active, as Lilly pointed out. New mountains are being formed right now as the old ones get eroded. Just ask the poor folks living along tectonic fault lines... (or even the one living far, in case of tsunami)

    J

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  18. Sorry, Lily, too many "l"...

    Jim,

    Let me tell you what evolution means, since you don't know. Evolution means change over time. That's why evolution is a scientific fact, since it is beyond doubt that organisms change over time. (now, exactly how changes happen, natural selection and other mechanisms and all that, is still being investigated, as well as all the steps between different life forms, like the new fossil and others to come, are being discovered and helping put together the picture).

    So "evolving" versus "devolving", as you put it, makes no sense at all - evolution has no direction and can't predict the future, remember. A very reduced, blind cave dweller, or a parasite that lost almost all its organs and just sucks everything out of its host are as evolved as anybody else. And if there was no selection for a "fallback" food, it will not, er, be selected... So it is contingent on history. Evolutionary biology is a HISTORICAL SCIENCE.

    The point Massimo makes, as I see it, is that a designed entity (specially one designed by an all powerful being, as the IDers surely want it to be) shouldn't have this kind of "relicts", non-functional, broken pieces of equipment lying around the organism. Otherwise, the design is broken, right? A perfectly designed entity should have maximal efficiency, nothing missing and nothing in excess - otherwise it isn't perfect, by definition. Would that be a prediction based on ID, I wonder? No, I guess.

    Evolutionary biology, on the other hand, states among other things that species evolve from other species, and we all go back in time to a single life's origin. Therefore, as a logical consequence, with a change in lifestyle - start eating meat instead of fruits, for example - there will certainly be some changes in the population being selected for, while other characteristics will become obsolete. If these obsolete things break, who cares? It's not going to affect the survival of the meat-eater, for example. Therefore, the observation of broken genes (among a huge amount of other things, of course) supports evolutionary theories' predictions.

    Now please let me know where you found any IDer predicting anything testable, if you may? I still say IDers do not predict anything, since they don't even have a theory.

    J

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  19. "All that I would like to insist on in this discussion is that facts (or artifacts), such as fossils have a certain resistance to manipulation by our thought processes, basic empiricism (garden-variety empiricism) if you like; or the idea that there is no view of fossils that a "right-thinking man" must take."

    Okay.

    To me, fossils are a bit like snapshots of various species taken at different times. The snapshot could mean any number of things, but mostly it just means that the organism flat out died. Sometimes the fossil happens to be in the right place, the place were the animal actually was laid to rest. Possibly 30 % of the time the fossil is moved for a variety of reasons. Predators, water, erosion, natural disasters and a few others I'm probably not even thinking of.

    There is even the possibility that some species which existed in the past, have never been fossilized and may never show up on the fossil record. And that's just being realistic.

    Is it true that 90% of the fossil record represents species which are already extinct? I think I've heard that stated on more than one occasion. So we can be certain that extinctions do happen. But what we cannot be certain of, is if those extinctions realistically do give way to a newly evolved species. It would be to me, a doctrine of exceptionalism. Exceptional, because after all is said and done, any honest biologist will tell you(no matter what his belief happens to be) that life propagating mutations are against the odds. In establishing other theories in science, no serious scientist would take heart in the fact that he spent 40-50 years of his life searching out the exception, and never focusing in on the actual rule!

    Tho that isn't impossible that a sane person would do this, it just seems a bit strange.

    I know what the hypothesis about relatedness is based on DNA studies. But that cannot possibly mean that the previous 90% of species which are extinct are genetically responsible for the 10 % of remaining species. The %s should virtually be flip-flopped for evolution to make any cumalative, mathamatical sense at all.

    Thank you for the thoughts on the Huxely writings. I like old authors very much and own quite few ancient books myself. Have none of Huxely tho. I know that the older authors were not as sold out secular as most who write on such matters today.


    Most importantly, the very best of luck to you and your mother.

    cal

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  20. J,
    I think you may have missed one of Massimos earlier posts " Revealed truth, a logical fallacy", where we debated the issue pretty extensivly. Since then I have perhaps become more of an IDer, but I do accept what I still dare to call micro evolution. I am glad you set out to explain evoltion to me, but trust me, I do understand the theory and the processes involved.
    There are IDer that believe that the second law of thermodynamics applies to biological nature as well. If you have been involved in the debate for any amount of time, then you have heard this. So this being the case. The same prediction Massimo showed would be proof of I.D. just as much as evoltion. Yes I used the term devolved, I understand this is still a process of evoltion. The reason I used this term is because I aim to seperate What I believe is true in the current theory from What I believe is false. I dont want to repeat previous arguments from previous posts. So if you want to know the details of it, you can read the previous debate. My point here is that entrophy would better explain why the cat lost its ability to taste sweets. How does selection do this. It is kind of like this rediculous new theory about blond haired woman. Supposedly they came about because women need something to sperate themselves from the average. So the blond was selected and eventually grew over certain northen Europe populations. But now since the blond is so common it is no longer an advantage and will slowly dissapear. Explain to me why the blond will dissapear. What will prevent the blond from having blond offspring? Why would evoltion remove the cats taste of sweets. Why would the cat that can't taste sweets ever have some advantage over the cat that can taste sweets. Just because the cat doesn't need sweets, doesn't make it an advantage not to taste them If anything it should be a disadvantage. Entropy would in my opinion better explain it. All biological systems eventually fail on some part of the organism. If it doesn't affect its survival needs, then that failure will eventaully overcome the species. If it does affect the survival, than micro evoltution will only allow the members without the failure to survive insuring the species stays intact. So the reason I call this devolving rather than evoltuion is because that is how I see it. To me evoltion is the process of keeping species intact or having them change only slightly by size, shape or color. What I don't believe about evoltion is its ability to add new features.

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  21. Here is a prediction from the I.D. standpoint along with entropy. You will see every possible defect that can be imagined. Discoloration of every part of the body, missing and deformed fingers, toes and any other part of the body. You will see deformaties that have never been seen before. And if that deformation does not hinder the survival of the species (like tasting sweetness) you might see it stick around. It may not replace the entire species since whether or not it survives is random. Just like, I bet you can find a cat that can taste sweets. Another prediction.
    What you will not see is any of these deformaties (unless it is just size shape or color) present an advantage and change the way an animal performs a peticular function. Such as the fin become a hand or vise vesa.

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  22. Jim,

    I did read that previous exchange, and wrote some things there myself.

    But sorry, you DO NOT understand what you're talking about. It's clear from your posts. Sorry again if that sounds rude or arrogant, maybe it is anyway, but that's the truth - and I'd rather be sincere, you know.

    1) let's use a very simple analogy: let's say every piece of equipment in your household, from car to toaster, if broken, only gets fixed by you if you use them regularly. If you never use them, you don't fix them, and they might even decay further until they are not even repairable anymore. OK, now suppose you completely gave up drinking coffee. Your coffee maker will sit there doing nothing forever. It might very well still be functional 5 years down the road. But it might be that it broke - let's say ants bulti a nest inside it, or a thunderstorm toasted the transformer, or whatever. Now you have a broken coffee maker at home, but that makes no difference, since you do not drink coffee. And you won't fix the machine, given the rule I stated above. And your life won't be affected by the missing coffee machine, since you didn't use it anyway. You don't use the coffee maker anymore. Does that mean you have to go there and break it? No, you just don't fix it.

    OK, now put "genome" in the place of "house", "gene" instead of "equipment", the "sweet tasting gene" instead of "coffee maker", and "selection" instead of "you". Selection did not break the gene. It just did not care it was broken and left it there rotting. And yes, you might find some cat that still has the gene workable, as well as you could find your coffee maker still functional.

    2) forget the second law of thermodynamics as a crutch for ID. If you knew what that law says, you'd remember that it states that, IN A CLOSED SYSTEM, entropy always grows. Biological entities are NOT closed system - there's energy input when they feed, and that settles the case, nothing to see here. By the way, there's a good website around which explains this myth of "entropy" = "disorder" misunderstanding. I just can't find it or I'd send the link...

