What exactly is ID?

There are plenty of threads already dedicated to these subjects. For example, here is a thread dealing with the ERV evidence: threadThere are also numerous peer reviewed papers that discuss this evidence, one of which is here:"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)."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? Obsolete for all life? Yes, due to horizontal gene transfer among prokaryotes and basal eukaryotes. 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? A bush doesn't have branches? That's news to me. If ID is true then we should see an orchard, trees that do not connect. That is not what we see. Projection? 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. They are. Vertebrate eyes are only found in vertebrates. Cephalopod eyes are only found in cephalopods. Insect eyes are only found in insects. That is not what your quote says. The common ancestor had feathers as did the descendants. This is why ID can not explain the nested hierarchy. There is no reason we should observe one if ID is true, and yet we do. However, a nested hierarchy is the only pattern that evolution can produce among species that do not participate in horizontal gene transfer. Metazoans do not participate in horizontal gene transfer. What do we see? A nested hierarchy.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. As you have shown, ID can not even explain biogeography. Among metazoans there is a nested hierarchy. How does ID explain this? So says the guy who didn't even understand meiosis. C'mon, lets see the math. Yes it does select. It selects for penicillin resistant bacteria. What does the genetic data show?

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PLoS One. 2009;4(3):e4969. Epub 2009 Mar 23.

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Mutational meltdown in primary endosymbionts: selection limits Muller's ratchet.
Allen JM, Light JE, Perotti MA, Braig HR, Reed DL.

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Zoology Department and Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA. juliema@ufl.edu

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BACKGROUND: Primary bacterial endosymbionts of insects (p-endosymbionts) are thought to be undergoing the process of Muller's ratchet where they accrue slightly deleterious mutations due to genetic drift in small populations with negligible recombination rates. If this process were to go unchecked over time, theory predicts mutational meltdown and eventual extinction. Although genome degradation is common among p-endosymbionts, we do not observe widespread p-endosymbiont extinction, suggesting that Muller's ratchet may be slowed or even stopped over time. For example, selection may act to slow the effects of Muller's ratchet by removing slightly deleterious mutations before they go to fixation thereby causing a decrease in nucleotide substitutions rates in older p-endosymbiont lineages. METHODOLOGY/PRINCIPAL FINDINGS: To determine whether selection is slowing the effects of Muller's ratchet, we determined the age of the Candidatus Riesia/sucking louse assemblage and analyzed the nucleotide substitution rates of several p-endosymbiont lineages that differ in the length of time that they have been associated with their insect hosts. We find that Riesia is the youngest p-endosymbiont known to date, and has been associated with its louse hosts for only 13-25 My. Further, it is the fastest evolving p-endosymbiont with substitution rates of 19-34% per 50 My. When comparing Riesia to other insect p-endosymbionts, we find that nucleotide substitution rates decrease dramatically as the age of endosymbiosis increases. CONCLUSIONS/SIGNIFICANCE: A decrease in nucleotide substitution rates over time suggests that selection may be limiting the effects of Muller's ratchet by removing individuals with the highest mutational loads and decreasing the rate at which new mutations become fixed. This countering effect of selection could slow the overall rate of endosymbiont extinction.

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

That does not put their origin in doubt, nor common ancestry in doubt. I don't see how ERV's evolving function puts evolution and common ancestry in doubt. We observe these organisms participitating in HGT. That would seem to be a pretty big hint. That would be your fantasy world. In reality there is a nested hierarchy for metazoans. You continue to dodge this by conflating a lack of a nested hierarchy for all life when prokaryotes are included as a lack of any nested hierarchy for any group.Go here. The nested hierarchy for metazoans. Peer reviewed articles please. This is from "New Scientist" which can be horribly inaccurate, not to mention that this is pulled from the DiscoTute which is also known for bending quotes. At the individual level, you are right. However, due to sexual recombination individual alleles are selected for at the level of the population. They are found in the same lineage. That inverted retina type eye is found just in the vertebrate lineage. The forward facing retina eye is found in the cephalopod lineage. The compound eye is found in the arthropod lineage. These are lineage specific eyes, just as you would expect from evolution but not from ID.Can ID explain why every animal with a backbone also has an inverted retina? What was stopping a designer from mixing a backbone and a forward facing retina in a single animal? That's a bunch of woo. It has nothing to do with how flagella work, how they are constructed, how they differ from species to species, etc. This has nothing to do with biology at all. It's nothing more than word games. What it shows is that genetic entropy hits a wall. There is a certain point where additional slightly deleterious mutations are strongly selected against, much more so than earlier in the lineage.Edited by Taq, : No reason given.

