dscccc, “the molecular tree contradict the genetic one”
The molecular tree is the genetic tree. It is possible to infer trees for individual genes which sometimes don’t agree with the tree inferred from whole genome sequences or from large sets of gene sequences for various reasons, including the incomplete lineage sorting mentioned by Dennis, but they are all molecular genetic trees.
You quote a paper which says in the title that the degree of convergence is unusual, so it’s not a general explanation for any similarity which is seen in different genomes. They made clear that the convergence seen was due to similar selection at high temperature, and that not all the mutations were convergent. That virus has a very small genome - only a few genes, which overlap with each other. As a consequence there are not that many possibilities for mutations to optimize for a new condition, so it’s not too surprising that some of them should repeat in an experiment with enough repetitions.
You don’t think evolution happened at all, so why do you think convergence by selection somehow accounts for similarities in genomes? Even if it was all by selection, that wouldn’t support your rejection of evolution. You would be invoking evolution to disprove evolution.
“so its indeed a belief and not part of science because we cant test this claim in experiment.”
Just before you made this statement you were arguing based on the observed sequences of mammals. Those were observations, not experiments. You need to make up your mind whether inferences from observations (based on understanding gained from experiments on present day organisms) are part of science or not. You can’t have it both ways. Those of us who have actually been scientists are clear that this is part of science, and declaring that it isn’t is just a rhetorical strategy, not a serious argument. You can’t do experiments with stars, planets, black holes, etc. in astronomy - that doesn’t keep it from being a science.
“1) the rat population is huge, so the fixation time for new mutation will take more time in the rat genome then the cavia one”
It doesn’t matter. Huge numbers of neutral mutations happen in a population. A small proportion of them get fixed by chance. There has been plenty of time for fixation of a few neutral mutations in the GULO gene in rats.
“Almost always” is what you need to account for the similarities between genomes. An occasional parallel occurrence of the same mutation in different species (the technical term is homoplasy) can’t come anywhere near to accounting for what we see. I have seen a paper describing independent insertions of a transposon at the same site in 2 different species, but even then it wasn’t the same kind of transposon, so the events were easily distinguished.
“even so- according to the claim here of “15% prediction” we will need to find a 100%changes in the genomes of 2 animals that split before 50 my… we know that isnt true- then its wrong.”
This isn’t how this works. The multiplication isn’t valid. The 15% is not a prediction based on how many mutations are expected in a given period of time. It has to do with the fact that two speciation events occurred close to each other in time, with the relative times estimated from coalescence theory.
Of course, mutations do accumulate with time. Mammals have a lot of similarities in sequences that have no functional effect, that are the result of recent common descent, but if you go as far as comparing a bird and a mammal there is little sequence similarity outside of coding and regulatory sequences. There are blocks of similar gene order, and of course it’s easy to detect the similarity in sequences that code for most RNAs and proteins and some regulatory sequences. Dennis was right that the mammalian and plant genomes are not 50% identical. That article was probably referring to the most highly conserved genes, but those are a very small portion of either genome.
There’s not any possible biological mechanism for the repeating of millions of complex mutations in multiple species. Targeted mutation can’t do it, because enzymes are just not that accurate (and there’s no evidence for it anyway.) Natural selection can’t do it, because in complex organisms there are way too many ways for it accomplish similar functional results. Whichever one happens first is going to be selected.
I have to agree with Dennis that, if you are really interested in this stuff, you are going to have to go beyond news articles and creationist websites and take some college courses in molecular biology, or if you are capable of teaching yourself, get good textbooks in genetics, biochemistry, population genetics etc. and work your way through them.