    I gotta go now, so I can't comment on your "predictions" now, but seems like there's a pretty low standard on your part on what a theory's prediction would be... I'll elaborate on that later - but in a word, your predictions are not predictions, and they've got nothing to do with ID's "theory" anyway.

    J

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  23. "OK, now put "genome" in the place of "house", "gene" instead of "equipment", the "sweet tasting gene" instead of "coffee maker", and "selection" instead of "you". Selection did not break the gene. It just did not care it was broken and left it there rotting."


    RE: Utility
    Mendel’s laws do not agree with Darwin's.

    Darwin’s reasons for traits sticking around are very superficial and environment oriented. Which is, of course, only a fraction of the entire biological picture. Mendel's ideas were deliberately divergent (and correct, incidentally) stating that the recessive and dominant traits have very specific internal, predetermined reasons for being retained or lost. And those reasons and mechanisms are not necessarily either environmental or "selective pressures", if you will. They are based on orderly internal information.

    We don't pass on resistance, for instance, to diseases that we are vaccinated from. But according to evolution, Darwin style, we should. It is not that we have ever lost the ability to fight the specific disease, but we are instead trying to exploit and optimalize the way an immune system works. Is this a good idea? Probably not.

    Selection, Darwin style, was supposedly about optimalzing genetic traits. (even tho some people seem to distance themselves from such conclusions anymore) But in reality, I think that selection is more about predator /prey relationships (food chains) and how the environment may tweak the way genes work from time to time. But next to this smaller subset of factors, Mendels' laws are infinitely more reliable in structure and sequence, and thus changes to a genome tend to only flow in one direction. If a gene becomes "broken" it is the unmistakable equivalent of information loss.

    cal

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  24. Okay, the following doesn't have much of anything to do with cats and sweets. But it sure was sweet what the cat did happen to do. I wonder what the cat perceived about the baby lying at the door that made it carry on loudly till somebody responded. Interesting.

    "BERLIN (Reuters) - A cat saved the life of a newborn baby abandoned on the doorstep of a Cologne house in the middle of the night by meowing loudly until someone woke up, a police spokesman said Saturday." ...

    http://today.reuters.com/news/articlenews.aspx?type=oddlyEnoughNews&storyid=2006-04-16T022631Z_01_L15718549_RTRUKOC_0_US-GERMANY-CAT.xml

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  25. Second part, Jim.

    Now, the ID standpoint, as you put it... What is it? As far as I've seen so far, the only thing the ID "theory" says is:

    "The biological world is too complex to have evolved by natural means, therefore there must be an inteligent designer".

    (this statement is ridiculous both phylosophicaly and scientifically, but let's ignore this for a moment)

    Would that be a fair picture of ID's tenet? So far, I haven't seen "they" say anything that wasn't this, in a form or another, so I guess that's about it.

    In science, a theory's prediction is some logical consequence of the theory itself. Gravitation theory: mass atracts mass. Prediction: two bodies will atract each other and come together. Just let go of an apple and this prediction is confirmed, or watch a comet go arond the sun, etc. Evolutionary theory: all life has a common ancestor, from which we are all descendants. Prediction(s): if you go back in time, lineages will "join" - therefore, younger fossils will look more similar to the currently living species, with older fossils looking more and more different from what we have today. Some descendant lineages will die without leaving any descndents themselves (extinction), for any number of reasons. Species alive today will not be found as old fossils. One should find intermediary forms in the fossil record. Now, just get any paleontology book to see these little predictions being confirmed massively, beyond any sane doubt.

    Is it clear now how predictions based on scientific theories are made? They have to be directly related to the theory's statements (duh).

    Now, the "predictions" you gave, and said were based on an ID standpoint, have NOTHING to do with the only ID "theory" (unless your understanding of ID is quite different from that of Behe, Dembski, et al.). If you think I'm wrong, and I could very well be, please let me know how "too complex to be natural only" can lead to a (wrong) application of the second law of thermodynamics, and them to the (unrelated and disconnected) prediction of loss of genes and organismal features. Completely unrelated things, if you ask me.

    Nothing personal at all, most believers seem to do this at some point or another, but to me those "predictions" sound more like a desperate way to rationalize your beliefs, by loosely (and inadequately) using some scientific jargon to try fitting the religious beliefs into the world as seen by your eyes and informed by the science and technology you enjoy every day. You don't need that, Jim. Nobody does. It's OK to have your religion, relax. Trying to rationalize, "prove" your faith only belittles the faith. That's in the Bible itself, isn't it? You ought to believe not just in the absence of evidence, but even against any evidence.

    Cheers
    J

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  26. J,
    As I have said in previous debate. I grew up believing in evolution. Yes I am a Christian. But I feal the creator can use any means it wants for creation. So it is not a matter of religion. So you obviously did not read the previous debate or I wouldn't be repeating this. I would have no issue being a Christian and believing in evolution as the two beliefs coincided with me for many years. Where I came into issue with evoltution is when I actually tried to imagine species changing to a higher form and gaining more complex geometric shapes in features. It is not the actual complexity that I take issue with. it is the lack of geometric mutations to accomplish a change. For example take any two species in the same lineage. How did the Jaw change just right to get the new function or shape? The differences between the two geometrically are extreemly significant. In order for that to happen by a random process, shouldn't there be every possible geometric shape mutations of the jaw that did not work? Nature would have to be an ugly monster contantly mutating every part of every species. Most people will say that all changes come in such slight differences that they dont require a significant geometric change. Well then. How can it present an advantage? and enough of an advantage that the members that dont have this slight change can't get to reproduce. So its one or the other. Mutations are so slight that they could never maintain enough of an advantage to allow it to replace the species. Or mutations are significant enough to give the members who have it a good advantage, but if this is so, there should be millions of significant mutations that are not usable. Hence nature would be an ugly monster. If you drop millions of tooth picks on the floor you will eventually get the letter "G" needed. But you will also get every other letter and possible configuration not needed. Mutations can not think what to do and which direction to go. So in order for evoltion to be possible you would have to have mutations that are exatreemly slight in difference from the origional product, bu tyet give the membes who have this extreemly slight difference a huge advantage over the rest of the members, so much so that they would die out. This is impossible.
    As far as entropy or evolution for the cats loss. Either way we are describing the same thing. Use it or loose it. To me, the loss of function is not proof of evolution.

    You say I do not know what I am talking about. So explain to me where the missing mutations are. Evoltion must happen one mutation at a time. Does it happen with just that one mutation? Where are the millions that are not sucessful?

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  27. J,
    Here is a prediction that I think would better suit the ID theory. I am not sure it is valid. Kind of just thinking out loud.

    As technology advances, we will discover that all parts of all species will serve its origional function or very closely related function. Parts can become vestigial but not serve a pupose other than what it was designed for. All parts must have an origionally designed function. Since all species piece parts are specifically designed to serve a purpose, whenever the enviorment changes in a way that prevents a piece part essencial for survial to accomplish its job. That species will die out in that enviorment. Unless the species can adapt by behavioral changes. If survival means a mechanical change in the species. It will die out completely.

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  28. Jim, wonderful! Such prediction has been refuted several times, since there are plenty of examples of re-use of parts during evolution. The case of the reptilian-jaw turned mammalian-ear is just one of the best documented in the fossil record.

    OK, ready to give up ID now? :)

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  29. "Is it clear now how predictions based on scientific theories are made? They have to be directly related to the theory's statements (duh)."

    Watch it now! There is no rule to forming hypotheses that says that general statements (as Jim made)are erroneous and irrelevant. Furthermore, your whole list of descriptions here is about as open-ended and false as anything I've ever seen!

    Example:

    "Some descendant lineages will die without leaving any descendents themselves (extinction), for any number of reasons. [open-ended]
    Species alive today will not be found as old fossils." [false]

    Funny thing is, I have my own collection of fossilized sea life that does represent VERY similar species still alive today.

    Everything that is fossilized isn't necessarily old. Everything that is old, isn't necessarily extinct. Mendels laws (recessive traits, etc.) explain a lot of this. But you are not saying anything profound or specific enough to form patterns for concrete predictions here.

    "Gravitation theory: mass atracts mass. Prediction: two bodies will atract each other and come together. Just let go of an apple and this prediction is confirmed, or watch a comet go arond the sun, etc."

