Cool new paper by Robert Asher

if we both agree that similar morphology is connected to similar sequence then is see no real difference in our explanations.

That’s a problem for you. Perhaps you have lost sight of why you started this argument in the first place?


my argument was that there is a connection between similar sequence and similar morphology. since we both agree about that i see no real issue here.

What was your purpose in making that argument? Try to think back.

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Your statement surprise me. I would have thought that phylogenetic relationships were determined based on some degree of similarity, be it molecular, morphological or otherwise. Can you explain to laypersons why it is not the case and on what basis phylogenetic relationships are then determined ?

On the contrary, it seems to me that under a design perspective, it makes perfect sense that genes in anatomically/physiologically similar species would display more similarities than with the same genes in species more distant anatomically/physiologically. Indeed, for a given function, it is expected that the designer would fine tune the genes involved in that function according to the specific physiological needs of a given type of organisms.

And that is the classic misconception, which I’m sorry to say is still just wrong. Yes, the genes would be “tuned” to perform their functions for the organisms. But that doesn’t explain why they yield similar trees. The “tuning” is expected to be towards function, not tree topology. Only given common descent do you expect the tree topologies from different data sets (different genes, or morphology) to agree.

You, like scd, don’t seem to understand the difference between the sequence performing the function(and how the sequence relates to the function), and the phylogenetic tree derived from a set of different similar sequences.

The fact that more similar organisms are more likely to have similar physiologies does not explain why the sequences yield similar phylogenetic trees, particularly when we know what the genes do, how sequence affects the function, and that many genes are known to have completely unrelated and independent functions (some times none at all, aka junk-DNA).

I quote again from Theobald’s 29+ Evidences for macroevolution:


One common objection is the assertion that anatomy is not independent of biochemistry, and thus anatomically similar organisms are likely to be similar biochemically (e.g. in their molecular sequences) simply for functional reasons. According to this argument, then, we should expect phylogenies based on molecular sequences to be similar to phylogenies based on morphology even if organisms are not related by common descent. This argument is very wrong. There is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry. Though this logic may seem quite reasonable initially, all of molecular biology refutes this “common sense” correlation. In general, similar DNA and biochemistry give similar morphology and function, but the converse is not true—similar morphology and function is not necessarily the result of similar DNA or biochemistry. The reason is easily understood once explained; many very different DNA sequences or biochemical structures can result in the same functions and the same morphologies (see predictions 4.1 and 4.2 for a detailed explanation).

You really should also take the time to read predictions 4.1 and 4.2 mentioned.

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Let me see if I get this right(ish). The genetic similarity between similar species isn’t as interesting to understanding common ancestry as the the way the differences between the sequences of different species can be arranged in a tree-like relational structure. This would imply either a common ancestor or something that would have to be intentionally made to look like a common ancestry, it’s much more than similar function = similar sequence.

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The point really is that there is an enormous number of different possible and functionally equivalent sequences for any given gene sequence. So from a functional perspective, it is entirely conceivable that the DNA sequence of some gene could be different from what it is, yet still encode a functional transcription factor, or enzyme, or what have you, that would function just as well as the one it happens to have.

And while many of these different possible and functionally equivalent sequences would be similar to each other, it would be very unlikely that if you were to pick one among this set of similar and functionally equivalent sequences at random, to stick into your organism, that it should happen to be the one that ends up yielding the same phylogenetic position in relation to all other similar species, as the tree derived another gene would.

It is trivial to find examples of genes who’s function and sequence is pretty much totally independent of the sequences, functions, and physiology of the rest of the organism. I’ve mentioned this earlier, but the salivary amylase gene is an enzyme secreted with spit that breaks down chains of starch into it’s monomers. Clearly this gene doesn’t make you human, or even a mammal. It’s in spit because it does something in spit, it helps digest starch. Every organism that eats something starchy secretes this enzyme with spit. Yet the gene encoding it is not identical between these species.

