What exactly is ID?

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That's obviously false for a start.

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So some are left? Which are those?

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I'm not making up anything. I'm just keeping it to what we DO know about. The known function, the one tested for was lost. Unknown functions - whether existing before or gained as a result of the mutation - were not tested for and obviously could occur in some cases even if they did not appear in this particular set of experiments. So we don't know anything about those other than that they could be present.

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The point, is that this one was lost. Regardless of what else happened, this one was lost. The point of the article was to show how much you can mutate a particular function before it is lost. That is all.

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The 50 proteins in the E coli flagellum are all distinct.

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It doesn't matter. I'm talking about those same proteins. Just more of them.

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And if the proteins WERE identical there would likely be very little difference in "complexity".

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First of all, it's not "complexity" it's complexity. And it's obvious that there would be vast differences in complexity. More dies more complexity. More proteins more complexity.

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(It would be more like all the dice being dice rather than all the dice coming up with a particular number !)

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It's both. You both have to get the same number. With 1 die, or with 5 dice. If the number you want is 6. It's obviously harder to get number 6 with 5 dice, on every single die, than with just with one.

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Since you don't actually use evolution in any of your calculations - no, it isn't obvious.

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Evolution is the chance hypothesis in this case. You don't use it. You calculate the probability based on it.

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So, according to you, Dembski makes this assumption because the argument needs it. That's not a good reason.

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No, he does it because that's how statistical calculations are done. If you have no prior knowledge of the sequence space you are searching, you assume uniform probability. Everyondoy does that every single time they do a statistical calculation.When you calculate what the probability of throwin 1 die will be, and you than calculate the probability of throwing 5 dice. You ASSUME uniform probability. But this is the most reasonable thing you can do. And if you don't assume it, if you just impose your own probability, than on average, you will get even worse results. That's why this is a standard procedure in all statistical calculations.

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And his real reason (he's attempting to provide an estimate of *general* performance with limited information) makes it inapplicable to a situation where we need the real numbers for a specific case.

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Umm no. Generalization means that this works for all cases. Like General and Special relativity. General relativity does not mean that it does not work when you need specific numbers. It just means that it's a generalization of the principle of relativity extended to non-inertial frames of reference.

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I already did.

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Poit out where.

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I'm afraid that is another silly argument, since the English language allows for more than one way to describe a thing. In fact deleterious mutations could easily be described as "noise" in the genome. So merely NOT using the word "noise" in the definition does NOT mean that "noise" can't be used to refer to genetic entropy.

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They are the noise. I never said they are not. But the point I'm trying to make is that genetic entropy itself means deterioration of genetic information due to accumulation of mutations.

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Because you only have models that state that large populations can, under some conditions, die out from mutational meltdown. Those models can't tell you if those conditions apply to any real populations.

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They were modeling real populations. Not aliens or mythical beings.

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Of course the relevant measure is not any "absolute" measure of information. A non-viable embryo cheetah, doomed through mutational meltdown, would still have far more "genetic information" than the single RNA strand. And it wouldn't make the slightest difference.

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The point is that the doomed cheetah lost vital functions. You can keep loosing genetic information and not die out for a very long time. Loosing the ability to produce melanin is not going to doom the population. Loosing hair is not going to doom the population, loosing the ability to produce some vitamins is also not going to kill off the population.But loos of vital information, like those genes that code for reproduction will certainly kill teh population. Genes that code for breathing, if lost, will kill the population. The same goes for digestion.

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I'm not an expert on RNA life, but there's no clear barrier against increases in functionality.

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Yes there is. It's called probability. The probability of finding functional biological sequences is too small for the darwinian mechanism to actually find them.

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In reality, genetic entropy doesn't even stop increases in functionality occurring and being selected.

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In reality it does just that. Like I said. The probability is to small. Simple RNA chains won't find any new functions. And even if they did, they wouldn't be beneficial enough to actually outperform other and take over the population.What would actually happen is what we saw in the Spiegelman's experiment. The chains would keep getting shorter, and they are the ones that would overtake the population.

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Since you couldn't be bothered to read it the first time, or go back and read it when I asked you to why exactly should I repeat it again ? If you really ant to read it just go back through the chain of posts.

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So you refuse? Fine...

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I already explained. You responded by asserting that I must be assuming that the nucleotide was the unit of selection and that I must be ignoring the random mixing of genes. Neither of which was true at all.

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Okay fine, forget about that. Explain to me how is natural selection supposed to be working on the level of the gene? How? How are the genes the ones that get selected and not the genome?

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Of course, you are exaggerating here. While idealisations make for an easier mathematical treatment, none of these have to be absolute.

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Just remember that I didn't make this up. This is from Sanford himself. He know what he's talking about.But let's say that we will look over the points 3, 4 and 5. You still have 2 FACTS that make your idea of genetic selection false.1.) Genes are inherited in blocks. These things do not go under genetic recombination. So if one of the genes in such blocks has a beneficial and the other a deleterious mutation, they both get passed on.2.) Nucleotides do interact. The ENCODE project has shown that genes are polyfunctional and poly constrained. Which means you can start translation of one gene, hop on on to another and finish the translation. You can also read them in the opposite direction. Nucleotides do interact in just such a way. That means, that the gene can not, in any ossible way be the unit of selection.The genome is. The genome gets passed on in full. Natural selection does not pick out the best genes and drops the rest. To claim the opposite is to be in argument with reality itself.

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What I said. CSI is not measured in bits. Information and Specified Information is measured in bits. Complex Specified Information is any Specified Information with more bits than the bound (or has a probability below the bound - which is the same thing).

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Something is or is not CSI, that's true. But something can contain more or less CSI. That's also obvious. And since information is measured in bits. CSI is also.

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In fact I keep explaining why. Your calculations keep trying to pull in irrelevant details which aren't part of the specification. That's obviously invalid.

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Such as?

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The idea that genes are not rearranged by genetic recombination is simply wrong. What do you even think genetic recombination means if not that the genes are recombined? The closer genes are to each other the less likely they are to be seperated by crossing over, but that is just a question of probability, it doesn't mean that they can't be seperated, even different regions of the same gene can be recombined. And that is without even beginning to look at other mechanisms which can lead to changes between complementary gene regions.

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Where did I say that? Please point ot where I sad that genes are not rearranged by genetic recombination? I never said that. So why would you claim I did? Is it because you misunderstood me? Probably. What I said is that linkeg genes in genetic blocks do not undergo recombination. Do blocks themselevs do, but not the genes inside the blocks.

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All this shows is that you A) don't understand what ENCODE was looking at, and B) dont understand genetics at all.

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Or, that a) You're full of yourself, or B) You're full of it.

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The main problem is that 'unit of selection' is not a very useful term. A single nucleotide change can certainly produce the neccessary phenotypic difference to form a basis for selection to act on.

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And you miss the point completely. I never said that a single mutation won't have such a strong effect that it won't cause the individual to be selected. Maybe it will. I never said it can't be done.But what I said, is that, even thoug that might happen, let's even say that it happens most of the time, natural selection is going to evaluate the whole organism, and than it's either going to select it or not. What this means is that however great the effect that single mutation had, let's say it was beneficial, all the other deleterious mutations the individual had within it's genome, are going for a ride! They all get passed on together. This is what it means that the genome is the unit of selection. Not the gene, or the nucleotide. Because natural selection is going to evaluate how the whole organism (genome) is compared to the other organisms and select it. It's not evaluating specific genes, or nucleotides against genes or nucleotides of other individuals.Either all genes and nuclotides are selected and passed on, or they are not. This means that the genome is the unit of selection.

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The whole point is that the mixing of different complements of genes within a population's gene pool does allow a degree of seperation between genes allowing us to look at the increase in specific alleles rather than looking at whole genomes. It is impossible to make any sort of case in sexual organisms that whole genomes are inherited.

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So let me get this straight. When meiosis occures, the mechanisms inside the cell, PICK OUT THE BEST GENES, and pass them on to the next generation? OBVIOUSLY NOT!

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In terms of the ENCODE data what you are talking about is presumably the identified ransripts, the thing is that the ENCODE data showed that the majotrity of the genome is transcribed, but only 5% of it seems to have any sort of selective constraint suggestive of function. This makes it a pretty substantial leap to go from the existence of transcripts to their having a functional role which would be destroyed by any single nucleotide changes.

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I never said anything like that. Why do you keep misrepresenting me?

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As genes, mRNAs, and eventually complete genomes were sequenced,
the simple operon model turned out to be applicable
only to genes of prokaryotes and their phages. Eukaryotes were
different in many respects, including genetic organization and
information flow. The model of genes as hereditary units that are
nonoverlapping and continuous was shown to be incorrect by
the precise mapping of the coding sequences of genes. In fact,
some genes have been found to overlap one another, sharing the
same DNA sequence in a different reading frame or on the opposite
strand. The discontinuous structure of genes potentially
allows one gene to be completely contained inside another one’s
intron, or one gene to overlap with another on the same strand
without sharing any exons or regulatory elements.

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What is a gene, post-ENCODE? History and updated definition What I was talking about is this. Genes are not descrete units of code. There is no such a thing as one gene one trait. Biological functions are coded for by lot's of genes that are either a.) placed on different sites on the chromosome, or b.) overlap each other. Meaning that 2 different functions can share a single gene. Not only that, but some genes are also coded for by the intron regions which were thought not to contain any code at all.So any talk about a gene being the unit of selection is painfully wrong by today's standards.As for the 5% number of functions you cite, I have no idea how you interpreted that, or where you got that, but it seems to me, that you are talking about this quote right here.

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Moreover, comparison of the human, dog, mouse, and other vertebrate genomes showed that a large fraction of these was conserved, with ∼5% under negative selection since the divergence of these species

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What this shows is that they are simply assuming that there is 5% of code that is conserved since humans, dogs and mice diverged. This is obviously an assumption. Since they don't actually know this to be the case.

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It is important to understand that when the ENCODE project talks about functional areas of the genome they are talking about biochemical function in the context of transcription or identifiable binding sites, this doesn't mean that these regions actually perform any functional purpose in the life of the organism. Indeed one of their conclusions is that there is a large amount of functionally active but selectionally neutral genetic material.

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I don't care. Those are still functional regions we are talking about. I don't care if they are selectable or not. I was the one who was claiming that selection is almost non-existnt from the start. What we have is almost constant geentic drift or near neutral selection.