    But this is only a generalized assumption about generalized phyisics, and as such is no more profound or explanatory than Jim's generalized claim. He observes things in nature that he keeps thinking look intellegent to him. You keep seeing things that seem to be falling towards earth!??? But beyond everything you've just said, you really know nothing and can explain NOTHING about PRE-BIG BANG physics. Can you?

    cal

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  30. Jim, wonderful! Such prediction has been refuted several times, since there are plenty of examples of re-use of parts during evolution. The case of the reptilian-jaw turned mammalian-ear is just one of the best documented in the fossil record.

    OK, ready to give up ID now? :)

    Massimo,
    On your previous post I explained why I did not believe that the reptilian Jaw turned mammalian ear. I still haven't heard a decent responce as to why I say its not possible.

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  31. Jim, it is simply amazing to me that you say that somethig that is under your very nose, available in most museums, is somehow "impossible." But I guess I shouldn't be surprised.

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  32. "...that is under your very nose, available in most museums, is somehow "impossible."

    There isn't much in museums that isn't subject to layers of interpretation, politics, matters of funding, etc..and especially one having to do with biology or evolution.

    And I know that you can produce evidence for anything you want, if you have the will to do it. So as Alice Cooper, whose article I quoted earlier today said about being the inventor of certain games...I know that you're 100% capable dealing with what Jim asked, so why not?

    Tho I'm not even nearly as nice as Jim, you know we'll respect you even if you're not perfect. If there is no answer, it's quite okay. It just looks like you lack credibility if you get short-tempered and cranky about simple stuff.

    that's all.
    cal

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  33. Massimo,
    to save time and re-explain my arguement for why this example you have shown means nothing to prove evolution. I have cut and paste my previous arguement.

    Looking at the first transition (same example I pointed out before), look at the quadrate. It changes severely. I was asking for the advantage of this change. You guys say we can't know what every advantage was. I will buy that. But we agree their must have been some advantage even though the actual function of the quadrate did not change (as unlikely as that is, I will buy it). My point is that the geometric change between the two parts is huge (especially on the second transition of the quadrate). In order for that change to take place by random mutations there must have been thousands of other mutations that did not work in order to get that one change that did work. There must have been every imaginable geometric configuration to the quadrate and all but that one, did not work. This is where I say nature would have to have a super high mutation rate to make this change (so much we could constantly witness it). You could argue that there are many mutations between these two fossils (that havent been discovered yet)so they are much more subtle changes that is why we don't see the mutations (non-beneficial ones) constantly. But if the changes were so subtle then how could they have a real advantage in the environment to make them survive? This is kind of a paradox. Do you guys see my point?
    Where are all the mutations that don’t work? If you say they are just the tiny variations that we witness every day, then how could any present an advantage. There has to be something significant to allow it to replace the species. And if it is significant enough to allow it to replace the species then there should be many more significant ones that don’t work. Evolution does not know which way to go. It is by chance. To hit the lottery you must play a lot of tickets.

    March 18, 2006 1:24 PM

    Explain to me massimo, where are the mutations? You say "I shouldn't be surprised" as if my blind faith in God is keeping me from seeing the obvious. Which either means you don't believe me when I say that believing in evolution has no implications to my religous beliefs whatsoever. God can use any process he see fit. I still don't know how I feel about the old testament, and have not personally accepted it as fact. So I am not bound by any starting point for my beliefs. The other possiblilty for why you said that is that you just deem me unitelligent.Which ever the case, the answer to my arguement must be a simple one. Would it be so difficult to write it?

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  34. Jim
    I'm not sure if Massimo would have been following that whole discussion from last February, so

    here is the link we were discussing then.

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  35. Jim,
    Where are the missing mutations?

    They're there all the time, but since they are not selected for, they don't accumulate, so they don't become noticeable. They just wash out from onegeneration to the next.

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  36. Also Jim,
    "But if the changes were so subtle then how could they have a real advantage in the environment to make them survive? This is kind of a paradox. Do you guys see my point?"

    If there is a selection pressure in favor of a new feature, selection will "see" it, no matter how small the change. Most of the time an organism is already adapted to its environment, so selection just weeds out mistakes. But if conditions change, e.g', new types of vegetation that might call for a different jaw, then selection will favor even the tiniest changes in the direction of that kind of jaw.

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  37. Varus,
    You are assigning "selection" intelligent traits, by saying things like - Selection will see-, or -Selection favors-.
    It is strictly a random process. So each favorable mutation (as you put it) would have to have such an advantage that the members of the species that dont have it(which in the beginning would be all but one member) would have to die out because it didn't have that peticular mutation.
    So look back to the case of the reptilian jaw turning mammalian ear. The quadrate changes quite severly from one species to the next. If this was one single mutation, well then fine, I suppose it could be such an advantage that somehow all the members that dont have it would not make it to reproductive age (I realize this could take generations to elimate all the members without the mutation). But the geometric change is huge, in order to get it in one mutation, there would have to be thousands of other geometric mutations that did not work, and they would be just as significant as the one that worked. So nature would have to be nothing but huge mutations to bring about a change.
    Ok, so now you'll say it did not happen in just one mutation. That there are many more transitions of the quadrate between each of these found species, we just haven't found their fossils yet. My point is that if these changes are just extreemly subtle, then they won't be enough advantage so that the members who don't have it will not make it to reproductive age. How would the member of the species that had just a slight variation in its quadrate manage to somehow survive so much better than the others. Does that slight variation allow him to run faster to the pray and beat the others? Does it allow him to chew his food way faster so the others don't eat enough? see my point? in order for a mutation to overcome a species, it has to have something that gives it a great mechanical advantage in its enviorment, so much that others in that species can't compete and eventually the one member that had the mutation become the father (or Adam) to that whole species.
    So varus, you saying that the mutations I am looking for are there all the time, they just don't get selected, doesn't cut it. In order to get selected it would have to be a great advantage.

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  38. That's rather erroneous information, Varus. The genetic trait/info. instructions, what have you, existed in the genome before the effects of the "pressure" manifested itself. 'Selection' alone is an incredibly limited, dependant on a whole host of other scientific contingencies , factor.

    Beak sizes may change. But they're still beaks, and they still belong ON BIRDS!

    cal

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  39. Jim,

    "Selection will see-, or -Selection favors-. It is strictly a random process."

    NO! This is sooo frustrating. Why is it that creationists have such a hard time realizing that natural selection is most definitely NOT a random process? That's why it's called "selection" and not "lottery."

    Selection is a shorthand for a correlation between certain biological characteristics (say, having a better eye) and reproductive fitness. When biologists use anthropomorphic language, such as "selection sees" something they don't mean it literally. It's a metaphor for whatever traits confer higher reproductive fitness. Once again, randomness has nothing to do with it (in case you are wondering, there is of course a place for randomness in evolution: that's in producing mutations, the raw material on which selection -- non-randomly! -- acts).

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  40. "When biologists use anthropomorphic language, such as "selection sees" something they don't mean it literally. It's a metaphor for whatever traits confer higher reproductive fitness."

    Let's make an effort to put the imprecise language behind us. "Selection" is an intelligently chosen word, and you know this as well as I do.

    Secondly, there are matters to which one thing must necessarily come before the other. Food (energy) is an initial condition, or requirement, far more so than reproduction. If the food source isn't there, the individual species (or organism) doesn't reproduce. Period.

    Tho reproduction and energy sources both seem to be part of the same parcel package, they are not. Hybrids can be useful, yet they obviously require food. And of course, since they also clearly represent genetic incompatibility, they will not necessarily reproduce. So how can reproduction be the singular goal when it requires a hybrid, which will likely not reproduce, to cause leaps between species?

    someone is asking for miracles here
    cal

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  41. Jim,

    Sorry if I put you in a bin, but all I have is what you write here. I obviously do not know you. If you're using the (exhaustively and repeatedly refuted) arguments and reasoning of the "desperate religious people" against science, I can't help but conclude you're one of them. If you're one of them or not, that's none of my business, of course.