No one is saying that direct ancestry can be proven. What we are saying is that fossil species should have a mixture of characteristics in keeping with the pattern predicted by evolution. As a rough example, we should see fossils with a mixture of basal ape and human characteristics. We should NOT see fossils with a mixture of ape and avian features. The fact that we only see the mixture of characteristics predicted by the theory of evolution tells us that the theory is on the right track.So what mixture of characteristics does ID predict? Should we or should we not see a mixture of avian and mammal features, and why? Can you tell us? This model predicts that I should not see a frying pan with toothpicks in it, correct? So if I find a frying pan with toothpicks in it then I can conclude that they didn't evolve. See how evolution is falsifiable? We do not claim that things evolved because they are similar. It is the PATTERN of similarity that points to evolution.Also, are you saying that we should NOT see transitional fossils if evolution is true?

We can even go one further. We can pull an ERV out of the human genome and make it into a retrovirus, and then observe how it behaves.

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Genome Res. 2006 Dec;16(12):1548-56. Epub 2006 Oct 31.

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Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements.
Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T.

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Unit des Rtrovirus Endognes et Elments Rtrodes des Eucaryotes Suprieurs, UMR 8122 CNRS, Institut Gustave Roussy, 94805 Villejuif Cedex, France.

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Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral "progenitor" element of one of the most recently amplified family - the HERV-K family - and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. We also show that this element amplifies via an extracellular pathway involving reinfection, at variance with the non-LTR-retrotransposons (LINEs, SINEs) or LTR-retrotransposons, thus recapitulating ex vivo the molecular events responsible for its dissemination in the host genomes. We also show that in vitro recombinations among present-day human HERV-K (also known as ERVK) loci can similarly generate functional HERV-K elements, indicating that human cells still have the potential to produce infectious retroviruses.

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If it quacks like a retrovirus, walks like a retrovirus, and flies like a retrovirus it's a . . . magically inserted piece of DNA performed by an unevidenced magical designer. At least, that's what the ID people are trying to argue. Perhaps they could make millions of dollars as defense attorneys arguing that fingerprints found at the scene of the crime are actually the product of Leprechauns.

That is not what the evidence demonstrates. The evidence demonstrates that these sequences started out as a retrovirus that then inserted into the genome. That these DNA sequences acquired function after this event casts no doubt on their origin.And as it stands, ID still can't explain orthology, divergence of LTR's, or divergence of overall ERV sequence between species. They somehow think that pointing to some function in some ERV's somehow makes the phylogenetic signal go away. It doesn't.These are retroviruses that randomly inserted into these genomes. The only explanation for finding the same retroviral insertion at the same spot in two genomes is a single insertion in a common ancestor. The LTR divergence and overall ERV divergence back this up. Can ID explain why the long tandem repeats of an ERV are more divergent if the ERV is shared by all apes than in an ERV shared by just chimps and humans? No, it can't. Evolution can explain this, and it is predicted by the theory. Common ancestry is the only thing that can explain shared metabolic pathways and shared genetic systems. If you found an organism that did not use the same codons or metabolic pathways I would happily admit that this organism does not share a common ancestor with the rest of known life. Actually, that's not true. What you are looking for is the signal. There will always be noise in any phylogenetic tree, especially given the vast distances between the existing branches. This is unavoidable due to the large distances between branches. This noise is called homoplasy. This is a well known effect that all geneticists are aware of. What geneticists look for is the overwhelming signal, and that overwhelming signal is a nested hierarchy. Peer review please. Sorry, but the DiscoTute is infamous for pulling quotes way out of context. These are subspecies. This is variation WITHIN a species. I keep saying that metazoans fall into a nested hierarchy, and then you quote a paper that deals with fungi. Go figure. Yes, after selection is done to the WHOLE POPULATION. In order for gene frequencies to change YOU NEED A POPULATION. That population will have a mixed genetic background. If a gene confers an advantage then that gene will be seen at a higher frequency for each generation IN THE POPULATION. Each lineage has a different type of eye. Each lineage has a LINEAGE SPECIFIC EYE. You might as well cite insect wings and bat wings as homologous structures. These eyes are NOT homologous structures. They are analogous structures. The cephalopod eye and the vertebrate eye are not homologous. They are analogous. They us different ennervation, different developmental pathways, and different cell types in the retina. The only similarity is in their overall shape which is limited by function to begin with. Do you understand the difference? Are you also going to claim that an insect leg and a mammalian leg are homologous simply because you can call them both legs? Is that the length of your phylogenetic analyses, the ability of the English language to describe two structures? Really? That's your argument? You put words in my mouth and consider that an answer? How dishonest is that?Imagine if you were a defense lawyer in a murder case. "Your Honor, if my client's fingerprints were NOT at the crime scene you would just invent some other evidence, so I call for the dismissal of the fingerprint evidence." Do you think that would work? Do you really believe that this is a rational or logical argument?So I will ask again. How does ID explain the fact that an inverted retina is only found in animals with a backbone? Can you answer this or not? Or is this another item that ID is incapable of even approaching? So you are saying that if humans evolved from a common ancestor with chimps that the theory does not predict that we should find a fossil with a mixture of human and basal ape features? Really? Are you really serious with this? Convergent evolution does not produce homologous structures. A toothpick of the exact same nature in both lineages but not in the common ancestor would be a violation. It is falsifiable. So what is stopping a designer from putting a toothpick in a frying pan? Care to explain? No, it isn't. Life could have shared similarities that didn't fall into a nested hierarchy. In fact, humans do it all of the time in genetically modified organisms. If you can't distinguish between similarities and a pattern of similarities then you really can't make any arguments against evolution. That's a lie, as I have already shown. A bird with a mammalian middle ear would falsify evolution. According to ID, why don't we see a living of fossil species with feathers and three middle ear bones? Or is this another fact that ID can't explain?

