I believe this is not true. Have you really thought about it?
I’ve already granted the first point. As for the second, what is the current understanding in science?
It is the theory of relativity, not Einsteinian physics. It is Quantum Mechanics, not Planckian theory. It is the Germ Theory of Disease, not Kochian theory. It is genetics, not Crickian theory. I have thought about it.
Your’e joking, right? 
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That a tree is only a first-level approximation of how to describe genetic data. Several well understood processes cause violations of the tree, both in experiments and simulation. The argument being made here by DI is to attack a straw-man we already rejected a long time ago.
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So, then, this must be a rare opportunity for unilateral agreement! 
I have no clue what you are talking about. 
You can’t possibly be talking about the DI “argument” that “Darwinists” need to deal with Ewert’s paper, because that is a rather recent development. Which DI argument are you talking about?
And you seem to be saying that the tree is the current model, but just a first order one. That violations to the tree are known, which I have acknowledged. How do we know they are “violations” and how common are are these violations of the tree model. We count them as violation because of the tree, and they are not so frequent as to destroy the signal of the tree. It is that the tree must be “perfect” that is the straw man.
When you say you that accept common descent, what is that based on if not the tree-like pattern of life? Would you say that the nested hierarchy is not a tree?
I am so puzzled just now.
I’m talking about this article.
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“Darwinists” is an anachronism. It is like posturing against Newtonians to come to terms with the evidence for relativity.
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We figured out a long time ago that a tree is not what evolution predicts, a long time ago. @Winston_Ewert did not know this, it seems, till our exchange with him here.
Now, in their defense, a lot of evolution-defender sorts have incorrectly argued that life is in a perfect tree. That was in error. It is an example of a bad argument for evolution. They are wrong, and any biologist can and should tell them otherwise.
You have a lot of catching up to do on population genetics.
You’ve been learning a cartoon version of evolution from ID, so of course you are puzzled.
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Seriously, how would you know where I get my “version of evolution” from? This is just a massively unwarranted assumption on your part, one that is exacerbated by the fact that it is so wrong. I get my understanding of evolution from reading books written by “evolutionist” authors. Please stop.
Well, you think that evolution predicts a perfect tree and is well described as Darwinism. That sounds like ID.
This is false. I think no such thing. I have never stated that evolution predicts a perfect tree and I would never say such a thing because I think it’s nonsense.
However, I have seen “evolutionists” consistently argue that common descent predicts a nested hierarchy.
So why don’t we begin with that statement:
- Does common descent predict a nested hierarchy?
- Is a nested hierarchy a “tree”?
In the future, before declaring that I hold some position, perhaps you could first ask me if I hold that position. Please? 
Apologies. I thought you were making a rhetorical point by asking an obvious question. I misunderstood.
A nested hierarchy is a tree. Common descent predicts a nested hierarchy, and a tree, but not a perfect tree/nested hierarchy. It all hinges on “perfect” vs. noisy.
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Well, I hope I have settled what I think in that regard. I can think of a number of things that might lead to a tree that is not “perfect.”
- horizontal gene transfer
- symbiosis
- hybridization
Do you agree with those and are there others?
It doesn’t sound like ID to me because I have never encountered an ID author who clams that “evolution predicts a perfect tree.” You seem to have been learning a cartoon version of ID. 
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I presume you’ve heard of Casey Luskin? He wrote several articles on ENV about phylogenetic incongruence, always with the message that the lack of a perfect tree (because of incongruences) was a problem for evolution. E.g. here:
“At the end of the day, the dream that DNA sequence data would fit into a nice-neat tree of life has failed, and with it a key prediction of neo-Darwinian theory.”
I have never seen him qualify his statements about incongruence with something like “some degree of incongruence would be expected, but this much is too much for evolution”. Even if ID authors don’t believe, deep down, that evolution predicts a perfect tree, I’d say they do a pretty good job of giving their lay readers that impression.
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And I’ve made that argument many times myself, though I try to say “‘Tree-of-life’ pattern of common descent.” No one has called me on not-a-tree yet, but I should be more careful how I say it.
“Tree” now only approximates a very broad view, up close it’s Tangled Vines.
Thank you for linking that article! I need to read it carefully but I can see from just a brief examination how Joshua (and others) could take the article to be setting up a “perfect tree” as a straw man and then beating that straw man. From what I’ve read so far I disagree with Luskiin’s approach.
However, and here is the danger in actually citing ID articles, did you happen to also notice the following?
“derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change.”
Jeffrey H. Schwartz, Bruno Maresca, “Do Molecular Clocks Run at All? A Critique of Molecular Systematics,” Biological Theory , 1(4):357-371, (2006).
I need to see if I can view that paper.
Schwartz’s point is that we shouldn’t believe any molecular phylogenetic results because they rely on false assumptions. But his real point is that we should believe that orangutans, not chimps, are the closest relatives of humans, and any analysis that says otherwise must be wrong for some reason or other. @swamidass, what’s the polite term for “crank”?
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The ones you mention are quite rare in most taxa. The common ones are random homoplasy, incomplete lineage sorting, and errors in data coding and analysis.
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The title of Luskin’s article at ENV is Molecular Biology Has Failed to Yield a Grand “Tree of Life” But then the remainder of his article absolutely requires the existence of such a tree in order to spot the anomalies that his article depends on. There is an internal incoherence to the argument.
My opinion is that the best way to address that is to acknowledge the tree model and point out the logical inconsistency rather than denying that the model is that of a tree.
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This is how it is often communicated to the public. It’s a lot easier to grasp than “common descent predicts a statistically significant phylogenetic signal that rises above the noise caused by mechanisms such as incomplete lineage sorting and homoplasies”.
Right or wrong, communicating science to the general public can involve sacrificing accuracy for clarity.
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