    Regarding me saying that you do not really know evolutionary biology, I thought it was obvious why I wrote that: you keep saying blatantly wrong things about the basics of it, and then basing all your reasoning on these wrong assumptions. What's that supposed to mean, if not that you don't know evolutionary biology??? You also say some things that are right sometimes, so you do know some of it, obviously. But if you want to discuss some scientific topic, and specially challenge the overwhelmingly accepted theories, I guess you would agree that it's a basic need to at least know the basics very well, right?

    Massimo gave one example of a common misconception: evolution is NOT random (it has both random and non-random components). Another one that I keep repeating but people keep ignoring: selective advantage is NOT everything! What I mean is that there's no need for every modification to be advantageous. Neutral modifications can stay in the population very well, and even take over (and later become an advantage, or a disadvantage, or still be neutral). Actually, even disadvantegeous modifications can survive for quite a long time, and later happen to become an advantage. You'll probably ask how that is possible - well, organisms are pretty big bags of characteristics, and some can "hitchhike" with others, for example (an organism happens to have a bad mutation, but also a very good one, so in balance it's still better than other organisms). Second, a disadvantage is not always fatal: it might just reduce the organism's success by, say 4 or 5% (which is not very low, but I wouldn't say it's spectacularly high either). In some cases it WILL be really bad and kill quickly. No wonder 50-60% of all pregnancies end in natural abortions (how's that for a good design?). There are many of your "missed mutation", for example. For more mutations that weren't really missed, and sometimes even spread, check out the book "Mutants" by Armand Marie Leroi - lots of "weird" human mutants. We are all mutants.

    Your second prediction, about the designed parts becoming obsolete and then dispearing, but never changing function, is a much better one. It does relate to what ID says. And as Massimo and others pointed out, it's already been proved wrong lots of times. One example from the biochemical world is the coagulation cascade - yes, the one Behe uses in his book as an example of "irredutibly complex". It has been already shown that there's nothing irreductible about it, and it's not even that complex at all. There are species (like lobsters) that do have reduced versions of the coagulation system. And more, the enzymes that do the work are modifications of digestive enzymes. So there goes the prediction of "no change in function" out of the window - at least I can't see how blood clotting enzyme can be considered even close in function to liver-produced enzyme for food digestion.

    For much more detail on this one, here is a good description of it all. It's a bit technical and lenghty at times, but who said knowledge is supposed to be easy to acquire? :-)

    Cheers
    J

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  42. Jim,
    Massimo was right. I was using a metaphor, that's why "see" is in quotation marks.

    You talk as if an individual with a selective advantage has to somehow leave all his kin in the dustbin of history in the very first generation. Think of all the individuals in the population as an advancing cloud, some of whom have the advantageous mutation, some not; sometimes they interbreed with each other, or not. In the long run the cross-section of the crowd (or cloud)that has inherited the good mutation will do better than the others.

    Cal,
    It would be nice if you could sit back in your armchair and tell Natural selection what it can and cannot do, but I swear by my pet spider's jaw that Natural selection doesn't give a hoot. (Yes I'm personifying natural selection.)

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  43. Jim

    A while back I was trying to make the point that the genome is a recipe rather than a blueprint, and that mutations are mutations in the developmental process, rather than mutations in the adult organism, and that this would probably mean that there is no need to go through a limitless number of mutations because only some mutations are likely, more or less production of a protein, etc.

    I know I did not explain it well, but since then this article has appeared on the PZ Myers blog. How to make a bat.

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  44. Jim

    I meant to point out this sentence from the article.

    "The proliferation of the early cells is a key control point. Keep them dividing longer before replacing them with bone, and the digit grows longer. Start the ossification process earlier, and you end up with short digits by truncating the proliferation process."

    But the whole article is interesting.

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  45. As far as me saying evolution is a random process. I understand what decides if a mutation survives or not is not random. They are factors controlled by the enviorment. What I strictly mean is that the mutations are COMPLETELY random. And mutations are the have no way of knowing what direction to go.
    J,
    you are still not sufficiently anwering my question.Someone explain in the case of reptilian jaw turning mammilian ear. How does the mutation of the quadtate change so drastically without there being every other possible geometric shape of the quadrate being formed in other mutations. If you answer with, the changes are more subtle, than how can they be an advantage? its that simple. Instead of talking about concepts, we have a peticular example that is a supposed proof of macro evoltution. Someone explain how that perfect shape of the quadrate was formed by a random mutation. for that to happen huge random mutations that don't work would be everywhere. Not only do you have this huge geometrical change, but on some of the changes that quadrate never even changes its function.
    Lily,
    I think I get what you are saying about a recipe rather than a blueprint. We know when certain genes are altered they affect unrelated parts of the body. So this kinda fits in with that discription. I don't think that really affects my delimma at all. Since I dont have an issue with how mutations are formed or why. I just can't see mutations causing a complete change in function of a mechanical feature.
    You link about bats is a good example. They showed the bats forelimbs have a 35% higher bmp2 levels than the mouse limbs or the bats hindlimbs. This explains how the limbs grew longer. My point is that random mutations would not just expirament and only use the 35% difference in bmp2 levels for the forelimbs. In order for that to happen ( bat come from the mouse) there wouldn't be just that one mutation. There would be a mutation that is 22% greater bmp2 on the forelimbs. there would be a mutation that is 45% greater bmp2. There would be a mutaton that is 45% less bmp2. And so on and so on. And the mutations would not know to just affect the forelimbs. All those random mutations would also expierament with the hind limbs as well. In order to finally get the long forelimbs that are suitable for flight. You have to get every other possiblilty of bmp2 amounts. And that is just for the forelimb length to be correct never mind the many other changes that would have to take hold to form the wing. Like webbing between forelimbs, muscles, and so on. In order for this to happen nature would be an ugly monster constantly producing significant mutations.
    Back to my old saying. If you want to get a letter "G" by dropping random toothpicks on the ground. You have to drop thousands of toothpicks, and you will probably get many other letters you don't need.

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  46. Jim,

    "What I strictly mean is that the mutations are COMPLETELY random. And mutations are the have no way of knowing what direction to go."

    So???

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  47. Well, Jim

    You seem to have forgotten the previous discussion, where many of us said that you were demanding an unreasonable thing: a minute by minute account of what happened, exactly how and why. You are still doing that, and it makes it look like you don't WANT to consider any evidence unless it is detailed to an impossible level. We give you 1 intermediary form, you demand 10, we give you 10, you ask for 100 - and with detailed information about everything from molecular function to ecology in the life of a 200 million year skeleton. We give you examples of parts changing function, and you ignore them (remember the "mammary glands are modified sweat glands" example I gave in the earlier discussion?). I wish you would apply this same standard of absolute skepticism when evaluating the claims of IDers (not to mention the preposterous things claimed by religious beliefs, but let's stick to ID for now). But I suspect this does not really happen.

    Evolutionary biology is a historical science, do you know what I mean? What did Napoleon Bonaparte do on the morning of September 15, 1799? I have no clue, and probably nobody does. Does that make our understanding of history all wrong, then?

    Anyway, I guess I'm done with this discussion with you, since it's already been made clear that you still have some way to go before being able to meaningfully question the prevailing science.

    Cheers
    J

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  48. Jim

    "There would be a mutation that is 22% greater bmp2 on the forelimbs. there would be a mutation that is 45% greater bmp2. "

    Seems like a bit of an easier situation than trying out all the possible geometric configurations.
    And don't forget the moving cloud that Varus talked about. This could be where that figures in, with the "final average" of 35%.
    Just speculation.

    I guess I mean that the qualitative can be based on the quantitative, which might be an easier situation. Richard Dawkins wrote about spider webs in one of his books in just this vein. Unfortunately I can't remember which book.

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  49. My point is with all the different bmp2 levels that would have to be tried in order to come up with that 35% used only in the forelimbs. You would witness mice with a huge variation in hindlimb and forelimb length. that would be up to and over the 35% required for bat wings. You would still witness mice with these huge limb variations today. The other option is that there was an advantage to an intermediate stage (although your link is claiming it is possible to happen in one step). Where somewhere at one time there was some advantage to mice having slightly longer forelimbs only. This is where I take issue with evolution happening in tiny steps. There has to be something that allowed the mice with slightly longer forelimbs to either replace the entire species or get seperated and start its own new species. This just isn't practical.

