What exactly is ID?

All X are Y.Y.Therefore X.That is a logical fallacy no matter how it is dressed up with rhetoric. You are committing this fallacy. There is no two ways about it. You argument can also be shown to beg the question. This is where the conclusion is found in the premise.All known complexity is due to intelligent design.Life is complex.Therefore, life is designed.The conclusion and first premise are the same. There are about 6 billion different DNA combinations living right now that produce a human. 6 billion. That's not specific at all. Add to that the billions of species that have lived through time. There is no specificity. There is what works and what doesn't.Secondly, show me a 2 billion year old genome. If you can't do it then withdraw your claim. What we do observe is that genomes change in every generation. Therefore, there is no expectation whatsoever that genomes were the same 3.5 billion years ago. None. That's not what SETI is looking for. SETI is looking for a narrowband radiowave signal. That's it. They are looking for a radio transmitter within the clutter of broadband radio signals produced by stars and celestial objects. They are not looking for strings of prime numbers. They don't need any observations since it is a dogmatic religious belief.IDer's have not even been able to evidence CSI in real life genomes, so you seem to be jumping the gun a bit. Those fingerprints do not indicate the DNA sequence of their genome nor their intracellular organization. As for Mars, do you really think that if they do find stromatolite-like deposits on Mars that they will conclude that organisms with DNA identical to modern Earth algae produced those deposits?

There was no ID explanation, just a long diatribe against evolution. Where was this progression indicated? Here is the picture again: Do you see anywhere in there that says "THIS IS AN EVOLUTIONARY PROGRESSION"? I don't see it. These skulls are laid out in CHRONOLOGICAL order (except for the chimp skull in A).So you need to explain, using ID, why older fossils look more like chimps and more recent skulls look more like humans. How does ID explain this? Remember, "not evolution" is not an ID explanation. We want to know how it DID happen according to ID and the experiments we can do to test this explanation. How do you determine, using ID, which are disfigured and which are not? If I found a dog skull is it doubly disfigured because it isn't identical to either a chimp skull or a human skull? How do you distinguish which are separate species and which are not using the fossil data? How do you use ID to determine this? Did you? Let's take Henry Gee's words. These fossils do not come with birth certificates so how did you determine who was related to whom?And just so you know:

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The Discovery Institute’s Viewers Guide to the PBS Evolution series claims in several places (for example, on page 11) that the series leave(s) viewers with the misleading impression that the evidence for human evolution is much stronger than it really is. The Guide attempts to discredit the scientific implications of the human fossil record by quoting (on pages 11, 40, 47, 88, and 111) passages from the 1999 book In Search of Deep Time by Dr. Henry Gee, who is also Senior Editor, Biological Sciences, for the journal Nature. Dr. Gee has sent us the following comments:
1. The Discovery Institute has used unauthorized, selective quotations from my book IN SEARCH OF DEEP TIME to support their outdated, mistaken views.
2. Darwinian evolution by natural selection is taken as a given in IN SEARCH OF DEEP TIME, and this is made clear several times e.g. on p5 (paperback edition) I write that "if it is fair to assume that all life on Earth shares a common evolutionary origin..." and then go on to make clear that this is the assumption I am making throughout the book. For the Discovery Institute to quote from my book without reference to this is mischievous.
3. That it is impossible to trace direct lineages of ancestry and descent from the fossil record should be self-evident. Ancestors must exist, of course -- but we can never attribute ancestry to any particular fossil we might find. Just try this thought experiment -- let's say you find a fossil of a hominid, an ancient member of the human family. You can recognize various attributes that suggest kinship to humanity, but you would never know whether this particular fossil represented your lineal ancestor - even if that were actually the case. The reason is that fossils are never buried with their birth certificates. Again, this is a logical constraint that must apply even if evolution were true -- which is not in doubt, because if we didn't have ancestors, then we wouldn't be here. Neither does this mean that fossils exhibiting transitional structures do not exist, nor that it is impossible to reconstruct what happened in evolution. Unfortunately, many paleontologists believe that ancestor/descendent lineages can be traced from the fossil record, and my book is intended to debunk this view. However, this disagreement is hardly evidence of some great scientific coverup -- religious fundamentalists such as the DI -- who live by dictatorial fiat -- fail to understand that scientific disagreement is a mark of health rather than decay. However, the point of IN SEARCH OF DEEP TIME, ironically, is that old-style, traditional evolutionary biology