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ENCODE certainly showed that the transcriptome is much more complex than we would have expeected, but it doesn't show in any way that single nucleotides cannot form a suitable substarte for selection, or that genetic recombination cannot resegrate nearby beneficial and deleterious mutations.

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1.) Common sense is actually what I was appealing to to show you that. A unit of selection is what gets evaluated and passed on. Specific genes do not get evaluated and passed on, neitehr do nucleotides. The overall fitness of the organism is what gets evaluated together with beneficial and deleterious mutations.2.) If we are talking about physically linked genes that there is no way they are going to get recombined. Unless there is some new mechanism for that. Which I'll be glad to accept once it has been found.

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Clearly there are deleterious mutations which hitchhike to fixation, but it would be very hard to make a coherent case for any way in which this could happen unless the beneficial mutation they are accompanying outwieghs them.

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This pretty much happens all teh time. You do know that deleteriious mutations are way, way more overrepresented than the deleterious ones? And you do know that there are about 175 new mutations added to the lineage of human species with every brirth? And now you are going to tell me that deleterious mutations are not going for a ride together with beneficial ones? Are you seriously going to suggest that!?Edited by Smooth Operator, : No reason given.

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Great. So tell us what testable predictions ID makes.

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This is such an old topic? Must we really go over it?(1) High information content machine-like irreducibly complex structures will be found.
(2) Forms will be found in the fossil record that appear suddenly and without any precursors.
(3) Genes and functional parts will be re-used in different unrelated organisms.
(4) The genetic code will NOT contain much discarded genetic baggage code or functionless "junk DNA".FAQ: Does intelligent design make predictions? Is it testable?

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So now you're saying that ID *does* have something to say about evolution. Specifically, you're now saying that ID has something very precise to say about the history of life on Earth, claiming that ID says common descent is impossible.

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So here's the question once again, and please don't yank me through another series of three or four evasive and misleading posts: What is the ID explanation for the history of life on Earth, and more specifically, what is the ID explanation for why common descent is impossible?

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Wow, just wow.I mean... wow...Really? I said that ID says that CD is impossible? Where, oh where did I say that? Except never. Actually, what I did say is THE COMPLETE OPPOSITE! Yet you somehow missed that. Let my quote myself now...

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No, it's fine by me. I like the discussion to be as broad as possible. However, ID is clearly compatible with CD. Michael Behe accepts both ID and CD. So no, there is no problem in accepting both.

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EvC Forum: Message PeekHow exactly did you miss this one where I said the exact opposite of what you claimed that I said?Once again, just wow...Okay, before this turns into an unnecessarily long discussion, which it basicly already is, let me explain myself thoroughly. I never claimed ID was no compatible with CD. It is compatible. It's also compatible with random mutations that would be acted upon by natural selection to increase the information in the genome. So, a sort of a darwinian evolution is also fine. The only thing that ID is not compatible with is that this kind of darwinian evolution did not have an intelligent cause. There must have been an intelligence at the start. That is what ID claims.And now, if you are goig to invoke a full darwinian evolution to falsify ID, and claim that there can be such a thing as a design without a designer, it's clear that to falsify your argument I have to attack it! Since a full darwinian explanation consists of 3 parts, which are 1.) Common descent, 2.) Random mutations, 3.) Natural selection, me falsifying any of those 3 will make your argument against ID fail.So, yeah if you are going to invoke a darwinian evolution to show that there is sucha thing as a design without a designer, than I have to discuss all 3 aspects of your argument, falsify at least one of them, and show that there is only design with a designer and that ID is correct.

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Then ID fails to explain biodiversity.

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Maybe because it's not trying to do such a thing? Evolution also fails to explain the origin of life? But is that any sort of an argument, since evolution isn't even trying to explain the origin of life. So why would you make such an argument against ID? ID explains the cause behind the design of patterns we observe in the universe. Some of them are found in living organisms. So ID also explains the cause of design in life, it doesn't try to do anything else.

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"We see in these facts some deep organic bond, prevailing throughout space and time, over the same areas of land and water, and independent of their physical conditions. The naturalist must feel little curiosity, who is not led to inquire what this bond is."--Charles Darwin, "Origin of Species", Chapter 11

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Ah yes, Saint Darwin and his Holy Book. Great read...

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Aren't IDer's curious as to biogeography? Is biogeography not something that ID must explain in order to explain modern biodiversity?

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Aren't evolutionists curious as to origin of life? Is origin of life not something that evolution must explain in order to explain modern biodiversity?

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As we have already demonstrated, due to the dogmatic nature of ID there is nothing we could ever show which would falsify ID.

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Either, a.) Show that an event is probable enough to be produced by chance, or b.) show that an event is due to high probability of natural laws. This is how you falsify the design hypothesis.

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Rather, the theory of evolution demonstrates that these observable and natural processes are sufficient to explain modern biodiversity in the same way that the Germ Theory of Disease is sufficient to explain infectious diseases but incapable of completely ruling out disease causing demons.

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Oh, really? Please than do explain the modern biodiversity. I'm waiting.

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In order to claim that mutation only results in a loss of function then you must know all functions that the protein has. Given the wide range of possible function it is extremely difficult to do this for every protein. This is why the "mutation only results in loss of information" is such bunk.

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My main argument isn't even about loss of all information. I simply said that all known functions were lost.

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Unless you designed your experiments correctly you would just notice the lack of methylation at the GATC sites. You would call this a loss of function. However, these mutations lead to a new function, methylation at GATT sites. Mutations can and do lead to specifity for new substrates, and given the vast number of possible substrates it is nearly impossible to claim that a protein of no known function lacks function in all situations.

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Did I ever claim that mutatoins can't leed to new function? I don't remember saying that. Maybe I did, but I really don't remember that.But what I do remember saying is that chance alone can not generate new CSI. Did your experiment claim that that happened? No, it didn't. What did it claim happened? That new functions evolved. Fine? But what kind of evolution was it? A full darwinian evolution, or a directed one? Let me remind you with a quote from your own article.

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We have changed the target specificity of EcoDam from GATC to GATT by directed evolution, combining different random mutagenesis methods with restriction protection at GATT sites for selection and screening.

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A directed one. And it was directed by what? What was the source of direction? What was the information origin for the direction of where evolution is going to go? An intelligence. So the conclusion is, that this is a clear case of intelligent design. Intelligent agents are the ones that produced new functions. Not an undirected process like a darwinian evolution.So you were saying?

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Do you have any evidence for this, other than your bald assertions?

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If you actually payed any attention to the thread you would have noticed the facts I presented a long time ago.Spiegelman's Monster - Wikipedia

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I think you are making the same mistake you made earlier. The paper you referred to earlier suggested that the SMALL POPULATION size of LARGE ANIMALS could lead to genetic entropy. They used the size of the animals as a proxy for their population size since larger animals need more territory, hence smaller populations.

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And after that I showed a paper that is a mathematical model of large sexual populations, which claims that such populations are in the same danger as small populations.Edited by Smooth Operator, : No reason given.Edited by Smooth Operator, : No reason given.

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If you think that the fact that you said all function is lost is sufficient to prove that some function remains you have great faith in your ability to get things wrong.

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I'm simply asking you to name teh functions that are left? Keep in mind that we are totally of the subject now. I neevr claimed that loss of all functions is my main argument. It's you who simply doesn't want to drop this. Why? I don't know. But please do continue, tell me which functions have remained.

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We're not discussing that at all, because that was accepted long ago. Instead we go round and round in circles with you switching between asserting that all function was lost and then trying to act as if you never said it.

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But I did say it. And I told you why I said it. So why again are we talking about it?

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It certainly does matter. Since the only "50 proteins" figure we have is the number of different proteins in the E coli flagellum - which is made up of a good many more than 50 protein molecules using that figure implied distinct proteins. But OK, why would 1,000,000 units of 50 distinct proteins be significantly more improbable than 1 of each ?

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What a question... For the same raeason that getting 6 of 5 dice is less probable than getting one 6 on one die.

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Given that the "complexity" we are talking about is a measure of improbability and not closely related to the normal usage then the scare quote are entirely justified.

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Excuse me, but it's your, not my problem that those two words, complexity and improbability are inversly proportional. When one increases, the otehr decreases. This is a well known fact of statistics. Increase the number of dice, the complexity increases, yet the probbili probability of getting a specific outcome decreases.

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Then it's a pity that Dembski did no such thing.

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Explain why. Point out where you did so, if you already did it.

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No, they don't.

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Where! Show me where is non-uniform pobability used without prior knowledge!

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At least not if they want the result that they get to be anything more than a rough estimate.

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Well, duh! That's what statistics are all about. It's about probability! It's not exact like standard algebra where 1+1=2. It's about approximation.

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For things like dice and coins we use a uniform distribution - but that's because of knowledge, not ignorance. (And even there we acknowledge that there might be subtle biases in the real objects).

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Of course there could be. Nobody is claimng that there couldn't be! I'm not claiming it. Dembski isn't claiming it! Nobody is!But we certainly are ignorat about teh principle of unifom probability of because of ignorance. That is a fact.

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As with coins, it is assumed that the initial conditions of throwing the dice are not known with enough precision to predict the outcome according to the laws of mechanics. Dice are typically thrown so as to bounce on a table or other surface. This interaction makes prediction of the outcome much more difficult.

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Principle of indifference - WikipediaAs you can clearly see, the principle of insufficient reason, or as it is also called the principle of indifference, is uset precisely because we do not know the laws of nature 100%. If we did, we would be doing a statistical analysis in the first place! We would just know what would happen when we threw the die!Anyway, the point I'm trying to make is that we use this principle because it's the best approximation. If you have a better one, please do share it with us. If you don't than we are sticking with this one. If you claim that this method is false because it's not perfect and it's not giving us exact results, than your criticism fails. Because approximations are not supposed to be exact. Approximations are by definitions not exact. And that is what the field of statistics is.So basicly you have no real argument anymore.

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In this case it means an idea that is often close to being right (but can be drastically wrong).

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But it's the best we have. Care to give us a better method? No? Didn't think so...

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Re: CSI & Genetic Entropy discussions (Message 1056).

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Please quote the relevant part.

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In fact you did say that and attempted to misuse Sanford's definition to back up your claim.

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LOL, accusing me of lying again. Goog, good for you...

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Please show that the figures used in the runs which lead to mutational meltdowns in large populations used figures derived from a real population.

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Umm... that's what the scientists were supposed to show not me.