    J, This is different than me asking for an minute by minute account. perhaps I am not explaining myself good enough. I am not looking for what each advantage was exactly. My point is how did the mouse know to use an extra 35% bmp2 level to get only its front limbs longer. It didn't. Here is my point Massimo, about the fact evolution is strictly a random process. The mouse had to try all different numbers of bmp2 levels until it found an advantage to the front limbs being a certain amount longer (in this case flight). So in order for this to happen mice bmp2 levels would constantly be varying, and you would witness mice with huge variations in hind and forelimbs, even today. And not just bmp2 levels would be varying, everything would.

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  50. J,
    Your still not answering my question, instead of looking to write me off, because of my ignorance about evolution (which you seem to state over and over). Explain to me why we don't see mice with significant varying limb lengths.

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  51. Jim, who says we don't? Limb lenght is variable in all vertebrates (and invertebrates) in which it has been looked. There is lots of variability in almost any complex character one can think of. Again, what's the problem?

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  52. Massimo,
    look at the link that Lilly provided about bat formation from mice. Do we see this type of variability in limb length all the time? No. My point is we would have to. The point of Lillys article is to explain why we find no intermediary links between the mouse (or mouselike ) mammel. It is explaining how it is simple for the limbs to take drastic leaps with few intermediate species. Which would account for how mutations present a real advantage and allow them to replace the species. My point is in order for that to happen we would have to see drastic mutations, like in mouse limbs, constantly. Not just the small variations we see. You dont have Small variations in limb size, then just all the sudden see bat size limbs appear one day. Variations of that appearence would have to be constant(happening all the time).

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  53. Jim, I'm sorry but nowhere in evolutionary theory it says that variation (of any kind) has to happen "all the time." Millions of years available for evolution means that even rare events will eventually happen. Indeed, they do, since we can document the appearance of rare mutations in both the field and the lab. Still don't see the problem...

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  54. I was just looking at the fossils relating to the reptile's jaw-mammalian ear. To me it seems they prove that the latter evolved from the former, if proof is not too strong a word. Also, they seem to show that the evolution was gradual. Thirdly, it seems that adaptedness is maintained throughout. So that we have evolution, gradualism, adaptedness (at least as a constraint). Now of the processes that might account fo these features- natural selection, orthogenesis, Lamarckism, vital force- it seems that natural selection is the only one that we know exists, i.e., we can observe it daily, albeit on the micro level. I do not think that the fossils themselves can prove natural selection per se, but it seems a pretty fair bet.

    The question I have though, and I'm hoping Massimo will know something about this, is "What was the driving force behind the jaw-to-ear development? Was it the improved ear? Or was it the improved jaw? Are they in fact improvements? Is there some vast change of habitat associated with these changes?"

    In short, can you fill us in on some of the specifics of the case?

    Paul

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  55. Paul,

    "What was the driving force behind the jaw-to-ear development?"

    Good question, and we can only speculate, because we know little of the ecology of these (extinct) animals. My best guess is that the driving selective force was the fact that mammals tend to rely more on earing than reptiles, and that this has in turn be caused by the different ecological environments occupied by mammals. We can measure natural selection acting on these structures now, but of course that's not the same as what drove the change to begin with.

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  56. Massimo,
    I realize that nowhere in the theory of evolution does it say that there has to be significant variations all the time. I am saying that. In order for it to work that would have to be the case. Yeah throwing in the millions of years is a great way of responding to my arguement. But it is just not practical, unless you can coax the enviorment into only changing over millions of years. Make sure there are no abrupt changes in the enviorment, because evolution won't be ready to respond. In order for evolution to be successful it would have to be able to respond to enviormental changes. Perhaps if something would tell the food source it can only change gradually over millions of years.
    It seems that the poeple that wrote the "how to make a bat" article are aware that in order for evolution to work it needs to be quickly responsive.
    Some how I think I am still not getting my point across of why there would have to be constant SIGNIFICANT mutations in order for evolution to work.

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  57. Jim

    My original reason from bringing up the recipe thing was to suggest that mutations are likely to be along the "axis of development" [my new scientific term, God help me] so that they can be significant. This changes the original problem of "bumps" {bumps everywhere, remember?} to the more quantitative one of how much bmp 22%, 35% etc. But there are probably just a range of percentages within the population {of the rolling cloud} and selection settles on one, or on a smaller range, that is best.

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  58. lily,
    I guess I still don't understand what you are getting at. I am not sure why it makes any difference if it where a blue print or recipe. How does this insure that mutations are along the "axis of developement"?(and that is a perfectly fine term, by the way).
    I must confess that I really did not understand what J meant by "rolling cloud" and comparing it to populations in a species. I have a very mechanical thought process. Perhaps explain it in a different way. Sometimes you gotta talk to me like I'm 2 years old (seriously).
    If nature doesn't try all (or most)combinations then statistically it can't find the ones that work. I dont see how the information is stored, whether it be blue print or recipe makes any difference. It has to find the right limb length for wings (along with many other things). If it doesn't try all possible combinations of limb length(or all posssible bmp2 levels), how does it find the one that works?

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  59. Jim

    I think the rolling cloud metaphor was just meant to convey that in any population there are a lot of things going on at once, that if there is one long-legged son-of-a gun, there's probably more of them, all slightly different, and if there are enough of them, they even start interacting amongst themselves, creating an average effect over time. This is in contrast to the hypnotic way of thinking we often develop from looking at specific examples, of thinking that there is one only line of descent in population x that developed such-and-such a mutation. In other words our thinking can get too linear.

    With the recipe thing, I was trying to get at the idea that some mutations are more likely than others, although their locations on the genome are random, and also that many of the qualitative effects we see are based on quantitative "production factors". There could be quite a difference between finding the best possible place for something, and finding the optimum amount of something. Richard Dawkins claimed that every spider web you've ever seen, no matter how intricate, could be plotted on a graph using three coordinates (quantites).

    I am trying to think up a good example using recipes or assembly instructions. when I do, I'll get back. I am on my Mom's computer (dial-up) and can't spend too long at any one time.

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  60. lily,
    I think I see what your getting at with respect to recipe getting to more likely mutations. That may work if you were just talking about bats limbs or certain fearures only, but keep in mind that every single part of every species is brought about by evolution at one time or another, according to the theory.
    I think I understand what you guys mean with the cloud. I understand that multiple mutations in multiple directions can happen in said species. The theory could even bring about more than one new species simulatanously. The complexity could be endless adding the different processes of evolution, genectic drift, selection and so on. I do get it. Thats not to say that piticular mutations can not be looked at in a linear fashion. The only way evolution can create a new feature or extensivly change the function of a existing feature (like bat wings) is to severly strain the survival capability through enviormental changes and have severe mutations to get something done about it. Keep in mind whatever causes the mutations to survive, kills the members without it. You need very significant mutations to accomplish this, and you need them constantly. Mutations don't know when the enviorment will be changed, so they just need to be happening all the time. And they have to be significant enough to present real advantages. We seem to be able to believe that the enviorment can stress an animals ability to survive and the animal has millions of years to catch up with the enviorment. We know this isn't true. Watch how many species go extinct in the future while man keeps stressing the enviorments of species. Here is a prediction. You wont see any new species come about as evolution predicts enviormental changes should bring forth. You see complete species wiped out. Does evolution have a disclaimer that if man changes the enviorment through things like global warming then all bets are off?

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  61. Jim,

    You are a broken record. You keep on repeating the same argument on this blog over and over again. "How could randomness do all that". "Where are all the random mutations".

    You just don't understand the role of randomness in the standard theory of evolution (and probably you have a very bad intuition about probability, but you're not alone in that).

    Selection is not random. Mutation is only partially random. Not every type of mutation is equally likely. Most will yield a phenotype quite like the phenotype of the parent(s). Many are neutral and get fixed by chance.

    Have you ever looked around at your fellow humans? They are all different, they are all mutants.

    It's so obvious you just don't want to listen carefully to reasonable arguments because they conflict with your religion. You are boring.