"Evolutionists" do deal with the origin of life, they just don't use the theory of evolution to do so. IDists claim that biodiversity is due to intelligent design. Part of that biodiversity is biogeography. It is firmly in the wheelhouse of ID, and they refuse to explain it. Well, actually they could explain it, but then they would have to admit that magical poofing is the mechanism of choice. Isn't it funny how ID supporters immediatly start talking about evolution when they are asked for an ID explanation? Can you give us the ID explanation or not? His identity is "an Adidas employee". The big "Adidas" on the front kind of gives it away. Even more, we can look at the holes in the seams to determine how they were made, look at the thread and deduce how it was made, and look at all of the materials and come to some very strong conclusioons as to the steps involved in constructing the ball. So where are these same ID explanations for how life was made?

We don't need to know if the fish had any offspring or even any ancestors in order to test the theory of evolution. What we need is the mixture of characteristics found in the fish, and those are quite apparent.Does the fish have a mixture of fish and mammalian features? Nope. Evolution passes.Can you tell us, using ID, what mixtures of characteristics we should not see in fossils and why?

Because an ERV-K can be reconstructed into a retrovirus. It's called Phoenix.

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Genome Res. 2006 Dec;16(12):1548-56. Epub 2006 Oct 31.
Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements.

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Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T.

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Unit des Rtrovirus Endognes et Elments Rtrodes des Eucaryotes Suprieurs, UMR 8122 CNRS, Institut Gustave Roussy, 94805 Villejuif Cedex, France.

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Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral "progenitor" element of one of the most recently amplified family - the HERV-K family - and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. We also show that this element amplifies via an extracellular pathway involving reinfection, at variance with the non-LTR-retrotransposons (LINEs, SINEs) or LTR-retrotransposons, thus recapitulating ex vivo the molecular events responsible for its dissemination in the host genomes. We also show that in vitro recombinations among present-day human HERV-K (also known as ERVK) loci can similarly generate functional HERV-K elements, indicating that human cells still have the potential to produce infectious retroviruses.

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PMID: 17077319 [PubMed - indexed for MEDLINE]

