If you find phylogeny to be "bullshit", your biology and microbiology professors have truly failed you. Evolution by natural selection has produced the wonderful diversity that is life. Phylogenetic reconstruction is the tool biologists use to understand the history of all life on the planet. The fact that some living organisms engage in lateral gene transfer, or that there is no definition of species that perfectly applies to all living things is no reason to abandon perhaps the most fundamental and central pursuit of biology. Who we are as humans is inextricably tied to our mammalian, primate, vertebrate and multicellular ancestry, and we know this by virtue of the wonders of phylogenetics.
well, they kind of are bullshit, in the same way that the bohr model is bullshit, and that quantum mechanics is bullshit, too. It's not REALLY what's going on, but rather a simplification that gets your feeble brain to the point where it can do something useful. You'll eventually learn a model that's less bullshitty, that gets you doing one slightly more useful thing, but it's still bullshit.
Still no. You'd be hard pressed to find any biologists left that would argue that discrete taxa exist, but whether or not humans are more closely related to chimps or gorillas is superbly knowable and certainly not "bullshit". Likewise, whether or not birds and dinosaurs constitute a monophyletic clade is not bullshit. Even with all the "exotic" stuff like endogenous retroviruses or whatever "exception" you think you can raise, the "Tree of Life" model still works very very well, it just complicates how the branching works.
I work with hydrogenases, and the amount of horizontal gene transfer is incredible. There are so many mobile elements in the environment... E coli, the humble gut bacterium, seems to have four copies of hydrogenase. Two come from the broad class of "formate hydrogen lyase"; the other two are "uptake hydrogenases". Almost certainly they come from horizontal gene transfer, because other gammaproteobacteria may or may not have some or all of these hydrogenases; and you will find uptake hydrogenases scattered through bacteria (and archaeal) phyla.
the hydrogenase that I work with is part of a mobile element; it's found in our organism in a gene island, but also straight up in the genome of another organism that was isolated 5000 kilometers away, in a totally different ecotype. both of these guys are found in the ocean, but none of the other members in the broad family that it comes from are oceanic: they come from terrestrial volcanic mats.
So obviously species-wise discrete or fuzzy taxa do not work for me; but even protein phylogenetics can be muddied by things like random gene fusions and convergent evolution. I'm not sure that some of the trees that I generate are actually taxonomic, but may be the result of selective pressure against a highly conserved scaffold.
Of course, they're still useful, even if they're bullshit... Because I don't care about phylogenetics, I care about function. If the tree that I make is an unfaithful representation of the historical record, no big deal, as long as it faitfully clusters function.
My undergraduate senior project was on the interaction between breast milk and microbial ecology in infants, so I can appreciate the difficulty of protein phylogenetics in non eukaryotic organisms. I think it's still important to underscore that simply because whatever tree I get phylip to spit out doesn't reflect the true evolotionary history of the organism/gene/whatever, doesn't mean that 1)tracing the evolutionary history of an organism/gene/whatever is "bullshit" (whatever you mean by that) or that 2)the evolutionary history cannot be elucidated by other means. Phylogenetics can be used to discover gene fusion events and convergent evolution.
I think another way to put this is, we've got many years of experience using various forms of evidence to make trees of life (originally character states such as morphogenic properties but now also including gene data and other molecular details).
And even though we've been able to build a great story and a great tree structure, those of us who have studied deep biology know that the tree structure is really muddied by some inconvenient phenomena; for example, using some tiny subset of genes to compute phylogeny generates a very different result from using all genes, or combining all the gene data with all the morphogenic data. Understanding the underlying phenomena which help explain the oddballs that don't fit into the Dogma is almost always useful, because it helps us go back and refine the Dogma.
It's really more of a graph of life when you include horizontal gene trasnfer; whether that graph is very much non-tree like is still an open question.
That's rather harsh, don't you think? All models have their limits and scopes, but that doesn't preclude them being useful in their own right. For instance, Newtonian physics simply can't cope with molecular-scale events, but it still gets used every day for the cases where quantum or relativistic effects don't matter. Likewise, phylogenetic classification is still a hugely useful tool within biology. The fact that it has assumptions and limitations merely defines it, rather than diminishing from it.
Just because it's bullshit does not mean it's useless.
The tree of life model is almost useless for understanding single celled organisms which vastly outnumber there multicellular counterparts. It also creates a lot of confusion where people assume the model matches reality instead of poorly mapping to reality. Consider species is a surprisingly vague concept where A and B may be compatible and A and C are compatible but B and C are not. The point is it's based on inaccurate assumptions, if you understand how and why the model breaks down you can extract a lot of value from F=MA or any other such approximation.
You seem to have allowed the intricacies of the subject to distract you from my meaning. All of that is true, and there are obvious macrostructures, such as those you mentioned, which are credible. However, the worship of phylogenetic classification schemes which attempt to disambiguate even the most minute details of living organisms are not useful except maybe in the nichest of fields and to boost bioinformaticists' egos.
I'm still not sure what the argument is that you're making, or who you are accusing, and of what. Minute details tend only to be relevant in niche fields. Isn't the study of minute details what makes them niche fields? When you compute the area of a circle, though you may only use a few digits of pi, surely you can appreciate how those that need to precisely calculate the area of a circle might use more digits than you do. The fact that pi is irrational, that neither of you are using the "real" value of pi, doesn't make what either of you are doing "bullshit" though.
