Discussion of Phylogenetic Methods

That isn't true at all. The higher rate of change in the cytB gene means it is more useful for more closely related species.

Is this an admission that creationism is incapable of making any predictions about what we should or shouldn't observe?

The point we are making is that only common ancestry can explain why species fit into clades. You have been incapable of explaining why creationism would produce clades, such as the mammal clade that humans belong to.

How so? Why would an individual coder produce code so that it falls into a nested hierarchy?

No, it doesn't. It means a loss of phylogenetic signal for distantly related species."There is one caveat to consider with this prediction: if rates of evolution are fast, then cladistic information can be lost over time since it would be essentially randomized. The faster the rate, the less time needed to obliterate information about the historical branching pattern of evolution."
29+ Evidences for Macroevolution: Part 1This is why strongly conserved sequences of DNA are used for phylogenetic reconstruction of species that share a distant common ancestor. For more closely related species, the phylogenetic signal in the cytB gene is still there. For more distantly related species, the phylogenetic signal in cytC is still there.We could use a crime scene as an analogy. If an expert shows up at a crime scene within hours of a murder then the expert can collect evidence such as fresh tire tracks, fresh shoe prints, and so forth. If the expert shows up weeks after a murder that evidence will be gone, but there will still be other evidence such as DNA and fingerprint evidence. Just because some evidence has disappeared does not make all of the evidence disappear.

The pattern of shared derived characteristics (i.e. an objective phylogeny) do show us that they share a common ancestor in the same way that a fingerprint shows us that someone touched a surface. Isn't that the impression you have been pushing all along? If a designer can mix and match design units freely, then creationism should not produce a nested hierarchy. We are saying that only common ancestry is able to explain why shared derived characteristics found in biological species form an objective phylogeny. Creationism can't explain it.

That is probably the most important point. You can take modules from several other programs and meld them into a new program. This would produce numerous and obvious violations of a nested hierarchy. Contrary to vaporwave's claims, if we took the tools we use to analyze phylogenies in biological species and applied them to software we would not conclude that software evolved through common ancestry and vertical inheritance.

Do we? For those frogs, what percentage of their genomes have been sequenced? How much phylogenetic coverage is there? If the divergence is ancient and you don't have lots of sister taxa coverage, then you might not have enough data. The deeper the node the more difficult it is to preserve a phylogenetic signal without sufficient coverage (at least from what I have read). To use an analogy, even though no one has found Jimmy Hoffa's body no one believes he was snagged by aliens and transported to another galaxy. We are pretty sure that humans are involved. In the same vein, we are extremely confident that these frogs evolved from a common ancestor.

We OBSERVE that it is well conserved due to the number of shared bases. There are no assumptions. It is a direct observation.

It is evidence for an evolutionary history. Also, your inability to explain this data using creationism further reinforces this conclusion. Linnaeus did not assume evolution in the 1700's, and he came to the same conclusion. The nested hierarchy is an observation, and creationism can't explain it. Evolution can.

What "dominant evolutionary pattern"? Why would a single programmer build several programs in a way that they would form an evolutionary pattern?

Why would it fall into a nested hierarchy?Let's say there are 5 different peripherals, A through E. A programmer could create these 5 programs with 2 peripherals each:1. A, C
2. B, E
3. A, B
4. A, E
5. B, CI can almost guarantee that those programs would not produce a nested hierarchy. There is absolutely no reason why a programmer would produce code that falls into a nested hierarchy because that programmer is able to mix and match peripherals in a manner that easily violates a nested hierarchy. Do you not understand what conservation of sequence is? You line up the sequences and see how many positions in the gene have the same base. It is an observation, not a conclusion. You can't subjectively weigh a DNA base. A phylogeny is evidence that common ancestry is true. It isn't an assumption.Do you have to assume that a suspect is guilty in order to get a DNA match? No. The DNA match is what evidences guilt. The same process works with phylogenies and common ancestry. The phylogeny is evidence of common ancestry. Why not a vertebrate-cephalopod template? Why not a mammal-bird template? Why not a fish-jellyfish template?All of these would violate a nested hierarchy, but there is nothing stopping a designer from making them. "The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991). "
29+ Evidences for Macroevolution: Part 1

There seems to be some confusion over what sequence conservation is. I will be using protein sequences here, since they are a 3rd the length of DNA sequences.Here is a comparison of human and chimp cytochrome B:

355/379(94%)
Query  1    MTPMRKTNPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDAS  60
            MTP RK NPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDAS
Sbjct  1    MTPTRKINPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDAS  60

Query  61   TAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYSETWNIGIILL  120
            TAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLY ETWNIGIILL
Sbjct  61   TAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYLETWNIGIILL  120

Query  121  LATMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFFT  180
            L TMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQW+WGGYSVDSPTLTRFFT
Sbjct  121  LTTMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWVWGGYSVDSPTLTRFFT  180

Query  181  FHFILPfiiaalatlhllflhETGSNNPLGITSHSDKITFHPYYTIKDAlglllfllslm  240
            FHFILPFII AL TLHLLFLHETGSNNPLGITSHSDKITFHPYYTIKD LGL LFLL LM
Sbjct  181  FHFILPFIITALTTLHLLFLHETGSNNPLGITSHSDKITFHPYYTIKDILGLFLFLLILM  240

Query  241  tltlfsPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRSVPNKLGGVlalllsili  300
            TLTLFSP LLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRS+PNKLGGVLALLLSILI
Sbjct  241  TLTLFSPGLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRSIPNKLGGVLALLLSILI  300

Query  301  lamipilHMSKQQSMMFRPLSQSlywllaadlliltwiGGQPVSYPFTIIGQVASVLYFT  360
            L  IP+LH SKQQSMMFRPLSQ LYWLLA DLLILTWIGGQPVSYPF  IGQ+ASVLYFT
Sbjct  301  LTAIPVLHTSKQQSMMFRPLSQLLYWLLATDLLILTWIGGQPVSYPFITIGQMASVLYFT  360

Query  361  TILILMPTISLIENKMLKW  379
            TILILMP  SLIENKML+W
Sbjct  361  TILILMPIASLIENKMLEW  379

Here is a comparison of human and chimpanzee cytochrome c (somatic)

105/105(100%)
Query  1    MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW  60
            MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
Sbjct  1    MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW  60

Query  61   GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE  105
            GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
Sbjct  61   GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE  105

Human and chimp cytochrome B is 95% conserved. Human and chimp cytochrome C is 100% conserved. We get these numbers by directly comparing the sequences. We say that cytochrome C is more conserved because 100% is greater than 95%. We do not change these values based on phylogenetic data.Any questions?

But we do produce well supported phylogenies all over the place. I have already cited the cytochrome c example.

You have been incapable of explaining why something other than common ancestry would necessarily produce a nested hierarchy. If you can't come up with a logical and valid reason why a process other than common ancestry would necessarily produce a nested hierarchy, then our point stands. Doesn't change the fact that all of the evidence supports common ancestry.