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These ERV's have the same features as retroviruses (e.g. LTR's, gag, pol, env), they can become infectious, their insertional biases match modern retroviruses, etc. It quacks like a duck, walks like a duck, and flies like a duck but you want to tell us that it was magically poofed into the genome and isn't due to a retroviral insertion.What I do know is that if I am ever brought up on murder charges I want you in my jury. All my attorney needs to do is claim that fingerprints are not evidence. They are merely swirls of oil that were designed to capture dust floating through the air. Any DNA match of hair left at the crime scene is not evidence of me being at the crime scene. Oh no. It is just evidence that the DNA in my body and the DNA at the crime scene had a common creator. So the goal of ID is not to explain anything in biology? That's news.Can you answer the question or not? Why is there more LTR divergence in an ERV shared by all apes than in the LTR's of an ERV shared by just humans and chimps? Evolution can easily explain this, but it appears that ID once again is incapable of dealing with evidence in the world of biology. Why is it a better explanation, other than just asserting it? Why is it that every time we observe retroviruses inserting into a genome they insert randomly among billions of bases in the genome, even in genomes that are 100% identical? Why is it that up to 25% of cancers can be directly linked to a retroviral insertion into an oncogene in a somatic cell? Is that part of the design, giving people cancer? Just ask anyone who has siblings if common descent is possible. Because you would need to start over. That is a drastic reduction in fitness. You would need to reevolve EVERYTHING. You would need to reevolve tRNA's, ribosomes, polymerases, DNA binding proteins, on and on and on.On the flip side, there is nothing stopping a designer from starting from scratch. In fact, for an omnipotent and omniscient designer starting over takes just as much time and effort as copying previous designs. Completely false. Homology DOES NOT IMPLY A NESTED HIERARCHY. Automobiles share homology, but they do not fall into a nested hierarchy as we would expect from a design process. A nested hierarchy is a PATTERN OF HOMOLOGY, not homology itself.Secondly, if evolution is true and if life shares common ancestry then we should observe a nested hierarchy among lineages that did not participate in horizontal gene transfer. This is the TEST. So we should not find any fossils with feather impressions and three middle ear bones. We should not find living bats with feathers. We should not find an ostrich with mammary glands. An ostrich with mammary glands would share homologous structures with mammals, but this would break the nested hierarchy and would falsify common descent. Do you understand this or not? No, the measurement tool is crude. This is also what the author said:"Just as it would be futile to use radioisotopes with modest half lives to date ancient rocks, it appears unrealistic to expect conventional linear, homoplasy-sensitive sequences to reliably resolve series of events that transpired in a small fraction of deep time." I thought we were talking about evolution which occurs at the level of the population, not at the level of the individual. So you are saying that if evolution is true that the next generation of humans could look like winged dogs and nothing like apes? Am I getting this correctly? Let's look at the Glofish. This is a fish that carries and exact copy of the jellyfish GFP (green fluorescent protein) gene. This allows the fish to glow under UV light. This exact copy of the jellyfish GFP gene is not found in any other vertebrate fish. It is a clear violation of the nested hierarchy. Guess how it got there? Human designers. Humans have no problem moving genes between species and in clear violation of the nested hierarchy. Humans have no problem with getting mice to express human proteins in vivo. "Humanized" mice have been a huge advance in biomedical research. GM foods have been a big step forward in increasing yields and quality of product.So why do we see a nested hierarchy if design is true? Why don't we see ostriches with mammary glands? Why don't we see bats with feathers? You are begging the question. Fish have a two chambered heart and gills. Mammals have fur and a four chambered heart. So where is the fish with fur or the mammal with gills? Why don't we see these things if design is true? So let's summarize. ID can't explain ERV orthology, biogeography, the pattern of homology, the fossil record, and really anything else in biology. So why do you feel it necessary to come into a thread and discuss ID and biology since ID doesn't address anything in biology?