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WHich of course means that the issue is not the loss of all genetic information, but just sufficient to disrupt one or more vital functions. Therefore the absolute measure of genetic information is not relevant (the more so because many of the "vital functions" will be "vital" because other aspects of the animal require them - the simpler the life form, the less it has to go wrong).

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We are still talking about the absolute measure of information. A specific vital fuction is coded for by an absolute, not relative amount of information. And no, it's the individuals with more genetic information that can survive longer while loosing genetic information. Because they can be loosing those functions that are not vital. Unlike simple RNA chains that can loose som much and practically be done with.

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You are also refusing to do the very same thing. But I am happy to let my argument stand unrefuted.

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What the hell did I refuse to do?

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If Sanford really claimed that population genetics really required all those assumptions to work at all then Sanford doesn't know what he is talking about.

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Of course, and that is because you are smarter than he is. You know better than he does. You invented the Gene gun, not him.

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1) is not strictly true since the chromosomes are broken up by recombination. Genes that are very close will tend to stick together but that is all. And even if this were not the case, then the most you could do is to take a chromosome as the unit of selection, not the genome.

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2) is just illogical. The fact that genes interact doesn't mean that they can't be the unit of selection.

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1.) It doesn't matter if the chromosomes are broken up or not. The blocks of genes stick together. And there is no way that the chromosome is the unit of selection. Does natural selection remove the bad chromosomes and sticks with the rest?2.) Uhh, yes it does. Because a gene is not a specific region. It's multiple regions which overlap. If one region mutates two traits can be affected. So there is not such a thing as one gene one trait.

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In sexually reproducing species the genome does NOT get passed on in full.

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By full I mean the half that gets passed on. That half is not examined by some mechanims inside the cell and all the deleterious mutations are not picked out. And again, by full, I mean that natural selection evaluates the full genome. It evaluates how the whole organism functions, and than it either selects it, or it does not. Only than does that organism pass on that half you were talking about. But first, thw whole genome is evaluated overall.

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And in the long term natural selection will tend to favour the better alleles.

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No it won't. Noise is too large for this to happen. Remember those 6 sources of noise I was talking about? Like epigenetics? It interferes with the selection.

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"Hitchhiking" relies on the linkage remaining intact, which is not guaranteed even for adjacent genes - and you've got nothing else.

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Umm... hitchhiking is what's happening all day everyday. It's caused by the 6 sources of noise I was talking about before. Nto jsut one you just mentioned.

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How many bits of having more bits than the bound can a thing have ?

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What?

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Requiring exactly 50 proteins - that isn't in the specification. using the same proteins as in the E coli flagellum or variants of them - that isn't in the specification either.

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And Dembski never said that 50 proteins is the specification. It's the complexity of the event D*.

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I am quite happy to leave it at the known function was lost, but we don't know if there were any other functions which remained or other functions gained. You, on the other hand will only leave it there if we hide the fact that you originally argued that ALL functions were lost.

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Why would I argue for that when I said before, and now, that that is NOT my main argument? My main argument is to find out how much mutations can a certain function take before it becomes useless.

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Because your reason was incorrect, but the closest you will get to admitting it is trying to conceal the fact that you said it.

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So you are again accusing me of lying...

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THe reason why it is more likely for dice is that the result of the throw is random. The production of proteins is not random - the structure is controlled by the gene. So getting multiple copies of the same protein is not at all like throwing dice.

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But genes are the ones that are under teh question of being designed. It's notl like they are a product of some natural law. There is no natural law that directs a DNA sequence to code for a flagellum. It was either produced by chance, or it was designed.

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Of course what you say is quite silly. If we simply consider Dembski's idiosyncratic usage of complexity getting 500 heads in a row is a "complex" sequence. But in normal usage it would be seen as simple.

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I see you basicly have no more arguments. You are not arguing with me anymore, nor with Dembski, nor with the whole mathematical community. You are now in an argument with the logic itself. As far as I'm concerned, our discussion is over. I'll continue it simply because I will do so, but in reality there is no real reason to do so.If you deny something as simple as the inversly proportional relation between complexity and probability than we have nothign to talk about anymore.If you want to get 6 on all dies you have the relationship between probability and complexity will be something like this.More dice, less probability.
Less dice, more probability.5 dice, a certain probability.
3 dice, more probable than 5 dice.
7 dice, less probable than 5 and 3 dice.This is what you are denying. You are denying pure logic. This is not something I or Dembski made up. This is something you learn in the first year of college.

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I wouldn't like to speculate on Dembski's motives here.

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Neitehr am I asking you about the motives.

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I didn't say that it was.

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Well you can't have it both ways! Either its used or it's not. Either you accept the principle of insufficient reason or you don't. Do you or do you not. If you do, than fine. If you don't, explan why.

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That's also wrong. Statistics are useful in dealing with approximations (e.g. calculation of error bars) but approximations are no better in statistics than in any other branch of maths.

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What!? What did I say that was wrong?

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And you will notice that your wikipedia quote says nothing about uniform probability or the reasons for assuming it... In fact all it does is give the reasons for treating dice in terms of probabilities instead of exact predictions. Maybe you should have quoted the previous paragraph, but then that contains a reason FOR assuming that each number is equally likely.

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Yes it does. It says that it's because we do not know the exact mechanics behind the dice roll.

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Dembski claims that his method produces a mathematical proof of design - so no, approximations aren't good enough,

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LOL! He never, ever said that. NEVER, as in NEVER. He actually said that the design inference is NEVER perfect. And that is why he compared the Explanatory filter with a net. He said that it catches some design, and leaves out other instances of design. He also said that some things are still possible without being probable. And his method would falsify such a hypothesis that is possible, but not probable. That's approximation.You have no arguments left. You are just making things up now as you go...

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I don;t see why they should be expected to come here to back up your claims. And if they were supposed to show it in the paper all you have to do is to find the section where they did it.

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What exactly is it that you want to see? They modeled that reproductive fitness with size of the population, reproduction, selective pressure and recombination as variables is this not a representative of a living population?

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Well that's a confused mess. Nevertheless it seems clear that even an inviable cheetah embryo will have more genetic information than a perfectly viable RNA self-reproducing RNA strand - so obviously the absolute measure is not what we need.

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No, you are the one who is confused. Please explain the following logic to me."inviable cheetah embryo has more genetic information than a perfectly viable RNA self-reproducing RNA strand THEREFORE there is no such a thing as an absolute information measure"Please do explain this logic. It's totally meaningless.

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The same thing that you asked me to do. That is what "you are refusing to do the same thing" means.

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You are making absolutely no sense anymore...

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Just two problems with that. On is that inventing the gene gun doesn't require a knowledge of population genetics. The second is that it is quite possible that Sanford doesn;t agree with you.

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1.) The gene gun is used to genetically modify genes. Genes are studied in population genetics, he studied about it, he knows it.2.) He agrees with me, because I agree with him. I actually quoted him here, but you obviously don't care much about that.

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In other words "reality itself" does not say that the full genome is passed on by sexually reproducing species. Only half the genes are, and those are mixed by recombination. This is why we can't use the genome as the unit of selection - it doesn't persist long enough for the statistical effects to build up and dominate over noise. We need something that lasts, something that can spread through a population - and the full genome obviously isn't it.

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You are missing teh point.BEFORE!!!Do you hear me!?BEFORE!!!!!Before that HALF of genome can be passed on, the FULL, do you hear me again, the FULL GENOME will be evaluated by natural seelction! Not HALF of the gene, but the full gene. Based on all genetic and non-genetic traits. The most "fit" based on all of those traits will be selected. Not based on how good individual gene is, but how good the whole genome is!And by saying soemthing so stupid as the genome is not lasting, you are just digging an even deeper hole here. Are genes longer lasting!? You said yourself that only half of the genes get passed on. So guess what? Some genes do not go to the next generation. Obviously they are even less lasting. So how in the world could they be a unit of selection!? Some are even destroyed by mutations in one generation! LOL! Who are you kidding?

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And that is simply an assumption.

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No, it's not an assumption. It's a fact. About 175 new mutations enter the human population with every new individual, how can natural selection remove that? It can't.

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Oddly enough the "noise" didn't stop the alleles producing the melanic form of the peppered moth from spreading, once pollution turned the trees black.

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You miss the whole point. No wonder you don't unedrstand the topic. You are totally clueless about what is being talked about. I never, ever argued that natural selection can't change the frequencies of alleles withn a population. Yes it can. But what it can't do, is keep the population on the same level of genetic information, or increase it.Genetic entropy is decreasing the informational content. And while this is happening, there is absolutely no problem whatsoever for shifting frequencies within a population.

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Natural selection can overcome noise.

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And do what? Shift frequencies from light do dark moths? Yes.Maintain or increase the original genetic information? No.

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And it also fails to happen every day. Recombination mixes things up.

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How is recombination going to overcome the effects of epigenetics? How is recombination going to overcome the effect of both parent's gene being mutated beyond repair? You can recombine it, but it still doesn't work.For an example, human GULO gene. ALL humans have this gene mutated so it doesn't work. How teh hell is recombination going to repair it? Guess what? IT'S NOT! It's stays dead! And it's passed on to every single offspring!

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It's a simple question. Being CSI is having more bits of information than the bound. How is that measured in bits ? Why would you ever need more than one ?

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Oh, I don't know. Maybe because we want to know how much CSI is there in a human genome and in some other genome. If they are different size, than there are different amounts of information. So we have to measure them in different amount of bits.

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If it's not in the specification his calculation of the probability can't use it.

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Than where is it?

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And do you really think that log2-P(D*) is 50 proteins ?

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It's actually P(T|H) in the new paper which would correspond to P(D*|H) in TDI.
Which, let me remind you, you agreed that these two are the same few posts ago!

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And that is what is wrong. There is no such thing as a genetic block which is immune from recombination. It sounds like you don't know what genetic linkage really is, it is no universal law producing indivisible genetic blocks, it is a statistical reflection of the distance between discrete genetic loci.

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These discrete loci could even occur within one gene. To state baldly that genes cannot undergo recombination Intragenically is simply to ignore the molecular biology in favour of your own fantasy.

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The fact that you wilfully ignore the reality of crossing-over naturally lead you to continue being wrong when you talk about natural selection.

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Once more. I never said that genes do not undergo recombination. Only you keep saying that I claimed so. Yes they do undergo recombination. But take a look at this.

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We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations.

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Just a moment...In other words, what this article claims is that there are recombinatorial hotspots, and cold spots. Some parts of the genome get constantly recombined, others do not. So you can't just invoke recombination on every single gene, to be recombined with every other single gene. Because there is no evidence that such a thing ever happened.