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  62. I find it amazing that if I see an issue with evolution it must be because I'm blinded by religion. Even though I have stated over and over that evolution does not conflict with my beliefs. I don't even belong to a church, Although I promised my wife she could raise my kids Catholic, so I must make periodic appearences (baptism, first communion, ect.), but I do not personally belong to any since I can't really accept all of the old testement it wouldn't be appropriate. Never the less, If I oppose your view about evolution, it can't be becuase of any intelligent thought I have on the matter, It must just be that I'm blinded by religion, what a cop out. The fact is, I can see the random mutations that we witness being responsible for keeping a species fit and even modifying it to some extent. It's funny that you guys keep saying how I just don't understand the process, and that I have it all wrong. In a mechanical sense the process is so simple. Complexity only comes in because the effects of evolution and mutations can be combined to make endless situations

    Ido said,
    You just don't understand the role of randomness in the standard theory of evolution (and probably you have a very bad intuition about probability, but you're not alone in that).

    I am an expert in S.P.C. (statistical process control) and have studied statistics at UMASS at Lowell . Randomness is part of my life on a daily basis and foreseeing the random is part of my job. I see bell curves in my sleep. So trust me I understand probability. Either you don't understand my arguement or perhaps I haven't presented it way that you can understand, because you are not answering it by saying-

    Selection is not random. Mutation is only partially random. Not every type of mutation is equally likely. Most will yield a phenotype quite like the phenotype of the parent(s). Many are neutral and get fixed by chance.

    Saying that mutations are more likely to represent the phenotype of the parents only enhances what I am saying. So instead of answering my arguemnt you must resort to name calling. Honestly, I did expect more. Its a typical response though, rather than refute the delemma at hand just attact me personally. If you can discredit the person than you don't have to worry about anything he says. And someone out there may have an answer as to why we don't see SIGNIFICANT mutations that are capable of changing the function of a body part all the time. Because PROBABILITY says we should if species should be ready to change when the enviorment does. If someone does give me a good answer perhaps, I will sway back to evolution.

    Try to write a story about evolution. Not the simple one about horse turning zebra. Write Of how the nose or foot came about or any complex feature. Write the whole story of each mutation and how each one presented so much of an advantage the members without it started to slowly die out. Write it mutation by mutation. And how the changes in the enviorment made those mutations an advantage. It does not have to be real and can be totally fiction. But it should be easily possible. For each mutation you use, it can't be anything more unusual than what you see today. Meaning they must happen in small incriments not larger than currently noticable variation between members. This is a simple challenge. This will be an impossible challenge. And I know some of you will say it has been done with things like the eye. I have seen a version of it and it never talks once about enviorment, and each mutation is way beyond anything we witness on a regular basis. I will leave you guys alone. To pat each other on the back when you post a new proof of evolution without anyone on the blog that disagrees, we don't want to bore anyone with disagreement about evolution. That would suck. It will be better if Massimo just post a new evidence of evolution and everyone just comments on how awesome it is. And you can all go "where are those stupid IDers now". We will all be on some other boring blog sounding like broken records and boring each other to death.
    God Bless

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  63. Jim

    Your background in probability has given me a thought.

    What is the probability of finding an inert element with 6 electrons on the second ring? Zero. Because there is no such thing as a second ring with only 6 spaces.

    What is the probability of a mutation giving 42% of bmP (as opposed to 35%)? We don't know! Because we don't know how many mutations are available. [ We do know however that all mutations, without exception, are discrete. The appearance of continuum is a product of the interaction of genes, not the mutations in a single gene.]

    Your argument that evolution is impossible appears to be based on the assertion that the whole possible variety of mutations should be, but is not, represented. But since it it completely outside anyone's capacity to say what mutations are available, it is simply outside our capacity to say that evolution is impossible.

    In fact, plenty of variation could be present, through the interaction of genes, to provide the raw material for evolution; while, at the same time, the limited number of mutations available, would relieve nature of the necessity of producing the endless spectacle of ugliness that you postulate.

    Interaction between genes would tend to reduce the extremity of variations due to mutation, rather than excacerbate them.

    Since there is no need to postulate the impossibility of evolution, there is no need to come up with complicated scenarios showing how, in spite of all, evolution is possible. Put quite simply, if it looks like the mammalian ear evolved from the reptile's jaw, it probably did.

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  64. Lily,

    I bet a lot of individuals who work in a field of that deals with probability come to the same conclusion that Jim did. That since nothing is truly random, that is, every event that occurs in the physical universe has a cause which can be both quantified and attributed to that cause plus forces a, b, & c, and so on….and thus the identical conditions, even in the genome, are likely to create the identical effect again, (tho some things we observe have the appearance of randomness merely because "we” don’t understand the whole process) unless certain types of information are completely missing, of course, as would the case with extinctions.

    I certainly wouldn't come to the conclusions about extinctions that evolutionists do. Extinctions have never meant that information is increasing, or can build itself back up, or anything of the sort. It means, in terms of probability, that information loss is just incredibly more likely than information gain!

    cal

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  65. Ah yes. Climbing Mount Improbable.

    paul

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  66. "Ah yes. Climbing Mount Improbable."

    But one 'improbability' is deemed more favorable than the other, solely based on the fact that one can live one's life anyway he sees fit?

    And that, apparently, is worth stepping over evidence for.

    cal

    The Anvil - God's Word

    Last eve I passed beside a blacksmith's door,

    And heart the anvil ring the vesper chime;

    Then, looking in, I saw upon the floor

    Old hammers, worn with beating years of time.



    How many anvils have you had," said I,

    "To wear and batter all these hammers so?"

    "Just one," said he, and then, with twinkling eye,

    "The anvil wears the hammers out, you know."



    And so, thought I, the anvil of God's Word,

    For ages skeptic blows have beat upon;

    Yet, though the noise of falling blows was heard,

    The anvil is unharmed--the hammers gone.


    Author unknown

    http://www.crossroad.to/Victory/poems/anvil.htm

    ReplyDelete
  67. Blog Techniques Lesson #1.

    You can always have the last word if you say something really dumb.

    [Oops. I'm snookered. She can have the last word by leaving me with the last word. Aw.]

    paul

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  68. Paul,

    I don't mind much one way or another. I know what the end of skepticim will be, and likely so do you.


    Excerpts from: Can Man Live Without God

    "In such fashion came the onslaught of all that had gone before; the pen became the sword and the professorial lectern, the pulpit. If young, fertile minds could be programmed into believing that Truth as a category does not exist and that skepticism is sophisticated, then it would be only a matter of time before every social institution could be wrested to advantage in the fight against the absolute.

    However, over time the sword has cut the hand that wielded it, and learning itself has lost its authority. Today as we look upon our social landscape, the answers to the most basic questions of life,from birth to sexuality to death, remain completely confounded.

    The very scholars who taught their students to question authority are themselves disparaged by the same measure. No one knows what to believe as true anymore; and if anything is believed, the burden of justification has been removed. Interestingly, the word university means "to bring unity in diversity," and the idea of the academy was to impart knowledge and virtue. Neither of these goals are recognizable today. The Sartrean longing to unify knowledge never materialized, and it is now a tacit assumption that the hallmark of modern education is skepticism, going back to the Cartesian model, in which the only thing one can be certain of is doubt. However, tragically unlike Descartes, there is no god to guard us against deception, and where Descartes began the modern skeptic has ended..."
    Ravi Zacharias
    http://www.rzim.org/publications/jttran.php?seqid=22

    cal

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  69. Lilly,
    I really appreciate your comment. I feel you really have a grasp on my dilemma.

    You said,
    What is the probability of a mutation giving 42% of bmP (as opposed to 35%)? We don't know! Because we don't know how many mutations are available. [ We do know however that all mutations, without exception, are discrete. The appearance of continuum is a product of the interaction of genes, not the mutations in a single gene.]
    I still don't understand how if all mutations are discrete, how that 35% bmp could come about? Without trying all percentages that are at least from negative 35% to positive 35%. This must be the range of mutations in order to get to the 35% needed. The range could be higher (say neg 53% to pos 53 %)but it could not be lower.