How does this put their origin and mechanism of insertion in doubt? If an ERV induces variation how does that discount their insertion through standard retroviral mechanisms? It relates to your use of magic to discount obvious conclusions. You have consistently shown that ID is not able to detect anything in biology. Therefore, I can only conclude that there is no intelligent design in biology, otherwise ID could explain these features. No, it is not. I am asking you to use ID to explain observations. That is what scientific hypotheses/theories do, they explain observations. The observation is that an ERV shared by all apes has more LTR divergence than an ERV shared by just humans and apes. Evolution can explain this. If common ancestry and evolution is true this is exactly what we should observe. You are saying that common ancestry is wrong. You are saying that ID explains things better. So how does ID explain this observation? False. The random insertion of retroviruses is OBSERVED. It is an observation. Even an ERV rescued from the human genome (i.e. Phoenix) randomly inserts into the genome just like its modern counterparts.So once again you have to ignore observations to make ID work. That doesn't bode well. How does that put the origin of the ERV in doubt? Can you please show us how it is impossible for an ERV that is produced by random insertion of a retrovirus into the germline CAN NOT result in a function in the lineage? How does function negate the very natural origin of these sequences? Based on what evidence? If they have degenerated then how do you explain the higher divergence in ERV's shared by all apes than in ERV's that are lineage specific or shared by just 2 species of ape? If they all degenerated from a set time in history then all of them should be equally distant, but they aren't. You stated that common ancestry is impossible. Are you retracting that statement? I already told you what is stopping it. A drastic reduction in fitness. Such an organism would be selected against, strongly. Evolution can't go backwards. You might as well claim that gravity can make rivers flow uphill. This forum is about ID. What does ID say? No it is not. A bat with feathers would violate the nested hierarchy and would falsify the theory of evolution even though feathers would be a homologous structure shared by bats and ducks. Homology in and of itself does not indicate common ancestry or evolution. Not every pattern of homology will indicate evolution. There is only one pattern that will indicate evolution, and that happens to be the pattern we observe. Cars and frying pans do not fall into a nested hiearchy. You have just supported my argument. Designed things do not fall into a nested hierarchy. If they did then only one lineage of cars would have airbags. Only one lineage of frying pans would have teflon coating. This is not what we see. For example, we can find a Mazda and Chevy that have the same tires, but different engines. We can find two Mazdas that have the same engine, but different tires. There is no nested hierarchy even though there is homology. Do you understand the difference or not? Because bats were never birds. Evolution doesn't work that way. For bats to evolve feathers you would need to give bats the same genetic background as the non-feathered ancestors of birds. It is impossible for a bat to have that genetic background. Not only that, but once the bats have this impossible to get genetic background they need to acquire the same random mutations in the same order, another near impossibility. So your only recourse now is to put words in my mouth in order to discount my arguments? That's dishonesty at its acme. Why don't you find an ostrich with teats and then see how I react. Or why don't you give us the ID explanation of why we don't see a single species with teats and feathers. Care to explain?Secondly, the vertebrate eye evolved once. The insect eye evolved once. The cephalopod eye evolved once. These are lineage specific adaptations. They have lineage specific anatomy, histology, and development. The only thing that ties them together is their end function. You might as well try to claim that the insect leg, bear leg, and squid leg are also homologous because you can call them legs. What is being said is that the tool is too crude to resolve branches that are very close together. You might as well claim that binoculars don't work because they can not resolve separate stars in the Andromeda galaxy. It's not the equipment. It's the lack of data. Modern species represent a tiny fraction of the species that have existed. Using their genomes as a phylogenetic tool will not be able to resolve branches of extinct species that branched very close to one another due to the missing data. What it can give us is a cruder, larger picture, and it does that quite well. Please show how all known kachina dolls fall into a single nested hiearchy. Please compare the characteristics of each kachina doll population and show how they fall into a single nested hierarchy.BTW, the ability of something to physically fit inside another is not a nested hierarchy. The individual is meaningless in terms of evolution. If all we look at is the individual then we have to remove two of the important mechanisms in evolution: differential reproductive success and competition between organisms. If an individual has two offspring, what does that mean? What if that individual has 100 offspring, what does that mean? How can we make heads or tails of what the individual means without comparing the individual WITH THE REST OF THE POPULATION? You tell us? Why call it design when you have shown that ID can not explain any observations in biology? That was my question. Why should we or shouldn't we? What does ID predict as to the existence of fish with fur, mammals with gills, birds with teats, bats with feathers, etc.? Why do we only see the combination of features predicted by the theory of evolution?

The problem is that scientists can use the characteristics of the radio signal to reverse engineer the mechanisms that the alien race used to create the design. From the strength of the signal and the frequency one can derive the types of coils used, as one example. One can infer the mechanism of design from looking at the design. IDer's can't or won't do this.You need to find a new example.

I see a lot of assertions and zero evidence. Can you show any evidence that the ancestors of modern mammals required these ERV sequences in order to reproduce? Any at all? The magical poofing of retroviral insertions into genomes by your supposed intelligent designer. We are talking about patterns of characteristics IN BIOLOGY. ID is incapable of explaining these patterns, as you have already shown. Therefore, I can only conclude that there is no ID in biology. When a retrovirus inserts into a genome the flanking LTR's are identical. This is due to the mechanism of retroviral insertion. If the retroviral becomes part of the genome, that is becomes endoegenized, then mutations will accumulate in these LTR's over time. More importantly, different mutations will accumulate in each of the LTR's. This will cause the LTR's to diverge in sequence over time. More time equals more divergence.By applying the theory of evolution you can determine when these ERV's were inserted. The patterns of orthology tell us this. If all apes have the same ERV at the same location in their genome then this insertion had to occur in the common ancestor of all apes. If an ERV is found in just humans and chimps then this insertion had to occur in the common ancestor just humans and chimps, a much more recent ancestor. Therefore, you should see more LTR divergence in ERV's shared by all apes than in an ERV shared by just humans and chimps. This is exactly what we see. LTR divergence matches the insertion time established by orthology. You can read more HERE Technologies | The world's #1 location platform.

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Third, sequence divergence between the LTRs at the ends of a given provirus provides an important and unique source of phylogenetic information. The LTRs are created during reverse transcription to regenerate cis-acting elements required for integration and transcription. Because of the mechanism of reverse transcription, the two LTRs must be identical at the time of integration, even if they differed in the precursor provirus (Fig. ​(Fig.11A). Over time, they will diverge in sequence because of substitutions, insertions, and deletions acquired during cellular DNA replication.

