A new article about a bird needs to be analyzed in an hour. I don't know if I can do it. I did.

I always suspect there is a hidden agenda when the New Yorker publishes a piece about pure science. The magazine isn't pro-science I quoted a colleague in a previous post.

The New Yorker is fine with science that either serves a literary purpose (doctors’ portraits of interesting patients) or a political purpose (environmental writing with its implicit critique of modern technology and capitalism). But the subtext of most of its coverage (there are exceptions) is that scientists are just a self-interested tribe with their own narrative and no claim to finding the truth, and that science must concede the supremacy of literary culture when it comes to anything human, and never try to submit human affairs to quantification or consilience with biology. Because the magazine is undoubtedly sophisticated in its writing and editing they don’t flaunt their postmodernism or their literary-intellectual proprietariness, but once you notice it you can make sense of a lot of their material.

. . . Obviously there are exceptions – Atul Gawande is consistently superb – but as soon as you notice it, their guild war on behalf of cultural critics and literary intellectuals against scientists, technologists, and analytic scholars becomes apparent.

What is the reason we get an article about the evolution of a South American bird? I don't know the author's brief or motivation, but judging from the title and the content, this is an article in the "Darwin-was- wrong" genre. It isn't, of course, but in trying to make his case the author creates a farrago of confusion that will confuse both Matthew and me. You can click to read.

One of the world's strangest birds is called the hoatzin. The South American range is here.

The video shows the strange climbing behavior of the chicks, who have ancestral claws on their wings, and it is below. The clawed chick, whose nest is built over water, simply drops into the drink, swim to the shore, and use their claws to get back to the nest.

There is a video that shows the climbing behavior.

The front claws, which made people think the bird is primitive, isn't the only strange thing about it. The Audubon Society features Elizabeth Deatrick's article on sketch.

Hoatzins are the only birds in the world that eat nothing but leaves, which, compared to seeds and fruit, aren’t very nutritious, and are hard to digest. So to accommodate this diet, the Hoatzin has evolved a multi-chambered digestive tract with lots of little “stomachs,” where the leaves can sit for a while and be digested by friendly bacteria. During the digestion process, the bacteria release methane that the bird then belches out, producing an olfactory aura that’s landed the Hoatzin a less-than-flattering nicknamed: the stinkbird. So much for fitting in.

It is also known as the "skunk bird."

We have some intriguing facts. It is very difficult to place the hoatzin on the family tree of birds. It is not useful because it is a different bird from other birds so long ago. If you use enough of it, you should be able to tell you what species the hoatzin is most similar to. Various analyses, depending on which parts of the DNA you look at, have suggested that it may be related to the ancestors of cranes and shorebirds. Depending on what part of the DNA you look at and which bird species you use, you can get different answers to the same question.

We can usually place a bird near its closest relatives if we use a lot of the bird's genetic material. peregrine falcons are more closely related to parrots than to other birds of prey. The correct place for falcons is on the bird evolutionary tree.

The idea of a branching tree of life, even though it is difficult, is still valid for we are using a phylogeny of genes to determine the population's location. The evolutionary history of the organisms that contain the genes does not match the evolutionary history of the animals that contain them.

There are several reasons for the discrepancies between the genes and organisms.

In incomplete lineage sorting, the first is. Let me tell you what's going on. If an ancestral species has two different forms of a genes, what would it look like? Let us assume that the branch that leads to X is separated from the branch that leads to Y.

The history of the species shows that Y and Z are more similar to each other than X is. The species X and Y are more closely related to Z than to A and B, for they both have form A, while Z has form B. The species X and Z are more closely related to each other than the species Y is.

It is not likely that you would find such discrepancies since there are so many genes. There is only one evolutionary history for the species and it is based on which populations evolved into new species. The trees can be different.

The way to solve this is to use lots and lots of genes and show a lot of phylogenies that match the tree of species. Barriers to gene exchange are involved in the definition ofbiological species.

That is what we find. Humans and Chimpanzees are more closely related to each other than the gorilla is to them. All of these species are related to the orangutan.

Depending on which species and which genes you look at, the hoatzin has genetic similarities that are discrepant if you look closely. It is not possible to show a general similarity between the genes of the two species. We don't know the nearest relative of the hoatzin. It's possible we won't know.

I don't think I have done a good job explaining this. In one sentence, the author refers to incomplete lineage sorting as a type of genetic scrambling. The evolutionary history of individual genes is different from the evolutionary history of the populations of organisms that contain those genes.

Heterogeneity, which can transfer genes between species that aren't all that closely related, is one of the factors that causes discrepancies between tree species. The transfer of bits of DNA into a species that doesn't reflect their evolutionary history is confusing I don't think it's a problem to place the hoatzin.

This is an example from Humans. I won't get into the issue of whether they're different species, though I don't think they are That would be correct. If you wanted to make a tree out of just the genes from Neanderthals, you would find out that every single one of us is more Neanderthal than the other way around. All of us are more closely related to each other than to Neanderthals, if you look at the whole genome analysis.

The author was able to conclude that the idea of a branching evolutionary tree may be overstated. Here's how he says it.

The tree is so ingrained in evolutionary biology that scientists encourage “tree thinking.” By learning to think in terms of trees, students can avoid the common fallacy of reading evolution as a ladder in which simpler organisms become more complex, as in the famous image “The Ascent of Man,” which shows a knuckle-walking ape evolving into an upright human. For all its pedagogical value, however, the tree also embeds subtle assumptions about evolution. The tree tends to downplay the genetic variation within species, which can obscure the fact that common ancestors are actually diverse populations that can pass on different versions of a gene to different descendants. It tells a story of endless partition and diversification, with branches that diverge and never reticulate.

The idea of evolutionary trees is questionable. The idea of trees for species, which is the way Darwin meant it to be construed, is doing well, but it just doesn't always fit with trees for some genes within a species. Tree thinking is good and likely to stay that way.

The outlines of animal evolution still look a lot like a tree in many places, which is why scientists continue to spend so much time developing and debating different branches. But, if tree thinking taught biologists that everything is connected, genes are suggesting that the connections can run even deeper than a tree can capture. To gain a more complete picture—and to answer questions like how such an unusual mix of traits came together in the hoatzin—scientists may need to think outside the tree.

He wouldn't have to create these apparent "discrepancies" if he was careful to distinguish between species trees on the one hand and genes on the other. In 2004, I wrote about this issue in my book Speciation with Allen Orr, and we have known about it for a long time. The appendix contains information.

I am not sure if sloppy editing made the confusions worse or if the author didn't clarify them. We're left with these facts.

a. The hoatzin is a damn weird bird. b. We haven’t been able to deduce its closest bird relatives.

c. There are evolutionary/genetic reasons for this difficulty.