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Since I am a microbiologist I will comment. Yes, eukaryotes and prokaryotes are very dissimilar, but not completely so. They also share basic, fundamental genetic systems such as ribosomes, tRNA's, and codon usage. Codon usage is the big one. There is no physical law that requires the DNA codon ATG to result in a methionine residue in a protein. NONE AT ALL. The relationship between codon and amino acid is arbitrary. To the microbiologist this is a huge clue, a clue that indicates shared ancestry.Just to back this up, there are "Indiana Jones" type microbiologists out there (as close as us real science nerds can get) who are searching for life forms on Earth that do not share the same codon usage. Such a find would probably win someone a Nobel and funding for life. This would indicate a second origin of life, a group of life that does not share common ancestry with the life we are all familiar with.

It is still a very subjective evaluation. A dog breeder would say that a Great Dane and a Chihuahua are very dissimilar, and no one would criticize them for saying so. In microbiology, we even consider closely related bacteria to be "very dissimilar" at times when trying to contrast the differences between them. It's a bit like asking someone a dollar value at which someone goes from being poor to being rich. It really depends on the person and the situation.

Do you have any siblings. If you do, what mechanism is responsible for your shared characteristics? Shared ancestry, is it not?Do you really think that common ancestry is not possible? Really? This is why ID is not scientific. Nothing can falsify it. 2 billion different species with no shared characteristics would also be consistent with magical poofing. A non-nested hierarchy would be consistent with magical poofing. Anything and everything is consistent with magical poofing.This is not so with evolution. The theory of evolution (a scientific theory) makes a risky prediction. It predicts that a nested hierarchy should exist among species that only participate in vertical genetic transfer (which is the case for metazoans). What do we see at the genetic level? An overwhelming signal for a nested hierarchy. How in the world do you think people determine that Rolex's are fakes? Or how old a pocket watch is? From these very things. It's not only possible it is done all of the time.Secondly, if I put two pocket watches in a box and come back 9 months later are there three pocket watches? No, there isn't. Watches don't reproduce. Life does. A designer could put feathers on a bat. There is nothing stopping it from happening. And yet, there is no feathered bats. Instead we see adaptations of a mammalian body type for flight without anything informing these adaptations from the bird lineage. Again and again we see this pattern. There is no reason that we should see a nested hierarchy in metazoans if ID is true. It is the only pattern that evolution can produce with a lack of horizontal gene transfer. Not for organisms that participate in HGT, no it doesn't. However, there is very little to no HGT observed among metazoans, and sure enough we see an overwhelming signal that is consistent with a nested hierarchy.Using ID, can you explain why we don't see birds with three middle ear bones? Why we don't see mammals with feathers? Why we don't see whales with gills? Why we don't see penguins with hair? How does ID explain why we see one pattern out of the billions that are possible?

How was this calculation made? More importantly, why limit this to a "bidirectional motor-driven propeller"? The function is motility. His calculations need to include all protein-protein interactions that could have led to a motility function. They pass on their entire genome? Really? You might want to think about that for a second. In sexually reproducing species only half the genome is passed on which means that a mixture of alleles is passed on. Therefore, different children from the same parents will have a different mixture of alleles.Secondly, there are very good examples of a single nucleotide difference being selected for. The hemoglobin S allele is a perfect example. In the heterozygous state it confers malarial resistance. In the homozygous state it causins sickling of the RBC's. Therefore, it has both beneficial and detrimental attributes depending on the environment. In environments with endemic malaria the beneficial attributes in the heterozygous state outweigh it's detrimental attributes in the homozygous state. The exact opposite occurs in environments without endemic malaria. So what do we see when we look at the geographic distribution of the hemoglobin S allele and endemic malaria? They match. Populations in areas with endemic malaria have many more individuals with the allele than populations in areas without endemic malaria. This completely falsifies your claim.