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So how does ID explain this? Any answers? Please show that this was so for all of the ancestors of modern sheep. From observing retroviruses inserting into genomes. Here is a really good paper showing a genomic map of the insertions for hundreds and thousands of HIV, MLV, and ASLV retroviral insertions conducted in the lab:Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences - PMCAs I showed earlier, an HERV-K (Human-ERV) was rebuilt from the human genome. It too showed this same pattern of random insertion:Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements - PMCSo modern retroviruses are observed to insert randomly. Reconstructed ancient retroviruses insert randomly as well. Shared codon usage, shared genetic systems, and shared metabolic pathways is the evidence. That is unless you can show a physical law that requires ATG to code for methionine. Otherwise we will have to conclude that the relationship between DNA codon and amino acid is an arbitrary one. Lungs didn't evolve from gills. There are even MODERN species with both a lung and gills. They are called lungfish. This didn't require a reduction in fitness since it didn't require the destruction of gills while the lungs evolved. A complete remake of the genetic pathways would require a complete destruction of all proteins. You would have to start over from an extremely simple replicator, possibly an RNA replicator. There is no way that this RNA replicator could compete with life that had already been evolving for quite some time.Like I said, you might as well expect rivers to flow uphill for 5,000 feet. A bat with feathers would falsify evolution because the genes for feathers can not move from the bird lineage to the mammal lineage through the mechanisms of evolution. However, a designer could easily move genes back and forth between birds and mammals.So I will ask again. Why, if ID is true, don't we see bats with feathers? A mother with a baby in her womb is not a nested hierarchy, and neither are Matryoshka dolls. A turducken is not a nested hierarchy. A twinky with creme filling is not a nested hierarchy. A nested hierarchy is not something physically put inside of another thing. What is so hard to understand here? Only one lineage of animal does have vertebrate eyes. The vertebrate lineage. Only one lineage of animals has the cephalopod eye. The cephalopod lineage. These are not homologous eyes. The airbags in different makes and brands of cars ARE homologous. Airbags in different makes and brands are often made by the same company. They ARE lineage specific adaptions, just as we would expect from evolution. Then do it. Show me a bat with DNA sequence that is more like a birds than it is to another mammal. And those features are only superficially similar. They are not homologous. The leg of the insect, bear, and squid are perfect examples. They can all be called legs, but they are not homologous. The same for the eye of the insect, the eye of the cephalopod, and the eye of the bear. These are different solutions for the same function.Using the bat and the bird, we could look at their wings as a very good example of this. Superficially, we can call them both wings. This simply refers to their function. They are superficially alike in that they projections outward from the lateral midline and involve the forelimbs. That is where the similarities end. The bird wing is an airfoil type wing with a reduction in phalanges and an air surface produced by the upper arm and lower arm bones in the front and feathers making up the rest of the airfoil surface. In the bat the majority of the wing is made up of the phalanges with a skin membrane stretched between the phalanges. They are not homologous by any stretch of the imagination. Because mutations can not jump between lineages. However, there is no such restriction for a designer. So I ask again, why don't bats have feathers? Why don't ostriches have teats? What was stopping a designer from mixing and matching design units just as human designers do? You can't determine what is being selected for or against by looking at a single individual, as I have already explained. We know exactly the technology being used is. We can know from the modulation, strength of the signal, and frequency the type of coils, voltages, and amperages being used. We can learn a lot about the designers by looking at their radio signals. This is completely different than IDers whose only goal seems to be ignorance.

You are trying to see stars in distant galaxies with binoculars. For branches close together the genetic tools would not resolve them EVEN IF THEY EXISTED. The phylogenomic tools used are incapable of resolving lineages that branched off close to one another in the distant past. However, these phylogenomic tools are capable of detecting a nested hierarchy WHERE THEY SHOULD DETECT THEM, in well resolved branches that are widely spaced.