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Yes, of course it is organisms that survive and pass on their genetic material, but they don't pass it all on and the allelic complements get rearranged by meiosis.

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Again, you miss the point. We are talking about natural selection, and what natural selection evaluates befre it let's it get passed on. Does it evaluate every single gene, or genome? Obviously it does so with the genome, not the gene.And the second point you missed is, that there is evidence that soem regions neevr got recombined. So you can't simply invoke recombination as a mechanism that would get rid of all mutations.

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It is this rearrangement which allows the breaking of linkage between alleles not genes and can allow us to consider the gene an appropriate level of selection.

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If all genes got rearranged than that would still not be true. Because individual genes are not what gets evaluated by antural selection.

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Obviously the genome isn't since the whole genome is never passed on,

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Again, please stop missing the point. It doesn't matter what gets passed on. What matters is what gets evaluated.

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your contention that a beneficial mutation must carry with it every deleterious mutation in its originating genome just flies in the face of so many basic principles of genetics it is hard to know where to begin.

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Like what? Name one.

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Um, for someone who likes to whine about being misrepresentied you seem to be doing a bang up job here yourself. The point is that selection is a statistical phenomenon, by breaking linkages between discrete allele loci mechanisms such as recombination allow for the alleles to be selected more independently.

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Fine I agree with that.

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No one other than you is positing any mechanism in the cell picking out the best genes. What I am describing is that within a population the various rounds of recombination will lead to a dissociation of particular genetic allelic combinations, which will be proportional to their linkage but still provides the possibility of even the most closely linked loci being seperated. Over time this means that selection will tend to lead a favourable allele to increase in proportion.

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I more or less agree. But the question is, what do you get out of it? What do you get over time by such a mechanism. Let's say you have a single cell 3.6 billion years ago. And that mechanism went on from that time 'till today. What do you suppose we are going to get with it?

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No one is denying the existence of deleterious hitchiking residues, there is plenty of genetic evidence for them although since you don't seem to accept gentic evidence, questioning as you do the idea of sequence conservation between mammalian genomes, I guess you must just be assuming this based on common sense since you deny the actual scientific basis which has allowed those determinations to be made.

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I accept genetic evidence. What I do nto accept is assumptions presented as evidence.Please explain the logic between mammalian conservation of genes. I would really like to hear it. You do understand that you first have to assume that all mammals were once one single species to be able to do that? Yet you have ZERO evidence that that was ever the case, or that it is even possible for such a thing to be true.

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Sorry about the mixup on the 5% thing, I was talking about the ENCODE data, which is what you claimed you were talking about. It turns out that in fact you were talking about a part of the review you cite which in fact had nothing to do with ENCODE. I think this rather supports my contention that you don't know what ENCODE did.

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Yes, so just becasue they mention the word "ENCODE" every few lines doesn't mean that they are actually talking about the ENCODE Project is, or what it did. Than what were they talking about? The Flintstones?

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What you are ascribing to ENCODE is research that has been ongoing for decades, the review itself discusses how Jaques Monod in the 60's was disrupting the naive 'one gene == one trait' conception. That doesn't make the idea of a gene being the unit of selection erroneous, although myself I think the nucleotide might be a better choice since it is a truly discrete genetic unit, it just shows that the historical conception of what constitutes a gene was erroneous.

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Yes, they mentioned him also. I never argued that they didn't. What I argued is that the ENCODE Project found out that the classical view of genes is obsolete. Which is what the article claims.

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The classical view of a gene as a discrete element in the genome has been shaken by ENCODE

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The ENCODE consortium recently completed its characterization of 1% of the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The ENCODE Project Consortium 2007). This project represents a major milestone in the characterization of the human genome, and the current findings show a striking picture of complex molecular activity. While the landmark human genome sequencing surprised many with the small number (relative to simpler organisms) of protein-coding genes that sequence annotators could identify (∼21,000, according to the latest estimate [see Ensembl genome browser 107]), ENCODE highlighted the number and complexity of the RNA transcripts that the genome produces. In this regard, ENCODE has changed our view of what is a gene considerably more than the sequencing of the Haemophilus influenza and human genomes did (Fleischmann et al. 1995; Lander et al. 2001; Venter et al. 2001). The discrepancy between our previous protein-centric view of the gene and one that is revealed by the extensive transcriptional activity of the genome prompts us to reconsider now what a gene is. Here, we review how the concept of the gene has changed over the past century, summarize the current thinking based on the latest ENCODE findings, and propose a new updated gene definition that takes these findings into account.

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This is the quote from the article. Are you still going to deny the mentioned ENCODE, and claimed that ENCODE changed our views on genes?

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You say you don't care about the distinction the ENCODE project highlight between biochemical function, a region of DNA being transcribed, and biological function/effect. But by this standard it is trivially easy to show the generation of novel biochemical function in the genome, many trx factor binding sites and transcription start sites are comparatively simple to create by chance and certainly may be moved around very easily.

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Show me some examples.

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All you are doing by talking about pervasive neutral evolution is agreeing that in fact most of the genome serves no biological function even if it is biochemically functional. I though the more common ID position was the exact opposite of that, that the majority of the genome does perform a neccessary function but that we just don't understand it yet.

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What I'm claiming is that positive evolution is almost non-existant. Majority of what exists is neutral selection. But that doesn't mean the majority of genome is non-functional. It' ssimply means that darwinism is false.

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Here you have confused weight for number, if I have 1 block of granite wieghing a tonne and you have 800 feathers weighing only a few kilogrammes then clearly my block outweighs your feathers for all that they outnumber it. It isn't the number but the effect that is important. Of course deleterious mutations are hitchhiking, and some are just being fixed by drift, it is the size of the effect of these mutations that is important.

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I totally agree, I never said otherwise. And the comparison between feathers and granite was unneccessary since I never claimed otherwise.The point is that beneficial mutations don't have such a strong effect, and are almost always drowned by the noise of non-genetic selective traits.And the other point is, that if we say that on average beneficial mutations will have the same strenght as deleterious mutations, than by simple shere numbers, they will overcome the deleterious ones.And the third point is, that they are more numerous however strong they are. Actually the less effect they have the worse it gets. Because than there is more chance they will get passed on, becasue they will be in the range of slightly neutral mutations that are invisible to natural selection.

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I think your problem is that you say whatever is expedient at the time. Here's you saying that common descent is impossible in Message 1038:

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You misunderstood me. I said that the notion of "design without a designer" is impossible, not common descent. I simply said that evolution is built on common descent and as such is tryng to be an explanation for how design comes about withoput a designer.

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So, reinterpreting the above in light of your reemphasis that you have no problem with common descent, this is apparently saying that ID states that evolution's removal of the designer from the process is impossible.

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I would say it a bit differently, that evolution is a theory that explains the evidence through a process of descent with modification and natural selection, while ID is a theory that explains the evidence through the intervention of a designer. You're in effect claiming that a theory that doesn't include a designer is impossible, so if ID has evidence of the designer then this is the time to introduce it, but what we usually hear from IDists is that we cannot know the identity of the designer or how he designed.

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ID is simply the science of design detection, and as such does not deal with the designer or it's mechanisms.Evolution on the other hand is trying to explain design without the designer. Which it fails to do.

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Yes, we know. And what happens if you project this requirement back in time? Let's say that life on Earth was created by an intelligence. Where did that intelligence come from? Maybe, following Shermer's example from the November debate, that intelligence came from Antares (a nearby star). Maybe intelligent aliens from Antares came to Earth a few billion years ago and placed the first life on this planet.

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But since there must have been an intelligence at the start, Antarean life must also have come from an intelligence, so where did the Antarean life come from? A planet orbitting a star in the Andromeda galaxy maybe? And where did that life come from? And the life before that and before that?

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After a while we're back to the plasma of the Big Bang before there were atoms, and there was no life anywhere to create the next life. So where did that first life in the universe come from?

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Your question is useless. It's totally irrelevant where the designer came from. The question is where the designed object came from, not where the designer came from.I'm not sayign that we should not ask where the designer came from. i'ms imply saying that it's irrelevant to ID. Imagine if you were walking down the street and found a pen. A guy asks you how did it come about. You say it was designed. But the guy say that it's not a good answer becaue than you would have to explain where the designer came from.That's totally wrong. Because you do not know where the designer came from, yet your answer that the pen was designed is true. It's true regardless of you knowing where the designer came from, or how. No infinite regress happened, and the pen is indeed designed.Basicly by asking the next question you would destroy science. You do not need to have an explanation for an explanation. When a first person proposed an atom, did he also have to propose the existance of the nucleous? Did he also have to propose the existance of protons, neutrons and electrons? Did he also have to propose quarks? You can go to infinity like that an never come to an end.Basicly, your criticism is invalid.

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At this point most IDists concede that they believe the designer is God, and at that point they've definitely left the realm of anything supported by scientific evidence, although they'd already done that when they posited a designer for life on Earth in the first place.

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You are wrong on both accounts here.Saying that God or anything else designed the universe is not unscientific. Simply becasue if the universe didn't create itself, and it's not eternal, it had to be caused by something outside it. So an outside cause is not an assumption but a logical necessity.Second part where you went wrong is saying that positing a designer for life is unscientific. Why would it be? Why is positing design in other branches of science scientific, but not biology?

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All four are predictions made after the fact and aren't predictions at all, plus all four are consistent with evolution. Does ID make any predictions that are different from evolution?

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1.) It was not known that molecular machines were irreducibly complex before Behe said it. The same goes for all other predictions.2.) Again, being consistent with evolution does not mean that any other theory is any less valid. General relativity and Newtonia gravity are consistent in some parts. That doesn't make any one of them wrong.3.) Evolution is a very, very broad term. You have to tell me what kind of evolution is consistent with these predictions. Please define the word "evolution" you are using here.

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To be more clear concerning point 1, evolution is consistent with specification and complexity, since evolutionary solutions must by necessity be very specific to the requirements of the environment and since competition generates increasing complexity in a way analogous to escalating arms races,

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So in other words, you are saying that evolution, again, I don't know what you mean by evolution here, generates CSI. Fine. Can you show me where has that been demonstrated?

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but evolution is not consistent with the irreducible complexity of Behe for which there is no evidence.

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The bacterial flagellum is a nice example.

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You mean evidence like orthologous ERV's, shared pseudogenes, etc.? We have that evidence in spades. The genetic evidence is conclusive.