Taq, you've got a very long section that is just a very long *UNQUOTED* excerpt from SO's post, or maybe multiple posts. It begins with "[qs]That's not what...". Please fix. --AdminYou do know that chihuahuas and great danes can not reproduce.And you never demonstrated why common ancestry is impossible, other than to just assert it. We do observe that common ancestry produces shared characteristics. We observe that all life shares arbitrary characteristics, such as tRNA's. 1) Since new information is produced by mutations, and mutations occur by chance, then ID is falsified.2) ID has always been about magical poofing. And in those species we see horizontal genetic transfer. In species where we do not observe HGT we observe a nested hierarchy, exactly as we would expect. This applies to the vast majority of metazoans. You have just rejected your own potential falsification. We observe natural processes producing a nested hierarchy. We observe a nested hierarchy in life. Once HGT stops there will be a nested hierarchy. [qs]That's not what ID is about. But nevertheless. The explanation is simple. They were not designed that way. But can you tell me what exactly would falsify evolution? What animal, and which characteristics would falsify common descent?

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Do you have any siblings. If you do, what mechanism is responsible for your shared characteristics? Shared ancestry, is it not?
Do you really think that common ancestry is not possible? Really?

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I'm talking about universal common ancestry. You know, the common ancestry of all life on Earth. You do know that bears and aligators do not and can not reproduce?

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This is why ID is not scientific. Nothing can falsify it. 2 billion different species with no shared characteristics would also be consistent with magical poofing. A non-nested hierarchy would be consistent with magical poofing. Anything and everything is consistent with magical poofing.

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This is where youa re wrong on 2 parts.1.) ID can be falsified. If an event is shown to be a producd of eiterh a natural law or chance, than ID is falsified.2.) ID has nothing to do with "poofing", whatever that is.

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This is not so with evolution. The theory of evolution (a scientific theory) makes a risky prediction. It predicts that a nested hierarchy should exist among species that only participate in vertical genetic transfer (which is the case for metazoans). What do we see at the genetic level? An overwhelming signal for a nested hierarchy.

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Except where we do not see a nested hierarchy. Did you read the article I quoted in my previosu post? A lot, and I do mean, a lot of speies do not fit the tree of life model you think they do. On the other had, I already told you, being consistent with something doesn't imply that this something is the cause.

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How in the world do you think people determine that Rolex's are fakes? Or how old a pocket watch is? From these very things. It's not only possible it is done all of the time.

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But it does not detect design. It presupposes design in the first palce. You already know a ROlex is designed. Now you just want to find out the mechanism.

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Secondly, if I put two pocket watches in a box and come back 9 months later are there three pocket watches? No, there isn't. Watches don't reproduce. Life does.

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If you put random atoms in that very same box, will they reproduce? No they won't. So why would you think a long time ago some atoms did just that and formed first life? But that's besides the point. How does reproduction have anyhting to do with design detection in the first place?

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A designer could put feathers on a bat. There is nothing stopping it from happening. And yet, there is no feathered bats.

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I know, why should there be?

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Instead we see adaptations of a mammalian body type for flight without anything informing these adaptations from the bird lineage.

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No you do not. You simply see, mammalian bodies that are able to fly. You have no idea of how that came about.

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Again and again we see this pattern. There is no reason that we should see a nested hierarchy in metazoans if ID is true.

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Except if it was designed that way.

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It is the only pattern that evolution can produce with a lack of horizontal gene transfer.

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You didn't even show that evolution is capeable of producing that in the first place! You can't ascribe an event to a cause that you do not know can even produce that cause.

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Not for organisms that participate in HGT, no it doesn't. However, there is very little to no HGT observed among metazoans, and sure enough we see an overwhelming signal that is consistent with a nested hierarchy.

