Posted: May 18, 2017 6:45 am
It's really much worse than that single post. You should, if you desire to facepalm so hard you'd need reconstructive surgery, take the time to read the thread through. There are in that thread, among other qualified people, Joseph Felsenstein, trying to teach this guy how common descent is inferred.
Joe Felsenstein wrote:Look Erik, I have worked for over half a century on the logic of methods for inferring phylogenies. Since back when there were about 6 people in that field. Up to today, when one of my papers is the 41st most-cited paper in all of science. I wrote the standard book on inferring phylogenies. And I distributed the first widely-distributed package of programs for inferring phylogenies.
So I know how the algorithms for reconstructing phylogenies work. They have gotten steadily more sophisticated and steadily better and better at assessing how conservative or how labile different parts of molecular sequences are. And no, they contain no step that tells the program to make sure to put anything called “chimpanzee” in the tree near anything called human. And yet, they keep doing that. Owing to the evidence.
Take a look at the evidence yourself. Try Orthomam, at
http://www.orthomam.univ-montp2.fr for example, a database of sequence alignments for (now) 14,526 protein-coding loci for 43 completely-sequenced mammalian genomes. And there they have trees, inferred automatically, for each locus. Or you can download the some of the aligned sequences, get one of the free phylogeny programs, and infer the trees yourself. Check out how similar the trees for different loci are. That’s important. Not just that they are trees but which trees they get for different parts of the genome.
If you have problems, ask an expert. Say John Harshman, who is an experienced molecular systematist who is a considerable expert on genomic and morphological evidence on bird and reptile phylogeny, and who uses phylogeny algorithms all the time. My 2004 book contains a section discussing, admiringly, his arguments about using bootstrap sampling with parsimony methods.
There are others here as well who have lots of relevant expertise. Stop lecturing them about how they are making elementary and fundamental mistakes. (In the passage you quote, Darwin didn’t make any mistake either, though you seem to think he did.)
I’m not trying to suppress discussion, just trying to urge you to look at the mass of evidence before making wild statements.
Yeah, I know, it’s always a mistake to “pull rank” and cite one’s own credentials in these discussions. Makes one look like a pompous defensive idiot. We do have to listen respectfully to any argument, no matter how little background the person has who puts it forward.
But in this case Erik is lecturing us about how we have all gone wrong, and when you look at his arguments, it’s like what Gertrude Stein said about Oakland, California: “When you get there, there’s no there there.”