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Well fine. Show me some examples. Listing them is not showing an example. Explain how are they evidence for CD:

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Ignoring the evidence is not helping you. We do observe a nested hierarchy. Yes, there is a little noise as would be expected from homoplasies and reverse mutations, but the overwhelming signal is a nested hierarchy.

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Let's see...

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For a long time the holy grail was to build a tree of life, says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. We have no evidence at all that the tree of life is a reality, says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

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Which part of "Many biologists now argue that the tree concept is obsolete and needs to be discarded" do you not understand? Do you have problem reading English? The tree concept is dead. It doesn't exist anymore. If you have anything to show against this conclusion, if you can show me the evidence I'm ignoring, than show them now.

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A bush is a nested hierarchy.

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No. A bush is an exact opposite. Branches is what was supposed to be seen, not a bush.

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They agree with me. The nested hierarchy is unambiguous.

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You don't get it. You are confusing interpretations and assumptions with evidence and facts.It is a fact that a tree of life is a bush, and not a branching tree. It is an observable fact. Meaning that you can't construct a unambiguous nested hierarchy. Those are facts.Assumptions and interpretations of those facts is that regardless of the facts, that chimps are our relatives. There is no evidence for that. That is an interpretation and an assumption.And no, they do not agree with you on the nested hierarchy part. They agree with you that humans and chimps are related, but in spite of there not being a nested hierarchy, but a bush.

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Why aren't airbags found in a single lineage of cars?

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Why aren't eyes found in a single lineage of animals?

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Why don't cars fall into a nested hierarhcy?

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Why don't all animals?

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Feathers are found in a single lineage of vertebrates.

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Yet they evolved independently few times. So what does that tell you?

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Powder down has evolved independently in several taxa and can be found in down as well as pennaceous feathers. They may be scattered in plumage in the pigeons and parrots or in localized patches on the breast, belly or flanks as in herons and frogmouths.

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Feather - Wikipedia

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Three middle ear bones is found in a single lineage of vertebrates.

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And it would seem they also evolved independently few times?

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Evidence that the angular (homologous with the mammalian ectotympanic) and the articular and prearticular (homologous with the mammalian malleus) bones retained attachment to the lower jaw in a basal monotreme indicates that the definitive mammalian middle ear evolved independently in living monotremes and therians (marsupials and placentals).

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Just a moment...

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So why aren't airbags found in a single lineage of cars, both morphologically and chronologically?

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Because they weren't designed that way.

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Why are there cars with jet engines? If cars can have jet engines why can't bats have feathers?

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Who said they can't? They simply don't.

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Why do human constructs consistently fail to produce a single nested hierarchy?

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Oh really? Since when?

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A nested hierarchy or inclusion hierarchy is a hierarchical ordering of nested sets.[5] The concept of nesting is exemplified in Russian matryoshka dolls. Each doll is encompassed by another doll, all the way to the outer doll. The outer doll holds all of the inner dolls, the next outer doll holds all the remaining inner dolls, and so on. Matryoshkas represent a nested hierarchy where each level contains only one object, i.e., there is only one of each size of doll; a generalized nested hierarchy allows for multiple objects within levels but with each object having only one parent at each level.

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Hierarchy - Wikipedia

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You tell me. Why can't a designer change the architecture at will? Why a nested hierarchy?

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He can. There is no nested hierarchy. Even if tehre was, what would that mean?

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Do you have any siblings? If so, the features you share are due to common descent. It really isn't that hard to figure out.

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I'm talking about universal common descent. It's very different than simple common descent. Because with universal common descent we are talking about species that were never known to interbreed, producing offspring. Is that even possible?

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At the same time, can you show how mutations that occur in one species can spread to another species? It doesn't happen in metazoans. This produces a nested hierarchy.

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What?

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You seem to be really mixed up here. A nested hierarchy can not be built for a bat with feathers. Can't be done. A nested hierarchy is clearly falsifiable.

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Why not? Explain why.

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A flagellum is just one possible solution for motility, and those odds are only for a flagellum like the one that appeared. I'm sorry, but your probabilities are built on baseless assertions.

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Listen, you don't know what you're talking about. The number 10^20 has nothing to do with the flagellum. It's the complexity of the specification. Please don't go into this, it's out ov your league.

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I already spelled it out for you with the hemoglobin S example. It is plain as day. You say it is stupid, and yet that is exactly what the data indicates. The single nucleotide change in hemoglobin S has been selected through positive malarial resistance selection (positive) and sickle cell anemia selection (negative selection).

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You miss the point. The whole organism was selected that contained that mutation. Not the mutation itself. The whole organism was evaluated. Do you think that mutation would be passed on if the organism was sterile?

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So ID is not trying to determine why bacteria have flagella? Really? So I guess we can say that ID explains nothing about biology?

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It simply explains the source of design.

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Evolution deals with CHANGE in life, not the origin thereof. Abiogenesis deals with the origin of life.

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No kidding Einstein, so if evolution doesn't deal with the origin of life and just deals with the development of life, why should ID deal with anything besides detection of design?

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My example demonstrated that the specificity of an enzyme changed due to random mutations.

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No. What your paper showed is that it changed due to random mutations and intelligent selection. Which is not equal to random mutations being operated on by natural selection.

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The authors simply created an environment where such mutants would be detectable using their methodologies. That's it.

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And they directed and selected which individuals get to reproduce.

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This is no different than penicillin intelligently selecting for resistance mutations in bacteria. Is penicillin an intelligent agent?

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Penicilin is not intelligent, and it's not selecting anything. It's simply binding becasue it's chemical properties.

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If you could be so kind, could you give the link for that paper again.

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http://hal.archives-ouvertes.fr/...53/PDF/ajp-jp1v5p1501.pdf

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Pretty much the same thing that is stopping all of the air molecules in your room from suddenly all being in one half of the room.

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But the fact is that youa re claiming that evolution did converge on a specific sequence once. So why not once again? So it's too improbable now? What, once is probable yet two times it's too much?

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I would strenuously object to the words "recruited for its role", but rather something closer to "given the role".

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My reading of the site leads me to believe that they dont have the "Tree of Life" properly defined in their heads, especially since their own words regarding Pax 6 would seem to imply common ancestry.

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But it's not people from Ideacenter that are saying that the Tree of Life concept is obsolete. It's other scientists.

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No - this just means that that particular sort of result is heavily favored when it randomly comes up.

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Being favored means being directed toward something, and from everything else. Which would imply design, and not randomness.

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No, no, no. You cant have your cake and not have your cake. All the research shows is that there are ZILLIONS of ways biology evolves. Fascinating.

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No, it doesn't SHOW that. you are just ASSUMING that.Can you tell teh difference? They ahve actually SHOWN that all tehse genes perform different and similar functions. Yet you are the one who is ASSUMING it's all evolved.And so what, let's even say it is evolved. That would just mean CD is unfalsifiable. Because you have every pattern covered. There is no falsifiable pattern.

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Just because they haven't gone back far enough in the "Bush" of life doesn't mean they've falsified it.

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It's because it's unfalsifiable.

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BTW Bush Of Life is probably a better way to describe it rather than insisting on only 2 branchings at a time.

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True. But that means there is no such a thing as a nested hierarchy.

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Yeah - it's way more complex than the untrained peanut gallery observers can imagine. There lots of systems that have "except when it doesn't" clauses that - upon careful educated scrutiny - turn out to be reasonable conclusions based the data to date.

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No surprises here.

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What I see in this site is an unbelievable amount of smugness on the authors. You can almost see them rubbing their hands and nodding to each other with grins "Oh - we got them now!" LOL

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They haven't made a point at all.

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Regardless of what you think of the author. Hi did nothing more than quote scientists who claim that the tree of life concept is obsolete. If that's not a point, I don't know what is...

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Hi Smooth Operator.

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'sup?

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I can, whether you will consider understanding it, or not, is the bigger question.

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Simply put, they died.

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As your great great ancestors are no longer able to reproduce because they are dead, so too are all organisms that have died.

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In this case, millions of years ago, including all the other dead ancestors of the living populations of bears and alligators.

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It's a simple concept. Each generation reproduces while that generation lives, not before nor after.

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Evolution is the change in proportion of hereditary traits in breeding populations from generation to generation in response to ecological opportunity.

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Okay, but you see, this doesn't really answer my question. You claimed that a species reproduced among itself. Now it can't. If that species is still alive. Not the old individuals, but the new ones, what keeps them from reproducing?

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ps - it's phenotype ...

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For another very simple reason: there is no (natural) mechanism that would cause this to happen. You don't need to worry about stopping something that will never start.

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There is no way for natural selection to operate, or any other mechanism known to biology and the real world, to draw the genes closer to similarity.

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DNA doesn't change because you want it to, the change is mostly random, and the results are then filtered by selection processes to adapt the organism to the ecology it inhabits.

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Both organisms are adapted to their ecology and don't need to turn into the other to be adapted to their ecology.

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But can it not happen by chance? If random mutations are random, can it not happen that while mutations are mutating the genome, natural selection will select those genes which are the best and in such a way to make 2 species identical? If it can happen for a phenotype, why not for a genotype? Are you saying there is such a mechanism that drives phenotpyes to similarity, yet tehre is no such mechanism for genotype?

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Because they found (and continue to find) skulls with this opening and arch belonging to therapsids and therapsid descendants, but not in ancestral species or in other hereditary lineages. In later descendants the opening closes, leaving the arch as a derived new feature in all descendant species. You have this arch, as do bears.

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For clarity, the arch "giving a superior bite" is present in the therapsids and descendants. Descendants can take advantage of opportunities to improve the jaw further, but they don't have to: not all descendants of therapsids evolved into cyconodonts.

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So you are claiming that they found more fossils, right? Okay, so tell me, how do you know that those fossils indicate a progression? How do you know those fossils are related? And how do you know, that they weren't always like that?

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By following the evidence of derived and inherited ancestral traits.

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How can you claim that two fossils that are actually related?

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The whole pattern of the fossils show many aspects that are not altered from ancestral forms (ancestral traits), and some that are undergoing transitions that become more derived over time (derived traits). The synapsid arch is a case in point: it appears in one species (derived), and then you see it inherited (ancestral) in descendant species with continued development (further derived) as the arch becomes more developed and the skull closes back together under the arch. This occurs through the evolution in many species, that each inherit their pattern/s of derived and ancestral traits as they evolve generation by generation.

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Aren't you first assuming that those fossils are actually related? Could it not also be the case that those fossils are species that always lokked like that? Maybe they are all simply distinct species that always lokked like that.