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But those animals you speak of were supposed to have evolved from those earlier that did participate in a lot of HGT. So if evolution was true, the later ones should obviously not be forming a nested hierarchy.Furhtermore, the idea that HGT is responsible for the noncorrelated branches is not enough. Simply because even the higher taxa is shown to not conform to a tree of life as envisioned if it was a slow gradual descent.

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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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A Primer on the Tree of Life | Discovery Institute

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That's not what ID is about. But nevertheless. The explanation is simple. They were not designed that way. But can you tell me what exactly would falsify evolution? What animal, and which characteristics would falsify common descent?

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Why weren't birds designed with three middle ear bones? Why weren't bats designed with feathers? What was preventing this designer from swapping design units between different vertebrate species? Why is the pattern of homology exactly what we would expect to see from evolutionary events?An animal, living or fossilized, that would falsify evolution would be an animal with a single lower jaw bone, three middle ear bones, and feathers. Another would be an animal with gills and hair. What was stopping this supposed designer from producing these animals?Edited by Taq, : No reason given.Edited by Admin, : Request fix.

So how many possible patterns are there and how was that determined?Frankly, I don't see how such a calculation can be done since it is nearly impossible to know which combinations of which protein sequences will result in any type of motility system. No, it contains half the father's genome. It's a haploid cell. Get thee to a biology book and learn about meiosis. Then please explain why the map of a single nucleotide polymorphism (SNP) matches so perfectly with the map of malaria distribution.Edited by Taq, : No reason given.

No, that is not what I meant.You are arguing that intelligences produce CSI. You then find CSI and claim intelligence. This leaves out the rather obvious possiblity that CSI can be produced by something other than intelligence. You forgot to add in the 150 or so point mutations that occurs in every generation, in addition to a handful of small and large indels. Adding these in and we come to the conclusion that each generation of human will necessarily be different than any generation that has lived before it. The gene pool from one generation to the next is not the same. So how can you claim that DNA is specific to humans when every generation is different from the last? As opposed to non-existent gene pools? What are you trying to say here? Prime numbers in what? We can find prime numbers in many things that are of natural origin. For example, tritium has three neutrons and three is a prime number. Therefore, tritium has an intelligent source, right?The prime numbers you are referring to would be embedded in a narrowband radio transmission. The first goal of the SETI program is to find that narrowband radio transmission. Only after they find the signal can they look for prime numbers. So IDers are looking for DNA that produces narrowband radio transmissions? Birds and stromatolites are nothing alike. Stromatolites are the excreted waste build up from metabolizing cells. That's it. They have no anatomy and they can not distinguish between the structure of the cells. What other people had to say about the picture has nothing to do with it. You still have not offered an ID explanation for the changes in morphology through time. You have not explained why skulls of more recent origin are more like modern humans while older skulls are more like other apes. You have not explained why we don't find modern human features earlier in the chronology. Now you have gone so far as to suggest that differences in morphology are NOT due to differences in DNA.
More than plenty for natural selection to work with in the existing gene pool to insure survival. But that does not mean that our genetic make up is not incredibly specific to our particular species. And the same argument applies for all the species. Not the same. There is no physical law that requires ATG to result in a methionine in the protein. For a wheel to roll it must be round, physics requires it.Also, there is nothing preventing a common designer from using different codon usage for different, and supposedly separate, creations. You might as well use GGG for methionine in birds and ATG in mammals. Why couldn't a designer do this? On top of that, common design does not explain the PATTERN of homology, the nested hierarchy that we keep talking about.Let's approach this from a different prospective. What potential observation would be inconsistent with common design? What combination of characteristics in a fossil would be inconsistent with design? What differences in DNA would be inconsistent with common design? Or are you going to claim that any and all observations, known and unknown, are due to common design? If so, then I can only conclude that common design is a dogmatic belief.Edited by Taq, : No reason given.