    You said,
    In fact, plenty of variation could be present, through the interaction of genes, to provide the raw material for evolution; while, at the same time, the limited number of mutations available, would relieve nature of the necessity of producing the endless spectacle of ugliness that you postulate.

    I think you are making a point of how the significant mutations are somehow there in the genes but we just don't witness them? Correct me if I am wrong about that.
    Either way, if the significant mutations are not physically present, how can nature experiment with them?
    The other point you made is that perhaps the significant mutations are actually there. Which gives me an idea. We need a system to measure mutations. If such a system could be devised, then evolution could be disproven or further validated. Since I do not have this system of measurement I can only speculate that the variation I see can not be large enough to account for an advantage when the enviorment changes.
    Another thing I thought of when trying to imagine a species changing through such small variation that we witness is, if evolution is true why are there any species? shouldn't every fossil be an intermediate. Isn't every thing we see, all fossils and todays living animals, just a snapshot in time. Or is it that the species only change when the enviorment changes? Shouldn't it really be impossible to group any animals into a species, since theoretically there shouldn't be any species. This is totally seperate from my previous argument, and I am not saying this disproves evolution.

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  70. Jim,

    I see ya. It'll be a few days before I can really say much, but I will get back.

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  71. Jim,

    You may know something about bell curves and moment generating functions, but you need to read up a bit on mutations and development. I can highly recommend Developmental Plasticity and Evolution, by Mary Jane West-Eberhard (2003, Oxford Univ Press). I have a feeling it will answer many of your questions.

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  72. Jim,
    You can google that book and see the table of contents and index on amazon, also read the first 6 pages. Looks interesting.

    here is an excerpt from a review:
    "The book's main contribution to modern evolutionary biology is the revolutionary idea that environmental influences on development, not mutation, are the first order cause of design. This view is a fundamental alteration of emphasis in a field obsessed with genes, genetic drift and mass selection. The book places major emphasis on the importance of genetic accommodation, which occurs when developmentally-mediated changes in the phenotype are molded by quantitative genetic change. The hypothesis of genetic accommodation can be understood as beginning when the environment induces a phenotypic change. This change imposes a new selective regime onto pre-existing polygenic variation. In this way, we are encouraged to understand genes as "followers", as opposed to "leaders" in evolution. The variants can be inherited in subsequent generations if the environmental conditions inducing them are recurrent, and if there is genetic variation underlying the population in the developmental capacity to produce them. Natural selection will favor the spread of a particular environmentally-induced variant when it has positive effects on individual fitness. Although both mutation and environmental induction are considered important modes of initiation of new phenotypic variation, West-Eberhard's argument is that environmental induction is in fact more important.

    This thesis challenges the modern gene-centered view of evolution, and in so doing, drives the final nail in the coffin of the "one-gene-one-phenotype" illusion. The book encourages the view that a unified science of evolution can only be achieved with a thorough integration of development into evolutionary biology. To this end, Mary Jane West-Eberhard's treatise is an enormous success. By showing how environmentally influenced development contributes to the origin of novelty in all organisms, the book provides a key missing component of a modern evolutionary theory that biology has been lacking since Darwin. The book is essential reading for all graduate students, researchers and teachers of biology."

    I notice that some of massimo's work is in this vein, if you look on his main website.

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  73. Jim,
    Before we get back to our discussion, I would like to give a sketch of where I think we are logically, and this will also give me a chance to summarize some points. I am going to use numbered sections. I probably won't get to where we left off before I reach number 4 or 5. This will have to be presented piecemeal over several days for reasons of time. It's not meant to be a scientific treatise. I'm assuming we are both just seekers and laymen trying to find what is trustworthy in the whole mass of data and opinion. Feel free to comment as I go, but I probably won't reply directly until I'm finished.

    1. I believe scientists see three major facts about evolution, which I will call (i)Tree of Life, (ii)Natural Selection, (iii)Genetic Fact.

    (i) By Tree of Life I mean the nested hierarchy exhibited in all biological classification. For example (following Theobald), plants are classified as either vascular or nonvascular , vascular plants are either seed or non-seed, seed plants are either angiosperms or gymnosperms, angiosperms are either monocotyledons or dicotyledons. Biologists believe that this nested hiearchy is not accidental but is the result of a genealogical relationship, i.e., Common Descent, or Descent with Modification. The evidence for this is morphological, geographical, molecular, and accords with the timely apearance of exemplars in the fossil record. Tree of Life is independent of any mechanism by which it is achieved. It could be the result of Lamarckian Inheritance of Acquired Characteristics, or some other mechanism.

    (ii) The second fact is Natural Selection, which I will divide into two parts, (a) observational & (b)theoretical.(a) Natural selection can be observed at the micro level on a daily basis, and can be the subject of experiments. It is the reason behind the resistance of germs to antibiotics, the size of beaks, the depth of fur, skin coloring, etc. It can be reasonably extended to such things as relative size of males and females, size of harems, etc. (b) When the Modern Synthesis combined Darwinian Theory with Mendelian Genetics to produce Neo-Darwinism in the 1930's and 40's, it was held that Natural selection was theoretically capable of explaining all the design there is, given deep time and gradual accumulation of changes. Of course this is only theoretical. Does natural Selection actually accomplish all these things?

    The denier says that despite (a) and (b): There is no direct evidence that Natural Selection can do any more than accomplish trivial changes in size and colour. Or something to that effect.

    (iii) Third is what I call the Genetic Fact, sometimes called the Central Dogma of biology. DNA transcribes RNA which translates to protein. There are no known exceptions. It is a one-way street. Roughly speaking the phenotype depends on the genotype, although this is subject to qualification (see below). This goes back to Weiszman's distinction between the germ line and the somatic line, and his refutation of Lamarckism.

    Each of these facts is an element in the overall theory of evolution, and each by itself has great explanatory power, i.e. organizes large masses of data.

    Now on to 2.

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  74. 2. Each of the three Facts has great explanatory power with regard to the data they encompass, but of course much of the data is common to two or three of these domains. Interesting things happen when the explanatory power of more than one fact is combined over a certain range. The explanatory power is augmented tremendously, but also at times made more supple and flexible.

    (i)For example when Natural Selection & Genetic Fact govern the same territory, something interesting emerges. It is something we haven't touched on, so this is a bit of a digression. it has to do with developmental plasticity, and the book that Raevmo felt would answer most of your questions. I won't say too much about it, because I don't know much, but I believe I would be safe in saying that Natural Selection does not have to wait for Mutation in order to come in to play. There is considerable variation in a given species even without genetic change, depending on how the "recipe" developed in relation to the environment. [It looks like some of Massimo's research has been taken down, so I can't link you to it, but I seem to remember a plant that developed into two distinct phenotypes, according to whether the environment was moist or dry]. As long as the same conditions remain in effect for a few generations, selection can operate, favoring a distinct type, and over time mutation can "catch up" to this status quo, and the range of variation will narrow down in a certain subset. It is called Genetic Assimilation. Some version of it has been floating around since the 1920's?, with a forerunner of the idea, named The Baldwin Effect. Baldwin felt it might be important for explaining instinct. [Not sure of this, but I think the phenotypes they talk about are discrete, you have either one or the other, because the organism develops in concert. This would have some bearing on the missing mutations problem.] Anyway, I think the idea is that Natural Selection would favor mutations that approximated to the norm of one of the phenptypes, if it was stable.

    (ii) What about when Natural Selection and the Tree of Life reign in the same territory? This is where I want to go back to the examples I used in our previous discussion (on another thread). Why I picked them, and what I think they prove.

    I mean, on to 3.

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  75. Wow, Lyly, very impressive sketch so far. Are you an alter ego of West-Eberhard? Keep up the good work.