Even if there are some sequence constraints operating on this gene that would explain why some species couldn’t have an identical one, that would still not explain why it yields a particular phylogenetic tree virtually identical to one derived from any other shared genetic locus.

We can certainly imagine reasons why it can’t always be identical, but it becomes very difficult to explain why that should yield trees with very similar topologies.
Let’s imagine that if this salivary amylase gene was encoded by an identical sequence in all species, then in one of those species some transcription factor (unique to and necessary) in that species would bind it on the chromosome and cause problems with transcription. Okay, that would explain why in that species, that sequence could not function properly if it was exactly identical to the sequence in all other species. But now we have merely explained why it isn’t an identical sequence, as there is SOME physiological reason why it can’t be. But we have not explained why it should be different in a way that yields a particular phylogenetic tree. It would be a grotesquely elaborate explanation we would have to come up with to explain why there are physiological constraints happening to constrain the sequence in all it’s phylogenetically informative loci in such a way that it sorts in a particular way.

And we’d now have to do this for all genes, in all species, in all their phylogenetically informative loci.


I can try. Basing relationships on similarity assumes that species that are more similar must also be more closely related. But that in turn assumes that evolution happens at a constant rate. If some species evolve more slowly than others, similarity may not reflect relationships. To make that point on the level of gross morphology, consider a shark, a trout, and a kiwi. The trout (at least on this gross level) is more similar to the shark than to the kiwi, but in fact it’s more closely related to the kiwi.

Instead, what we do is to consider the fit of the data to some tree, based on some criterion of fit, and choose the tree that fits best, i.e. the one that explains the pattern in the data. One of the simplest methods is parsimony: choose the tree that requires the fewest changes or, to put it another way, that requires the fewest separate gains or losses of particular features. If you do that with many sets of features (different DNA sequences, for example), and you get similar results consistently, you gain confidence in the tree.


What doesn’t make sense is why all of the genes produce similar trees. When we humans design organisms we often move exact copies of genes from very different creatures, such as taking an exact copy of a jellyfish gene for a fluorescent protein and putting it in mice or fish. Under a design perspective, there is no expectation of a correlation between genes. However, that is exactly what we would expect to see with evolution, and it is indeed what we see.

Under a design perspective, can you tell us why we would expect to see species with a mixture of reptilian and mammalian features, but no species with a mixture of avian and mammalian features?


Thanks @Rumraket, @John_Harshman, and @T_aquaticus! Those are three excellent and well explained posts.

Thanks a lot. I really appreciate.

As for kiwi, do you mean the bird below?


To make sense of this observation, I proposed that the designer would fine tune the genes involved in a given function according to the specific physiological needs of a given type of organisms. Under this fine tuning hypothesis, you would expect that genes involved in a given function would have more similar sequences in physiologically/anatomically closer species than in physiologically/anatomically more distant ones. Hence the observed tree like pattern.

Yes, but I could as well have been referring to a person from New Zealand.

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There’s no “hence” about it. First, have you already forgotten that phylogeny is not determined by similarity? Second, why should this fine tuning follow a nested hierarchy? Third, what about DNA that has nothing to do with physiology and anatomy?

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As @John_Harshman notes, why would this produce a nested hierarchy?

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are you saying that since there are so possible sequences that can perform the cytochrome c function, the chance of geting the same sequence/tree by convergent (design or convergent evolution) is extremly low, and thus it support common decent? is that your main point basically?

I am loss here! In what sense according to you is the trout more closely related to the kiwi than to the shark? Phylogenetically ? And in that case, what types of studies were used to determine this outcome? Gene and/or protein sequences studies? Others?

Yes. That’s what “related” means, you know.

Yes. All types of studies. There is zero controversy on this point. Feel free to look up any morphological or molecular study that includes at least one shark, one actinopterygian, and one tetrapod. Does this really come as a surprise to you?