Then ID fails to explain biodiversity."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 11Aren't IDer's curious as to biogeography? Is biogeography not something that ID must explain in order to explain modern biodiversity? As we have already demonstrated, due to the dogmatic nature of ID there is nothing we could ever show which would falsify ID. 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.

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.For example:

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J Mol Biol. 2010 Jan 8;395(1):79-88. Epub 2009 Sep 18.

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Changing the DNA recognition specificity of the EcoDam DNA-(adenine-N6)-methyltransferase by directed evolution.
Chahar S, Elsawy H, Ragozin S, Jeltsch A.

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School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany.

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EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the Escherichia coli genome. 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. By co-evolution of an enzyme library and a substrate library, we identified GATT as the best non-GATC site and discover a double mutation, R124S/P134S, as the first step to increase enzyme activity at GATT sites. After four generations of mutagenesis and selection, we obtained enzyme variants with new specificity for GATT. While the wild-type EcoDam shows no detectable activity at GATT sites in E. coli cells, some variants prefer methylation at GATT over GATC sites by about 10-fold in cells. In vitro DNA methylation kinetics carried out under single-turnover conditions using a hemimethylated GATC and a GATT oligonucleotide substrate confirmed that the evolved proteins prefer methylation of GATT sites to a similar degree. They show up to 1600-fold change in specificity in vitro and methylate the new GATT target site with 20% of the rate of GATC methylation by the wild-type enzyme, indicating good activity. We conclude that the new methyltransferases are fully functional in vivo and in vitro but show a new target-site specificity.

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PMID: 19766657 [PubMed - indexed for MEDLINE]

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

You mean evidence like orthologous ERV's, shared pseudogenes, etc.? We have that evidence in spades. The genetic evidence is conclusive. 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. A bush is a nested hierarchy. From that same article:"A phylogenetic analysis unambiguously confirms the conclusion that chimpanzees were our closest relatives to the exclusion of other primates and the relative divergence of the Homo—Pan and that of (Homo—Pan)— Gorilla are 4.93 million years and 7.26 million years, respectively."They agree with me. The nested hierarchy is unambiguous. Why aren't airbags found in a single lineage of cars? Why don't cars fall into a nested hierarhcy? Feathers are found in a single lineage of vertebrates. Three middle ear bones is found in a single lineage of vertebrates. So why aren't airbags found in a single lineage of cars, both morphologically and chronologically? Why are there cars with jet engines? If cars can have jet engines why can't bats have feathers? Why do human constructs consistently fail to produce a single nested hierarchy? You tell me. Why can't a designer change the architecture at will? Why a nested hierarchy? 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.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. 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. 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. 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).

So ID is not trying to determine why bacteria have flagella? Really? So I guess we can say that ID explains nothing about biology? Evolution deals with CHANGE in life, not the origin thereof. Abiogenesis deals with the origin of life. My example demonstrated that the specificity of an enzyme changed due to random mutations. The authors simply created an environment where such mutants would be detectable using their methodologies. That's it. This is no different than penicillin intelligently selecting for resistance mutations in bacteria. Is penicillin an intelligent agent? If you could be so kind, could you give the link for that paper again.

Just to help clarify this point, the reason that genes close to each other tend to be linked is that the chances of a recombination event occuring over a short span of DNA is low. The less DNA there is between two genes the less likely a recombination event will occur between the two genes. As the distance between two genes increases so too does the chance of recombination occuring in the gap between the two genes.

I reread it several times and it appears to be correct, but my mind could be playing tricks with me. I find that often happens when you read your own stuff, you project your intended meaning and can sometimes miss obvious mistakes. So here is a different explanation.Just to make the math easy, let's say the probability of a recombination event (i.e. a cross over in meiosis) occuring at any single base is 1 in a million (1 in 1E6 shorthand). If two genes (or more accurately, two alleles) are separated by 100 bases then the chances of a recombination event occuring between the genes is 1E2 in 1E6, or 1 in 1E4. If there are 1E6 bases between two genes then the chances of a recombination event between the two genes is 1 in 1. The more bases there are between the two genes the more likely they are to be separated during meiosis.