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See Derive - Wikipedia
for what is meant by "derived": "In phylogenetics, a trait is derived if it is present in an organism, but was absent in the last common ancestor of the group being considered. "

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An ancestral trait is a trait that is shared between the species and an ancestral species (common ancestor).

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When a fossil is >90% similar to an ancestral species with <10% derived (evolved) from the remaining ancestral features, as we see with the synapsid arch, then hereditary lineage is the most logical explanation. This is no different than looking at species that are all similar fossils and concluding that they are all the same species.

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Oh, I see it now! Yeah, I get it. You are basing your conclusions of relatednes on similarity.Well, yeah you see that's the problem. Similarity is not evidence that two species were related. It's evidence that they are similar.Similarity is not evidence for anything but similarity.You see, two cars are also similar. Yet nobody would claim that their similarity is due to common descent. But common design. So why would you claim that similarity in animals is due to common descent?

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When it is between an ancestral species and a descendant species in the development of the derived traits.

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See Transitional fossil - Wikipedia
or Page not found

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Let me first note that you based the idea of relatednes on a false premisse of similarity. Therefore an intermediate can not be known because you don't know any fossil is related.Second, could it not be true that this intermediate fossil is just a separate species that always looked like that?

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Again, it is a simple concept: species evolve, there is no species alive today that is not going through changes in the proportions of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Thus population A evolves into population B as the old members die and new members are born, and population B evolves into population C as the new members age, older ones die, and new ones are born: the members of population B are intermediate between population A and population C. Now introduce increasing numbers of generations between A and B and between B and C and you still have intermediate forms in population B that have ancestral traits in common with the ancestral traits in population A and derived traits in common with some of the derived traits in population C.

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I agree with this. This is a fact, and a common sensse conclusion. But what I disagree with is when you want to extrapolate this interpretation on polar bears and horses without any evidence. Since you ahve no evidence that either a.) horses and polar bears ever reproduced, or b.) they were one one species that reproduced, you can't use this interpretation.

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Oh dear, you've made the unfounded assumption that you are a reasonable person. The vast evidence of this thread and the one about the earth being fixed with the sun orbiting around it, speak volumes to your not being a reasonable person, but an unreasonable and obstinate person. I expect you will now demonstrate how unreasonable and obstinate you are.

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I'm sorry but you just presented a drawing. What else was there?

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The evidence is available in the information already presented, evidence that any reasonable person can take as a starting point and investigate further if they want to. Denying that this evidence exists is not being reasonable, and I'm not about to spend a lot more time on someone that I don't consider willing to confront the evidence realistically.

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I'm sorry, but it seems you are confusing evidence with assumptions. Let me explain the differnece.EVIDENCE - Observable facts which can be seen and studied.ASSUMPTION - ideas about things and objects that are not known to be true.You see, by saying that dogs reproduce and certain breeds of dogs are intermediate between a breed A and a breed B is a fact. It's an observable fact. Dogs do reproduce, they do change, and they do produce different breeds. This is evidence for their change over time. Call it evolution if you want.But, where you go painfully wrong. Oh so terribly wrong. Is when you apply this explanation for change over time, to species that were NEVER, and I do mean NEVER, EVER know, or have been seen to reproduce. You can NOT, say that the same applies to polar bears and horses becasue you do not know that they were ever able to reproduce. You simply ASSUME! I repeat, you simply ASSUME that they once could have reproduced, them being one species.But that's just it. It's a pipe dream. An illusion. An evolutionary just so story. With no evidence to back it up.

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Because there are no fossils of existing species in the fossil record at the time of the reptilomorphs, while there are fossils that show their evolution from the ancestral forms from reptilomorphs to today

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Wow, that's a great logic.If I go to the store and see they have no bread, it means they neevr had any bread.If I go to a school and see it's empty, it means nobody was ever there.If I go to my room and find no computer there, it means it was never there.There is simply no fossilesed animals of that kind at that period of time. That doesn't mean they were not there. Does not finding a Coelacanth prior to 1938 mean it's extinct? No it doesn't. It simply means we didn't find it before.

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Because there is evidence that shows the evolution pattern given and there is no evidence that shows your pattern.

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What patterns are those?

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I said that observing a bear and an alligator reproduce viable offspring would tend to invalidate common descent, not that any hybrid between closely related species would invalidate it.

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Tend to? Tend to!? Wait... tend to? Listen, something is eitehr falsifiable, or it isn't. Which one is it with CD, is it falsifiable, or not?

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So they are interbreeding between members of the same subfamily, not between organisms from different class levels of ancestry.

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What's teh difference? Why is one better than the other? Why does one falsify CD on other does not?

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There is much much more genetic difference between bears and alligators than there is between cows and bison.

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Where's the line? Where is the live where CD get's falsified?

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They are not much more different that the hybrids of horse and donkey and zebra, some of which are fertile.

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Interfertility does not necessarily cease between sibling species if there is no opportunity to interbreed and no selection pressure to change.

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The cow and bison did naturally interbreed, once they were introduced to the same area, but not all of the offspring were fertile, and it took a while for humans to develop a complete separate breed.

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There is also the "cama" - part camel part llama (only 3 so far, don't know if they are fertile).

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Great. The point remains that you don't know what a species is. A species should be a population that can't reproduce. Yet we have instances of different not only species but genera that reproduce. That just means that your whole idea of taxonomy is flawed. You can't consistently group animals into groups. So why would you thing you can group fossils into related species if you can't even with live animals?

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So we see that evolution doesn't necessarily change the ability to breed between species that do not normally come into contact.

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Yes, which makes the ieda of evolution totally useless. Sometimes id does do something, the other times by doing the same thing it doesn't. That's unfalsifiable.

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There have also been no successful attempts to mate cows and camels even though they have coexisted for thousands of years and belong to the same order level above family (but which excludes horses and bears). There have been no successful attempts to mate species at higher\older levels of ancestry, and the common ancestor level of alligator and bear is significantly higher\older than these examples.

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Again, great, I'm happy for you. This is all irrelevant information. The point remains you can't reliably group animals and infer their ancestry while they are alive. And than to turn and say you can do it for dead bones you find in teh ground is laughable to the highest extreme!

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If you don't know why you did it, why should I know ? And it still doesn't change the fact that you DID argue for it, and that is why this bit off the discussion has gone on so long.

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Who ever said I didn't know? What I actually said, is that I did know, and I told you that I did know, and I told you why I said it.

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But I did say it. And I told you why I said it. So why again are we talking about it?

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EvC Forum: What exactly is ID?See? This is my quote. I said it few posts ago. I never claimed that I didn't say it, or that I didn't know why I said it. I told you that I said it and I knew why I said it.

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This misses the point that we were talking about individual protein molecules, not genes. And in fact the version using 1,000,000 molecules need have no more genes than the version using 50 since you insist that each uses the same set of proteins.

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Why are you switching the discussion to DNA now? From the start 'till now, we were talking about proteins not DNA. DNA is irrelevant. Besides, there is a differnece in DNA if it's going to code for 50 proteins or 1.000.000 proteins.Anyway, that's irrelevant. The point is to get those proteins in the same place at the same time in the exact configuration. Which becomes more improbable with the increase of proteins.

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Even using Dembski's idiosyncrative definition of complexity the relation is not an inverse proportionality (the complexity is proportional to the logarithm of the inverse probability). Using a more normal understanding of complexity your assertion is even more laughable.

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1.) Tell me the difference between Dembski's definition of complexity and the "normal" definition.2.) You contradict yourself in one single statement. Saying that: "relation is not an inverse proportionality" and that right after that saying: "the complexity is proportional to the logarithm of the inverse probability" is a contradiction.A proportional relation between complexity and inverese probability is the inverse relation between complexity and brobability.So if you agree that complexity is proportiional to inverse probability, than you also agree with what I said which is that complexity is inversely proportional to probability. WHich are two identical definitions.Basicly what I'm saying is that you are confused.

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But if you won't communicate unless I agree with your silly assertion, all I can say is goodbye and good riddance.