Again, you are making assertions with no evidence. Please show that all of the ancestors of sheep were sheep, and that all of these ancestors required specific ERV insertions. Have you ever heard of creationism? So ID is not supposed to explain the pattern of designs in biology? Really? Why is it an assumption that every generation will accumulate mutations? That is what we observe. The more generations since the insertion of the ERV the more mutations the ERV will have, and the more divergence between the LTR's. This is population genetics 101. There is no living Coelacanth that is the same as today. Living coelacanths are in their own genus. No fossil species is in the same genus as the living species. There is no fossil species (which there are around 150 known species) of coelacanth that is identical to the living species.As far as divergence, you can not determine genetic divergence by comparing physical divergence. Those claims are highly suspect. Common ancestry is not assumed. It is tested for, and the test clearly points to common ancestry. If humans and other apes did not share a common ancestor then you would not expect to find ERV's at the same locations in their genomes, but you do. If there was no common ancestor you would not expect LTR divergence to produce the same tree as orthology. Due to the OBSERVED random nature of retroviral insertion finding multiple ERV's at the same locations in both humans and other apes is slam dunk evidence of common ancestry. No two ways about it. Did you look at the x axis? That's 10 million base pairs. For ERV's, we are talking resolution down to the same base, not within a few hundred thousand bases. Those hotspots comprise nearly half of the genome, as was stated in the reference I already gave you (the paper on HIV, ASLV, and MLV). That's billions of bases. ERV's shared by humans and other apes are found at the same base. Hotspots can not explain this, and it also can not explain LTR divergence which is an independent test that produces the same tree as orthology.Please explain this. How do hotspots explain the observation that ERV's that are shared by all apes have a higher LTR divergence than an ERV shared by just humans and chimps? Hotspots can't explain this. Again, what you are looking for is the signal. If 99.9% of ERV's fall into the predicted pattern and 0.1% do not what do you think the conclusion should be? I already explained this. This would require bats to re-evolve the genome of the common ancestor of non-feathered birds. Once that occurred bats would have to acquire the same feather mutations in the same order. Such a pathway is impossible. Evolution does not go backwards any more than rivers flow 5,000 ft uphill. Yes I did, especially this part:"For HIV the frequency of integration in transcription units ranged from 75% to 80%, while the frequency for MLV was 61% and for ASLV was 57%. For comparison, about 45% of the human genome is composed of transcription units (using the Acembly gene definition)."Only HIV showed a strong trend towards inserting into transcription units while MLV and ASLV only showed a weak trend. On top of that, these "hotspots" comprise 45% of the human genome. For a 3 billion base haploid genome, that's about 1.5 billion bases in these hotspots. That means the chances of a single ERV inserting into the same base through two different insertions is 1 in 1.5 billion. And that's just for one retroviral insertion. Humans and other apes share tens of thousands of orthologous insertions. Hotspots can not explain this, nor can it explain LTR divergence as discussed above. Then show how you can arrange Matryoshka dolls into a nested hierarchy using shared characteristics. Physically putting one inside another is not a nested hierarchy.If you arrange them by size then each doll is a separate lineage, not nesting. You also need to put ALL matryoshka dolls into your cladogram so you must list common characteristics (synapomorphies) and derived features for all matryoshka dolls and show how they form a nested hierarchy. Where is that nested hierarchy? Shared characteristics let me do that. A fish and human eye develop in the same way, share the same cell types, and share the same arrangement of parts. Both the fish and human eye differ greatly from the squid eye in all of these departments. Both the human and fish eye have an inverted retina, have the same retina cell type, and have the same developmental process as embryos. The squid and octopus also have similar development, cell types, and a non-inverted retina, but the squid/octopus eye differs from the fish/human eye in all of these categories. You can read more here.They eyes of all vertebrates are more similar to one another than any vertebrate eye is to a cephalopod eye. What more can be said? I already showed you a fish with a gene that is an exact copy of a jellyfish gene and not found in any other fish (i.e. Glofish). We know how that gene got there, through intelligent design. So why don't we see a gene in bats that is identical to a gene in birds but not found in any other mammal? Why don't we see this? Humans and fish are both vertebrates, and they sare the same eye with all other vertebrates. Enough common ancestry for you? Because selection is determined by the RELATIVE rate of reproduction. You need to compare the fecundity of the individual with the fecundity of the rest of the individuals in the population.Let's use an example. John competed in the 100m dash. His time was 11.23 sec. Where did John place? If you can't answer this for one person then how can you answer this question if I give you the times for the other competitors? It's simple physics, bro.