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  76. 3.
    (i) The example of the mammalian forelimb- bat's wing, whale's fin, human arm etc.- was raised explicitly to import natural selection into the Tree of Life. No major change in body plan was involved in these developments. They are all straightforward adaptations, easily seen as examples of Natural Selection at work. Yet they encompass the whole class of mammals and occupy a wide swath of deep time, thereby encompassing a pretty fair stretch of evolution. You have two possible responses to this: (a) you can say the changes are micro;or (b) you can say they are not the kinds of changes, i.e., changes in function, that Natural selection can produce. If you choose the latter you have to fly in the face of the evidence that this indeed happened, or challenge the aforementioned theoretical possibility, based in mathematics, that Natural Selection can achieve just about anything given time. If you choose (a) you have to be able to explain how a set of changes can be micro that encompasses an entire class. Note also that it is difficult to maintain both positions at once, because if you state the case against Natural Selection's ability to produce these changes, you are in effect denying the changes are micro. If you say the changes are micro, you have to minimize the extent of the changes, in order to contend that they are no problem after all. This is because the changes are of medium extent, which presents no problem for the evolutionist, but does present a problem for the denier. I do believe, Jim, that you have adopted both positions at one time or another, and that, at the very least you have to choose which one you want.

    Now I have to go away for a few days, and may not be able to continue for a while, but will return to 3 as soon as I can

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  77. Wow Lilly,
    Your are going above the call. Your mentioning of genetic assimilation has given me a little more to think about, since I havent really imagined evolution in quite that way. I am not sure how that thought process will affect my origional dillema, I'll have to mull it over.
    Raevmo,
    I will get that book. Most of my limited library is somewhat out dated. So its time to refresh. It will take some time since I will probably just order it from the local Borders.
    Lilly,
    I will comment more on your statements, as you I am out of time

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  78. Jim


    Check out the links in Massimo's latest post. They are the links I said were down

    Lily

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  79. 3.
    (ii) Here is a point that might be easy to miss, but which sums up the foregoing. The cat's leg, whale's fin etc. are all homologous. That is why their resemblance is significant. It does not matter whether you believe in evolution or special creation or whatever, a mammal would still be classified a mammal, a reptile would still be a reptile etc.. And since the cat, bat, whale etc. are all mammals, the homology of their limbs is significant, and constitutes evidence for evolution.
    (iii)The same goes for the transition from the reptile's jaw to the mammalian ear. They are all vertebrates. You can never get away from the fact that the reptile's jaw and the mammalian ear are homologous. it's just a question of counting and comparing bones. Therefore the series of fossils that indicate stages in a transition are highly significant, and constitute evidence for evolution. not only that, but the double-jointed jaw in the middle of the series is entirely consistent with what the theory of Natural selection would require, and constitutes evidence for the same.

    All of which alters the position with regard to the snetence I rendered in bold type previously.

    On to 4.

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  80. 4.
    The nested hierarchy of the Tree of Life is fact, in the sense that the same tree would be arrived at time and again, no matter how many times we started over. The homologies found within the tree are also fact. Fossils that demonstrate these homologies are certainly fact. From these facts evolutionists infer that evolution by natural selection is responsible for X.

    Given this showing of evidence, whether ultimately sustainable or not, the statement that follows is no longer adequate to the ID/creationist case.

    There is no direct evidence that Natural Selection can do any more than accomplish trivial changes in size and colour. [from before]
    Given the showing of evidence, something like this is required:

    Despite all appearances to the contrary, Evolution by Natural Selection CANNOT produce features of any complexity. This is impossible because...

    Notice, however, that this formulation imposes a considerable burden of proof on the ID/creationist advocate. By the same token the burden on the defender is light: he only has to show possibility. Of course it would be nice to know everything in detail, but this is not necessary in order to keep evolution in the game.

    The ID advocate almost has to prove his case, especially if he claims to have a "filter" that never gives false positives. (What if every living creature on the face of the earth was a false positive?)

    In short the following sentence has to be completed: This is impossible because...

    Jim, I suppose that this is where your points come in
    (a) the demand for scenarios
    (b) the missing mutations

    After the commercial....

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  81. Lily,
    For starters, thankyou for your effort to enforce your conviction of truth, and not just dismissing me as the ignorant bible blinded IDer. whether we agree or not aside, I need this dialog to find my own truths.
    Thinking what you said about the nested hierarchy of the tree of life being fact. If I were to design an animal right now. If I never had seen any other living species, but had absolute knowledge of what would be an ideal design for a specific purpose. Would that animal somehow fit into the nested hieracrchy tree of life? especially if the same designer was resposible for all the other species. What would a fossil have to look like to not fit somewhere into this hierarchy? Point being, the sheer volumes of species and varieties of shapes and functions kind of makes it impossible for something to be found that doesn't somewhere fit in. If you took every letter of all the different alphabets from every laungage, and arranged them by physical appearance, they would all fit in somewhere, but I guarentee they wouldn't all be in the correct order. You might see some English letters mixed in between the Russian and so on. I understand there is more involved here because of strata and such. I am just saying that, yes the fact we have a hieracrchy is fact, but that it is a correct hierarchy is not fact, even if evolution is true, don't assume that the way we arranged the fossil record is fact. And I am sure you will see changes in this hierarchy as well as changes have already been made. So I am not sure how we can just say it is fact. What is fact about the hierarchy when we can't know the actual scenarios that made it. Yes we have strata that can help with the scenarios. even amongst evolutionist, strata can be heavily debated. Aside from older is under, strata can have many different opinions. Especially when many times the fossil record is used to identify strata age.
    To say that we would arrive at the same hierarchy over and over again is fact is obviously something I would heavily disagree with. Thats like saying if you gave a group of young scientist all the fossils of the world and they havent seen any of them yet. And gave them all the information of how they were found, where, how deep, and so on. They would automatically produce the same hierarchy time and time again. Even if used differnet groups of scientist? I am not sure you really believe that. make no mistake about it, even if evolution is absolute fact, there are mistakes in our current hierarchy.
    I will write back more, out of time for now. Thnaks for hanging in there with me Lilly

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  82. Lilly,
    I have done some research on genetic assimilation. So it is not supposed to replace traditional evolution, it is just an additional process of evolution. In turn giving evolution more power by adding additional processes. I don't think this really changes anything in my way of thinking of mutational capability, since genetic assimilation must use a process that the species already contained. One of the examples that I read about is the ostrige. Many mammals have the ability to form callusis on their skin if repeatitive friction on a peticular spot occurs. The ostrige is born with these callusis already in place on its feet. It is believed this was selected out, but not from a mutation, but from the phenotype already available. This is similar to your plant example. So it is more like phenotype before genotype, rather than the other way around. I think this is one of the major points you were trying to beat into my thick skull in previous conversation. Keep in mind genetic assimilation is not a replacement for traditional evolution, it is only a additional process of change, but still relies on traditional genotype before phenotype evolution to be present. The ostrige still needed the ability to produce callusis prior to genetic assimilation. Or the plant still needed the previous mutation to survive in moist of dry climates. It is not believed by scientist that genetic assimilation replaces the need for the gnome to produce mutations. So this doesn't really change my yearning to understand why large mutations don't have to be constant in order to be ready for enviormental change.
    Genetic assimilation is also a little difficult for me to believe (just yet), since I find it difficult to see how an ostrige with perminent callusis is better than an ostrige with callusis that get formed shortly after birth? How would they replace the entire population? That is not to say it is impossible. Perhaps there is an advantage. Even so, I could still chaulk it up to micro.

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  83. Wow, you guys still here...

    Reading an old Science mag here in the lab, I just came across this review of an interesting book, which reminded me of this discussion: The Plausibility of Life, Resolving Darwin's Dilemma, by Marc W. Kirschner and John C. Gerhart. I don't know how much it relates to what Lily was talking about earlier, but sounds a bit similar, judging by the review. Seems to be an interesting book. This is how scientists disagree and try advancing new explanations.

    J

    PS: once again, forget micro and macro, gee...

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  84. J,
    I am glad to see the authors of "Plausibility" set out to answer unresolved questions on evolution. I have read a little about their "facilitated variation" on the internet, but haven't read the book yet. At a glance, they are saying exactly the point I think Lilly was trying to make. Although the nature of the cell is highly restictive, extremely subtle change in gnome will produce the novelty needed for selection. It seems the authors want to esacape from the linear thinking of mutation, one by one, leading to change (I confess this is how my brain likes to think it out). I will have to add the book to my list. My wife is gonna kill me, I need to find a way to steal this stuff of the net.

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  85. Here is a book review of another book by the same authors. Perhaps it gives an idea of what "Plausibility" would be like.

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