more evidence for shared ancestry (NOT similarity)

Its a very interesting paper and does provide convincing evidence for a common ancestor for humans and chimpanzees. But its by no means the only non functional shared derived trait we share with the apes these include thousands of pseudogenes and viral sequences as well as large amounts of conserved synteny (genes being in the same order on chromosomes) which decrease according to how distantly animals are thought to be related.this definition of cladistics might help people understand the paper:"Cladistics is a particular method of hypothesizing relationships among organisms. Like other methods, it has its own set of assumptions, procedures, and limitations. Cladistics is now accepted as the best method available for phylogenetic analysis, for it provides an explicit and testable hypothesis of organismal relationships. The basic idea behind cladistics is that members of a group share a common evolutionary history, and are "closely related", more so to members of the same group than to other organisms. These groups are recognized by sharing unique features which were not present in distant ancestors. These shared derived characteristics are called synapomorphies.Note that it is not enough for organisms to share characteristics, in fact two organisms may share a great many characteristics and not be considered members of the same group. For example, consider a jellyfish, starfish, and a human; which two are most closely related? The jellyfish and starfish both live in the water, have radial symmetry, and are invertebrates, so you might suppose that they belong together in a group. This would not reflect evolutionary relationships, however, since the starfish and human are actually more closely related. It is not just the presence of shared characteristics which is important, but the presence of shared derived characteristics. In the example above, all three characteristics are believed to have been present in the common ancestor of all animals, and so are trivial for determining relationships, since all three organisms in question belong to the group "animals". While humans are different from the other two organisms, they differ only in characteristics which arose newly in an ancestor which is not shared with the other two. As you shall see on the next page, chosing the right characters is one of the most important steps in a cladistic analysis."from: Introduction to Cladisticsand"clade -- A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig."from: UCMP Glossary: Phylogenetics

The examples of human chromsomes 4 and 17 are not very good because although they are different the differences have been well studied and charecterised and the differences are compatible with the current proposed evolutionary relationships of the apes (including humans). Its like saying that humans cannot be related to apes because human chromsome 2 was formed by the fusion of two ape chromosomes and therefore is different to ape chromsomes.There are examples of recurring breakpoints but these have specific features usually large duplicated segments that lead to unequal crossing over. These sequences or any others known to lead to chromsomal rearrangements are as far as i am aware not known to be present in the chromsomal region concerned. Also non random does not mean directed.This paper:
"Keller MP, Seifried BA, Chance PF. Molecular evolution of the CMT1A-REP region: a human- and chimpanzee-specific repeat. Mol Biol Evol. 1999 Aug;16(8):1019-26.PMID: 10474898"is interesting as it gives an example of a shared repeat between humans and chimpanzees only that can lead to genetic disease by enabling the duplication or deletion of the gene the two repeats flank. So the designer put a sequence in humans and chimpanzees the only known function of which is to cause Charcot-Marie-Tooth disease and HNPP. Intersting the gene these sequences flank (peripheral nerve protein-22) is particularly dosage sensitive, so these repeats are in just about the worst palce. The sequence does not cause these problems if present as a single instance as in the rest of the apes.[This message has been edited by Itzpapalotl, 10-01-2002]

Hi T.B.There are examples of organisms that occupy the same ecological nice are morphologically almost indistinguishable and yet are genetically diverse examples of convergent evolution. The bacterial group Bdellovibrio (originally classified on the basis of morphology and behaviour) are predatory bacteria that all attack similar prey in a similar way are almost identical physiologically and yet are highly diverse genetically with at most 35% genetic homology.Examples of convergent evolution of proteins in which only the funtional domains are similar are numerous and also show the similar appearance/function is not necessarily associated with genetic similarity. Therefore large amounts of similarity can only mean common ancestory if you want a scientific hypothesis or the designer wanted everything to be fairly similar and to look as if it came from a common ancestor but for no real reason if you can only accept divine intervention. Maybe the creator is trying to test our faith by making things look exactly as if evolution had happened .see:
http://lsvl.la.asu.edu/mic494/html/bdellovibrio.htmlandAppl Environ Microbiol 2000 Jun;66(6):2365-71
Prey range characterization, ribotyping, and diversity of soil and rhizosphere
Bdellovibrio spp. isolated on phytopathogenic bacteria.
Jurkevitch E, Minz D, Ramati B, Barel G.
PMID: 10831412

Tranquility Base,Of course my scenario is not the only possible one but i would maintain that it is the more likely one. Is there any evidence or experiment you can think of that could distinguish between the two theories?.Peter borger,The reason i mentioned these bacteria was that it was suggested phenotypically similar organisms in the same environment would have similar genomes due to design and these bacteria are an example where this is not true. Regardless of how the difference arose it raises doubts about the crationist argument that genetically similar organisms are designed to be similar because they live in similar environments. Convergent evolution is hardly an ad hoc explanation as it has been known about for a long time and is well studied. Of course mentioning ad hoc explanations means you don't have to commment on the actual evidence.What do you make of TB's:"If phenotypically similar bacteria for example share the same environment now that does not mean they always did. Due to potentially different past historiues they will have differnt gene loss histories."is that not an ad hoc explanation or don't the same rules apply? (this is not intended to be a criticism of TB's theory which must be considered on its merits rather that if it's ad hoc or not).

You say: "I can only conceive convergent evolution when the mutation are introduced non-randomly. Otherwise the odds are against it. Read Spetner, he did the maths on convergent evolution. Why? Since evolutionists never ever did any calculations on the odds of convergence."i say: look at the program called converge/CAPE available from: http://mep.bio.psu.edu/phanalysis.html
"CAPE is designed to test convergent and parallel evolution at the amino acid sequence level. It computes the probabilities that the observed convergent and parallel substitutions are attributable to random chance."The author Jianzhi Zhang has published/co authored several interesting papers on molecular evolution jou might want to look at.