To be accurate, it's crappy resolution. Do binoculars work? Yep. However, this doesn't mean you can resolve single stars in a distant galaxy. These tools work, but not at high resolution. Then don't claim it. You claimed that all sheep have always required a specific ERV insertion in order to reproduce. You have asserted this without any evidence whatsoever. Evidence please. Please show that all ancestors of sheep were sheep and not non-sheep.Chihuahuas give birth to chihuahuas, but not all fo the ancestors of chihuahuas were chihuahuas. So where can we find the MCS's (multiple cloning sites) in our genomes? Where can we find antibiotic markers used for determining of the plasmids have inserted into the genome? Where are there examples of clear violations of the nested hierarchy that humans can easily produce using genetic engineering (e.g. the Glofish)? Evidence please. Please link to the genome of the 100 million year old ancestor and the genome of the modern population. Please show that they are nearly identical as you claim.You are also making the mistake of correlating small phenotypic changes with small genotypic changes. Changes and phenotype and genetic divergence do not correlate. Never have. Identical to which of the 100+ species of fossil coelacanth? Give me a genus-species name and we will compare. You have changed your argument. You are arguing that genetic change occurs at the same rate as morphological change. Those do not correlate. A single mutation can drastically change morphology while a thousand other mutations can have zero effect on morphology. The rates of change (genotype and phenotype) do not correlate. The PATTERN of SHARED morphology DOES correlate with genetic divergence. DNA breaks down in much shorter time periods than millions of years. You are ignoring the much more likely conclusion that these are modern bacteria growing in salt that is millions of years old. I assume you mean common ancestry. Using ERV's, if two organisms share a common ancestor then you should find multiple ERV's at the same base in their genome (i.e. orthologous ERV's). Not only that, but LTR divergence should correlate with amount of time in the lineage as determined by orthology. These retroviruses insert among billions of potential insertion sites. These insertion sites make up 50% of the human genome, or about 1.5 billion bases. The chances of two independent insertions resulting in the same ERV at the same base in the genome are simply too high to explain the 10's of thousands of ERV's shared by humans and other apes. They are random among the insertion sites which comprise billions of bases. Once again, these hotspots comprise billions of bases. You might as well claim that everyone should have the same lottery numbers because the lottery balls are non-random being that they have a hotspot between the numbers 1 and 50. If the lottery were truly random then any imaginable number should be in play. All gravity has to do is move water uphill. Why can't gravity do that?It is not simple at all, despite your empty assertions. Bats would need to re-evolve the same genome as the non-feathered bird ancestors. How would that happen? After this long string of impossible mutations, bats would then need to acquire the same feather mutations leading to feathers, another impossible string of mutations. Using the lottery example again, you might as well ask why the winning lottery numbers are not the exact same for every lottery drawing. It does matter. Orthologous ERV's are found at the SAME BASE IN EACH GENOME. If you are going to refute this evidence you need to use the same level of resolution. It is not my responsibility to remove your blinders. That's your job. It is not my fault that you refuse to admit that a 1 in 1.5 billion chance of two ERV's occuring at the same base is not random enough. For just 10 ERV's occuring at the same spot in two genomes due to independent insertions this would require a 1 in 1.5 billion to the 10th power occurence, or 1 in 1x10^100 odds. And that is just for 10 ERV's. Humans and other apes share 10's of thousands of these ERV's. Then please construct a cladogram using shared characteristics that groups the human eye with cephalopods and the fish eye with vertebrates. Show it. So we should not see a nested hierarchy if common ancestry is true? Please explain. So you admit that the nested hierarchy is falsifiable. Because selection is determined by competition between individuals in the same way that a runner's place in the competition is determined by his time compared to the times of others. You can't look at the number of offspring that an individual has and calculate which genes are under selection in the same way that you can't use the time of an individual runner to determine his place in the competition.

Wrapping things up. Here are the general conclusions:1. ID can not explain the nested hierarchy. Humans easily violate the nested hierarchy by transferring exact copy of genes across lineages as one example of intelligent design. There is no reason whatsoever that we should see a nested hierarchy if ID is true. Any pattern of homology, morphological or genetic, is possible if ID is true. However, the nested hierarchy is the only pattern that evolution can produce among lineages that do not participitate in horizontal genetic transfer. The overwhelming signal in metazoans is a nested hierarchy within the resolution of the phylogenetic algorithms used.2. ERV's are unequivocable evidence of common ancestry, and their divergence over time illustrates how nested hierarchies work. The retroviral sources for these ERV's have been shown to randomly insert among billions of possible bases, negating hotspots as the cause for this pattern of orthologous ERV's.3. The same nested hierarchy is seen in vertebrate and cephalopod eyes. It is easily shown that the human and fish eye have the same arrangement of nerves, same cell types, and same developmental pattern. The cephalopod eye differs in all three categories. How does ID explain this? It can't. We have the same function (focused image of light) filled by two different designs, and not only different designs but lineage specific designs. If ID were true you would not even be able to describe a group of organisms as cephalopods or vertebrates, much less describe lineage specific adaptations in each group.