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Please don't misrepresent me. It's obvious that you are confused. So let me explain myself in more detailI never said that I do not want to communicate with you unless you agree with me. A debate precisely because people do not agree. So it's fine if you don't agree with me. What I actually said is that if you attackl logic itslef, you are not arguing with me anymore, you are arguing with logic. Se your debate with me is over, youa re now debating logic itself. Which is totally inappropriate. Why is that so? Well, please do let me explain.You see, in order to have a debate we have got to agree on something. And those are basicl rules we are going to follow while debating. If we are going to have a scientific debate, than we should agree that we are going to follow the rules of science. Those are not under the debate, otehr ideas within science are, but not the base of science itself. Yet, you are doing just that. You are attacking the base of how we are doing science. Like I said, this is inappropriate at this moment. That's not the issue at hand.What I have problem with are 2 things. First your unwillingness to accept teh principle of insufficient reason. Which is not something that is under debate, but a rule we should follow. If you attack it, you are not debating me. You are not debating Dembski. You are than debating the whole statistical community. Which is not what we are supposed to do.Now don't get me wrong, I'm all for turning over methods that do not work. I like to do so myself. But everything has it's time and place. And just to show you that I'm all for it, I'll give you my example of criticising base rules of science.For an example. I criticize maethodological naturalism. Which is fine to do. Why? Because it's not a fine method to be adhered to while doing science. Methodological naturalism claims that we should only include materialistic causes while considering causes for events we are investigating. This is clearly false, since we do not know that matter is all there is. Since we do not know that, there is no reason to artificially impose borders on what we can, and can't use as an explanation. We should be opet to all explanation.This is a valid criticism. Because in order to limit a possible source of explanations, you first have to know that something else is not responsible for the event in question. If you don't know it's not responsible, you can't say that it can't be used as an explanation.Now, you see, your are not doing the same thing. In order to give a valid criticism of a philosophical viewpoint, like a materialistic one, you have to either of 2 things.1.) Either show that what the method is claiming to do, can not do.
2.) Or show that you have a better method.Which is what I did. Simply by saying that ID provides an intelligent cause and increases the amount of answers we have while doing science, is presenting a better method than methodological naturalism. I provided a better method, with more possible solutions.What you did, with the principle of insufficient reason is the following. Yous imply said that there could be soem unknown factors so we can't use that matehod. Basicly what you are saying is that it's not perfect. Claiming that the method does not do what it's supposed to. This is point 1 of those two I mentioned. This is a false criticism. Because the method did not claim to be perfect in the first place. Statistics are about approximation. And that is what the method claims to do - it approximates.Second, you didn't say that you have a better method, and you didn't provide a better one. So as far as I can see, we are supposed to use this method because you have nothing to replace it. It's not perfect, it's not claiming to be, but it works. And that's why we are sticking with it.Let me give you a generalized example of teh use of this method, that I'm sure you'll agree with.Looking at the Sun, we see it goes around the Earth every 24 hours. We know it did so every single day for past few thousand years at least. We know that because we saw it. It's a fact. And from this fact, we produced a description of natural laws that claim that Sun is going to continue doing so in the future. You see now, this is called an inference. This is a part of the scientific reasoning. We infer things from past events. We no not know for sure the Sun will rise up. Maybe, tomorrow it will stop in the middle of the day, and start jumping up and down for 5 minutes, and that keep going as nothign had happened. And will do so for another few thousand years.So you see, in this case, we would rewrite our laws and we would than for a law of motion of the Sun that claims that Sun goes around the Earth for few thousand of years, and that starts jumping up and down for 5 minutes and than continues for another few thousand years to orbit the Earth.Yes, we could be wrong. Sun could do exactly that tommorow. But tell me, is it reasonable to thik that it's going to? IS it reasonable that tommorow is going to do something else? No it's not. That is why we say that in absence of prior knowledge we use unifom probability. And in this case, we infer, we do not know for sure, but we infer that the Sun is going to do the same thing tommorw, as it has been doing for at lease few thousands of years. But a much higher probability is that tommorow is not going to be different that the last few thousands of years. So the beast reasonable thing to infer is that it's not going to be any different. Why do we do this? Because it's the best method we have. And it works. So untill we have a better method, we arte sticking with this one. It's not perfect. It's not supposed to be. It's good, it works and that's all we want.I'm sure that you awould agree with this inference. And what bugs me, is when you claimed that this same inference can not be used which calculating the difference in probability between 50 and 1.000.000 proteins. If you with one use of the method, I'm sure you have to agree with the other instance. If not, than those are double standards. Which are not something we want.The second thign where you went wrong, is when you not only stopped debating me, not only stopped debating Dembski, not only stopped debating the whole statistical community, but you attacked logic itself. This, is not what we are supposed to do in a debate. We must agree that we are going to use the same logic. Science presupposes logic. You can't do science without logic. And when you say that probability is nto inversely proportional to complexity, you are attacking logic itself.Let me try to show you where you went wrong.Let's say that our targetwhile flipping coins is all heads. Heads are marked with H, tails with T. So basicly this is what we have. As you can clearly see, as the number of coins increase, the number of sides increase. The complexity also increases. Complexity in this case are all the sides that landed. The probability decreases. Therefore it's inversely proportional to complexity.1 coin - 2 sides, complexity = 1, probability = 1/2
2 coins - 4 sides, complexity = 2, probability = 1/4
3 coins - 6 sides, complexity = 3, probability = 1/8
4 coins - 8 sides, complexity = 4, probability = 1/16Here we have all possible patterns we can have. This here list shows you what ptterns certain complexities can express. 1 coin has a complexity of 1, it's either H or T. Two coins have a complexity of 2, they express either HH, HT, TH or TT. And so on...1 coin - 2 sides - H
2 coins - 4 sides - HH, HT, TH, TT
3 coins - 6 sides - HHH, HHT, HTH, HTT, THH, THT, TTH, TTT
4 coins - 8 sides - HHHH, HHHT, HHTH, HHTT, HTHH, HTHT, HTTH, HTTT, THHH, THHT, THTH, THTT, TTHH, TTHT,
TTTH, TTTTThis here is the inversely proporitional relationship between complexity and probability. I think that you would agree that when the complexity is increasing, the probability is decreasing.1 - 1/2
2 - 1/4
3 - 1/8
4 - 1/16And this is what you denied for the last few posts. You CAN NOT deny this. this is basic logic. Science can't work without basic logic. It presupposes logic. So when you disagree with something so basic as this. You are not arguing agains me, Dembski, thw hole of statistical community, but you are arguing agains logic itslef. And I would honestly pay to see you win that. In other words, it can't be done.So please, don't claim I said I won't communicate unless you agree with me. I simply said that our debate is over, and that you are now debating logic, not me. I'm still here, we can go on if you like. I never said I don't want to. But please be reasonable.

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Hi Smooth Operator,

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Yo...

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Thanks for confirming that you are simply unreasonable when it comes to understanding reality. I'll just hit the high points.

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Wait, what? i'm unreasonable? Why?

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It isn't. The descendants have become different species. That's what happens over long periods of time, such as the span of time between the common ancestor between alligators and bears to the present.

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But this is the problem. You dont' know that. You assume that. I know that it was supposed to have happened a long time ago, so we have no video tape showing us what happened. I know that. So I'm not asking you for that. But what I am asking you for is evidence that such things as aligators and bears being one speices and than splitting off. What's the evidence that this is even possible? What is teh evidence today, from which we can extrapolate in the past? Simply having assumptions that it can and it did happen is not evidnece. I need observable evidence.

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Nothing, but what they reproduce are their current species, not the original species. All the individuals in the population have evolved into a different species that continues to be a breeding population, but it is not the same as the ancestor population.

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Okay, so how do you know this is what happeend with polar bears and horses?

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Curiously, your opinion is completely unable to affect reality in any way.

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Excuse me, but no. I can't just let you go on this one. I was not unreasonable. I didn't express my opinion. I stated a FACT. A pure logical FACT. If you disagree with it, than fine, you should say why it's invalid, but don't say that logical facts are my opinion. They surely are not. It's like saying that 1+1=2 is my opinion. It's not, it's a fact.

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Below is an example of the type of evidence used by reasonable people to come to reasonable conclusions about reality:

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Let me please dissect your whole post and show you how you went from a fact to an assumption. Maybe you can't notice it when you are doing these leaps, but I'll show you when they happen.

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Here, not only do we see that the ancestral population had no trouble interbreeding among their members, and that the daughter species at the top are now reproductively isolated, but we also see the level by level transition from the ancestral forms to the derived forms.

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We also see that each level reproduces, but that at the top there are no more Pelycodus ralstoni being produced by that reproduction. This in only 5 million years, compared to the hundreds of million years between the common ancestor to bears and alligators and these animals today.

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This is your full quote. Let me now start slicing it up, and we'll ses where we end up. Okay?But before we do so, please do let me remind you what's the difference between evidence and assumptions.EVIDENCE - Observable facts which can be seen and studied.ASSUMPTION - ideas about things and objects that are not known to be true.

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Here, not only do we see that the ancestral population

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False. You see, you didn't even finish the statement you already made an assumption, and presented it as a fact. You do not know which bone in the ground is the ancestor of any other bone in the ground. This is a fossil bone A. This is a fossil bone B.You can not, I repeat, you CAN NOT, show me that the bone A is ancestral to the bone B. You can not show me that the bone A had ANY offspring. Do you understand that? Are you capable of understanding that? Can your brain process the information that I'm giving you? Can you comprehend the idea that the individual who was composed a long time ago of bone A could possibly have been sterile? Thus having no possibility of having any offspring.So, in short, you don't know that any fossil you find in the ground had any offspring. And you can't point to another fossil and show me that that fossil is it's offspring. You can show me no evidence of that. You can ASSUME, but you can't show me any evidence. And I asked you for evidence, not assumptions.But let's go on now...

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had no trouble interbreeding among their members

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You don't know that. You simply see a bone in the ground. Maybe those individuals all died before any of them reproduced. You are simply assuming that they reproduced. Again, conflating evidence for assumptions.

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and that the daughter species

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Again, false. Daughter species? How do you know they are daughter species? Where is the evidence? Where is the observeble evidence that a bone you found in the grand had any offspring? How do you know those species you are calling daughter species are offspring of those that you are claimng had the offspring? How do you know they are related? Do you know it? Do you have evidence? Or do you simply assuming it.Listen, a picture is not evidence. Bones in the ground themselves are not the evidence. They are facts of bones in the ground. How you interpret them is another thing. But for any interpretation, you need observable evidence.

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at the top are now reproductively isolated

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How do you know they are NOW reproductively isolated? Maybe they always were? Is it possible that they were always reproductively isolated?

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but we also see the level by level transition from the ancestral forms to the derived forms.

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NO! No we do not SEE theat! What's wrong with you! You are imposing that action on the pattern you found!What we SEE is a bunch of bones in the ground! Nothing more! Anything else is an ASSUMPTION without evidence. Claiming that animals on the bottom are ancestors of animals on the top is an ASSUMPTION! A baseless assumption!Now let me give you some facts.You have no obervable evidence that animals on the bottom were not sterile.
You have no obervable evidence that animals on the bottom were had any offspring.
You have no obervable evidence that animals on the top are offspring of the animals on the bottom.
You have no obervable evidence that animals on the top and the animals on the bottom EVER EVEN MET!
You have not evidence that the observed pattern is a pattern of transition from the animals on the bottom to the animals on teh top.
You don't have any evidence that any of those animals even died there!The only facts we have is that we have a bunch of bones in teh ground. And now we can do some scientific extrapolation. Since animals live today. They could ahve lived in the past. They also get buried by dirt and get fossilised. Layers of ground get worked up and down.So the only thing we can infer from this. Is that some animals lived in the past and than died. Before they decomposed they got buried by dirt, and got fossilised. MAyb some died before some later. Maybe those that are on the top died before. You see, layers can get reworked by earthquakes. Maybe some animals of those never even met. And they lived pretty much far away from others. But due to reworking they were found very close. So basicly this is all that we can reasonably infer.And to say that it's reasonable to say that we can actually SHOW, you actually claimed we can SEE, that animals on the bottom are the ancestors of animals on teh top, is pretty much insane. We certainly can't SEE that.

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We also see that each level reproduces

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No, we do not SEE that! Where do you SEE that! Show me the part of the picture where you SEE that!

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but that at the top there are no more Pelycodus ralstoni being produced by that reproduction.

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Maybe becasue they were neevr produced by that reproduction, but by reproduction of other Pelycodus ralstoni?

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This in only 5 million years

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Or 5 minutes of rapid layer deposition due to a catastrophe?

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compared to the hundreds of million years

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Such long time spans actually existed?

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between the common ancestor to bears and alligators and these animals today.

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For which you have no evidence. Simply assumptions.As you can clearly see, yes, you can actually SEE this, you confused assumptions with evidence. You confised ideas that are not known to be true, with observable facts. I asked you for one, you gave me another. When we do such thing, we get pretty wrong results.

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Except that it is much more than simple similarity - more than the similarity between sugar gliders and flying squirrels for instance (that you find curiously compelling) - rather it is based on a preponderance of homological identity. A fossil that is 90% homologically identical to a previous fossil is more than just similar.

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Yes, I agree. A fossils that is more than 90% similar to another is more than just similar. It's 90% similar! But what else is there to say?

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In the above example we see that there are many individuals at one level that could belong to the level above or the level below, and that it is only the ones at the end of the spectrum of change in the direction of the overall trend that lie just outside the parameters of the previous population, but within the parameters of the next. We know that they are related to the rest of their level population, and hence can readily conclude relation to the previous generation.

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1.) Yeah tehy could belong there. What exactly would an animal have to look like if it didn't belong there?2.) What are these parameters that show you a trent of transition?3.) How do we know they are related? Based on tehir similarity? No, we don't, we only know they are similar based on their similarity!4.) But since you can't even show that any single of those animals had any offspirng, or even could have them, you can't coclude that one generation was related to another.

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IMHO, any person who claims that ancestry cannot be logically and rationally inferred from evidence like this is not just smoking ignorance, but holding firmly onto delusion.

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Okay, let me turn this logic on you. Here you go. This is the evolution of frying pans from metal cups. The transition from one to the other is obvious. This is a FACT. They are related becasue they are similar. Our evidence for their relatedness is their similarity. Do you, or do you not agree with me. If yes, than fine. If no, explan what you did differently with showing me evidence for relatedness of distinct animals. But are you going to be so delusional and deny the relationship!?Edited by Smooth Operator, : No reason given.Edited by Smooth Operator, : No reason given.Edited by Smooth Operator, : No reason given.Edited by Smooth Operator, : No reason given.Edited by Smooth Operator, : No reason given.

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Right. But then you deny that ID has anything at all to say about a designer:

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Yes, exactly.

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The question I've been seeking an answer to for lo these many messages is very simple: If ID has nothing to say about a designer, how can it say that "design without a designer" is impossible. Isn't that saying something about the designer?

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It isn't. It's saying something about design. It's not saying that the designer is either: good, bad, tall short, blond brown, 4 legged etc...It's saying that design is a product of a designing intelligence. It says that you can't have design without a designing intelligence, whicever it was, whatever it was doing, however well it designed.It's saying nothing about the designer, but about design that can't exists without an intelligence.

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There are plenty of threads already dedicated to these subjects. For example, here is a thread dealing with the ERV evidence:

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thread

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There are also numerous peer reviewed papers that discuss this evidence, one of which is here:

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"Given the size of vertebrate genomes (>1 10^9 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14)."

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How does ID explain orthologous ERV's? How does ID explain the correlation between time since common ancestry and LTR divergence? How does ID explain the nested hierarchy produced by a comparison of orthologous ERV's?

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ERVs are widespread through all species. Ther are functional sequences whose operation is to modify the genome itself and adapt the individual to teh environment.

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Endogenous retroviruses (ERVs) are believed to be the selfish remnants of ancient RNA viruses that invaded the cells of organisms millions of years ago and now merely free-ride the genome in order to be replicated. This selfish gene thinking still dominates the public scene, but well-informed biologists know that the view among researchers is rapidly changing. Increasingly, ancient RNA viruses and their remnants are being thought of as
having played (and still do) a significant role in protein evolution, gene structure, and transcriptional regulation. As argued in part 3 of this series of articles, ERVs may be the executors of genetic variation, and qualify as
specifically designed variation-inducing genetic elements (VIGEs) responsible for variation in higher organisms.

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http://www.evoinfo.org/Publications/A/Borger4.pdf

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Obsolete for all life? Yes, due to horizontal gene transfer among prokaryotes and basal eukaryotes.

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How do you know it's due to HGT? How do you know, it's simply because they aren't related?

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Obsolete for metazoans? No, due to the lack of horizontal gene transfer among metazoans. So how do you explain the nested hierarchy found among metazoans? Can you answer this or not? Can ID explain this?

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The answer is that that there is no nested hierarchy. Just because you can't accept that is not my problem. Your objection was already dealt with. HIgher taxa also do not conform to a nested hierarchy. And your objection that HGT is the cause is falsified.

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Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.4 Hillis (and others) may claim that this problem is only encountered when one tries to reconstruct the evolutionary relationships of microorganisms, such as bacteria, which can swap genes through a process called horizontal gene transfer, thereby muddying any phylogenetic signal. But this objection doesn’t hold water because the tree of life is challenged even among higher organisms where such gene-swapping does not take place. As the article explains:

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Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirtsalso known as tunicatesare lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another, Syvanen says.

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Even among higher organisms, [t]he problem was that different genes told contradictory evolutionary stories, leading Syvanen to say, regarding the relationships of these higher groups, We’ve just annihilated the tree of life. This directly contradicts Hillis’ claim that there is overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence.

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A Primer on the Tree of Life2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes were compared. These species do not participate in HGT. Yet those 2000 genes do not match. They do not form a nested hierarchy. The article clerly says that this is does not only happen in lower taxa due to HGT. It happens everywhere.

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A bush doesn't have branches? That's news to me.

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It does but it's intertwined.

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But she dissents from that view and attacks the dogmatism of evolutionary systematists, noting, Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.

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A Primer on the Tree of LifeYou see, it's actually an intertwined bush. Basicly, not a branching tree, but an interconnected web. There is no such a thing as a branching molecular tree that conforms to a morphological one.

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If ID is true then we should see an orchard, trees that do not connect. That is not what we see.

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Who said that that's what we should see if ID is true?

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Projection?

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Show me an instance where is confused evidence with assumptions.

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What you seem to ignore is that the single hemoglobin S mutation has a lot to do with the survival of the individual in areas with malaria. This is why the frequency of the mutation is much higher in areas with endemic malaria.

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When did I ignore that? Where did I ignore that? I totally agree with that idea. But what you keep ignoring is that still doesn't me the gene the unit of selection. Individual genes are not evaluated one by one under natural selection before they get passed on. The whole genome gets evaluated. Do you thing that if an organism had this mutation, and it was either sterila, or born with defective lungs and could breathe, or it was born a paraplegic, that it would pass on that beneficial mutation?No, it wouldn't. Becasue overall his fitness is lower that the others are. Regardless of that beneficial mutation. And that is why it won't get passed on in this case. Becasue the whole genome gets evaluated before it's passed on.

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They are. Vertebrate eyes are only found in vertebrates. Cephalopod eyes are only found in cephalopods. Insect eyes are only found in insects.

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Which means they are NOT found in one lineage. If there was a nested hierarchy that eyes would ahve evolved only once. You simply chopped up few lineages and said that they all evolved few times and claimed that within them it evolved onl once. Well that's unfalsifiable. Becasue if you found an instance of eyes evolving withing vertebrates once more, you would simply take a lower taxa and claim that within that lineage,, there is only one instance of eyes. That's unfalsifiable.

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That is not what your quote says. The common ancestor had feathers as did the descendants.

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But they evolved independently, mayn times.

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This is why ID can not explain the nested hierarchy.

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There is no nested hierarchy to explain.

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There is no reason we should observe one if ID is true, and yet we do.

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What about Matryoshka dolls?

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However, a nested hierarchy is the only pattern that evolution can produce among species that do not participate in horizontal gene transfer.

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When did you see evolution produce an nested hierarchy int eh first palce?

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Metazoans do not participate in horizontal gene transfer. What do we see? A nested hierarchy.

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No we don't why do you keep making up this lie?Here is a clear cut example.

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For example, pro-evolution textbooks often tout the Cytochrome C phylogenetic tree as allegedly matching and confirming the traditional phylogeny of many animal groups. This is said to bolster the case for common descent. However, evolutionists cherry pick this example and rarely talk about the Cytochrome B tree, which has striking differences from the classical animal phylogeny. As one article in Trends in Ecology and Evolution stated: the mitochondrial cytochrome b gene implied...an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.

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A Primer on the Tree of LifeThe article claims that a nested hierarchy that implied nesting of cats and whales fell within primates, grouping with simians and strepsirhines to the exclusion of tarsiers. This is totally in opposition to what we see with cytochrome C, and totally opposed to a morphological grouping. Please stop claiming there is a nested hierarchy in higher taxa.

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ID can not explain why bats do not have feathers, why birds have a single middle ear bone, why fish have an inverted retina while squid do not.

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They were designed that way.

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As you have shown, ID can not even explain biogeography.

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Evolution can't explan the origin of life.

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Among metazoans there is a nested hierarchy. How does ID explain this?

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Where is the evidence?

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So says the guy who didn't even understand meiosis.

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Which part didn't I unedrstand?

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C'mon, lets see the math.

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Recall the following description of the bacterial flagellum given in section 6: bidirectional rotary motor-driven propeller. This description corresponds to a pattern T. Moreover, given a natural language (English) lexicon with 100,000 (= 105) basic concepts (which is supremely generous given that no English speaker is known to have so extensive a basic vocabulary), we estimated the complexity of this pattern at approximately ϕ
S(T) = 1020

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http://www.designinference.com/.../2005.06.Specification.pdfbidirectional rotary motor-driven propeller is the pattern in question. It's complexity is 10^20. How do we get this number? This is how.

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For a less artificial example of specificational resources in action, imagine a dictionary of 100,000 (= 105) basic concepts. There are then 105 1-level concepts, 1010 2-level concepts, 1015 3-level concepts, and so on. If bidirectional, rotary, motor-driven, and propeller are basic concepts, then the molecular machine known as the bacterial flagellum can be characterized as a 4-level concept of the form bidirectional rotary motor-driven propeller. Now, there are approximately N = 1020 concepts of level 4 or less, which therefore constitute the specificational resources relevant to characterizing the bacterial flagellum.

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So now you tell me, where did Dembski claim that 10^20 has anything to o with 50 proteins of the flagellum?

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Yes it does select. It selects for penicillin resistant bacteria.

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Explain how.

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The genetic data shows that negative selection slows down mutational meltdown even in large populations of asexually reproducing populations.

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THANK YOU! That's what I've been saying all along. Natural seelction can slow down genetic entropy. Yes I know, I've been saying it all along. But it does not stop it. Unless you take into account unreasonable variables like infinite population, infinite time for selection or perfect selection. Since we have none of those. The only thing we have is natural seelction slowing down genetic entropy but NOT stopping it.