One of the claims you make in your link is that “designer hypothesis” accounts for the fact that organisms with “similar mophology” have “similar biochemistry”, in reference to the conciliance between phylogenetic trees constructed using anatomical and molecular characters. This is untrue though. The only way the “design hypothesis” can explain such things is by saying “the designer chose to do it that way”, which is unfalsifiable and untenable as an explanation. It’s true that anatomy is not independent of biochemistry - obviously some anatomy is the product of particular biochemistries during development, but much isn’t. There’s no reason to expect that cows and whales should have more similar cytochrome b genes than cows and whale, for example, under the “design hypothesis”.
You also say that phylogenetic analyses assume common descent, so phylogenetic trees can be evidence of common descent. This is true at face value. Just taking a character and inferring a particular tree structure using it doesn’t “prove” that this structure is representative of the actual pattern of relatedness. However, when we get conciliance of multiple independent characters, both anatomical and molecular, the relationship suggested becomes better supported. ID proponents and creationists implicitly admit this when they point to incongruities in phylogenetic trees as evidence against the evolutionary relationship in question. If incongruence is evidence against the tree being real, then congruence is evidence for the tree being real.
(Edit: to be clear here, when I’m referring to the “design hypothesis”, this is obviously in opposition to “evolution including common descent”. I’m using the phrases in the way that @Nonlin.org is. Many other users here (not me personally) are perfectly comfortable accomodating evoution accommodating “design” in some form into “evolution including common descent”.)
Sure not equal, but would you say that gradualism is essential to evolution?
The shotgun marriage between Mendel and Darwin?
Strawmanning, “incredibly extreme”, “forbidding”? Is it too much to ask for ‘horizontal gradualism’ when ’ vertical gradualism’ is postulated? Read again 5.
Not just “intermediate in some way” but… in transition…
Not the version of gradualism that you’re working with, no, not at all.
It doesn’t follow that “vertical gradualism” neccessitates “horizontal gradualism”, even under your extreme version of gradualism. That being said, we do see a lot of “horizontal gradualism”, it’s one of the main reasons that the species problem exists. You didn’t address much of my point though, can you try again?
That’s what “transitional” means in the context of evolution. You asked what it would mean without that context, so I gave you an answer: it would mean that an organism’s form was simply intermediate between 2 other, without any genealogical relationship between them.
As I thought, you were talking about the latter of 2 options I gave you eariler. Coelacanth still is “transitional” in this sense: that the node it connects to in the phylogeny is between the node where earlier lobe-finned fish diverged and the node at the base of the crown tetrapods. The form of fossil coelacanths was also transitional, and since the extant coelacanth has a similar (in the grand scheme of things) morphology to its ancient, extinct, representatives, it represents a “living transitional form”. In the same sense, extant monotremes can be considered as living transitional forms between reptiles and mammals, and the extant spotted gar can be considered “transitional” between teleost fish and more basal ray-finned fish.
“The only way”? How so? Yes it’s not falsifiable but so is UCD since it’s used as assumption in cladistics - see links
See 1. - you just said “anatomy is not independent of biochemistry”
Can’t speak for others. My point with that OP is limited to “cladistics cannot prove UCD since UCD is an assumption in cladistics”
It seems you’re of the “blind, mindless, and purposeless environmental process” persuasion. I can see a guided evolution possible but that has nothing to do with the mainstream narrative.
See my quote that you’ve designated “2.” You can’t dismiss it by ignoring what I said about congruence and then cutting off my quote about the relationship between anatomy and biochemistry to make it seem as though I agree with you.
I just added the caveat so no one got on my case about making a dichotomy between evolution and design. Of course we’re talking about the “mainstream” model here, which doesn’t include a designer.
I’ve made up my mind, don’t try and twist things. I was quite clear in what I said about the relationship between anatomy and biochemistry. Some anatomy is dictated by some biochemistry, but nowhere near enough to explain the magnitude of congruence between molecular and anatomical character trees. I gave an example - the morphology of humans, cows, and whales is completely independent of the differences in cytochrome b between those species. If you think otherwise, feel free to try and make your case.
That’s a cop out if I’ve ever heard one. You didn’t seem to have much of an issue offering opposite views earlier.
How much “some”?
Can you quantify “nowhere near enough”?
You’re basically assuming cytochrome b gene is independent of the organism DNA. And then ask me to disprove? This is not how it works. The burden of proof is on those proposing the theory. However, it is trivial to show that all significant DNA segments are 100% correlated in an organism and including with morphology. IOW, any two significant human DNA segments will only be found in humans that also display human morphology. If the method is right or wrong, classifications based on one DNA segment are to be expected to match classifications based on any another DNA segment.
I have no issue with opposing views. Others have with mine.
Think about it. Molecular phylogenetic trees are usually constructed with protein-coding genes. We’ve known for decades that the vast majority of morphological differences between species are the result of regulatory changes, not changes in protein-coding genes. No, I can’t give you a percentage or something like that, but I don’t need to. There is absolutely no question that only a tiny number of molecular characters (used in phylogenetic trees) are responsible for the kind of morphological characters used (in phylogenetic trees). That’s a brute fact. If you want, we could go through an example of a phylogenetic analysis of a set of species, look at the molecular sequences used and the morphological characters used, and examine the literature for any link between the genes used and the morphology. But I can tell you know, we won’t find much, if any.
No, I’m not assuming it’s “independent of the organism DNA”, whatever that’s supposed to mean, I’m saying it’s independent of the kind of gross morphological characters used in phylogenetic analyses. This is trivially true - there’s no known mechanism by which the sequence of cytochrome b could influence the anatomy. That’s the evidence that it doesn’t, you disagree, so you need to give at least some reason why. You have made the claim that they are not independent, so back it up. This is analogous to you claiming that the number of blades of grass in your garden specifically affects the tides around the world. I say “no it doesn’t”, and your reponse is to say “you made a claim, back it up!” My evidence that it doesn’t is that there is no plausible mechanism by which it could be true, simple as that.
If I understand what you’re saying, I’d agree that they’re correlated (not 100%, mind), but the reason for this correlation is genetic drift and common descent, not some kind of functional necessity. You seem to be arguing that molecular sequences and anatomical characters can’t possibly be independent, because they produce congruent phylogenetic trees, which is obviously fallacious.
It might be helpful if you clarify what you mean by “significant DNA segment” though.
You’re saying that “human sequences are only found in humans” which is trivially true. The question is, do the human-specific differences in those sequences contribute specifically to the human morphology relative to other mammals? The answer is usually “no”.
Your link demonstrates otherwise. We are not assuming that fossils fit into a tree-like pattern. We are not assuming that evolutionary mechanisms will produce a tree-like pattern since we can observe that they do so in living populations. Furthermore, the null hypothesis is randomly distributed characteristics, so there is a comparison of models.
The fact that a designer can make any possible pattern of shared derived features means that it lacks predictive power and can’t be scientifically tested. Evolution does make specific predictions of what patterns you should and shouldn’t see which makes it scientifically testable.
You also claim that cars can be organized into an objective phylogeny with statistically significant phylogenetic signal, and yet no such tests are done. This is just an empty claim.
You then claim that anatomy is not independent of DNA sequence which is false. The vast majority of the human genome has no effect on anatomy. Genes like cytochrome c do not affect anatomy. On top of that, genomic features like transposons and introns do not affect anatomy, yet they correlate with phylogenies based on anatomy.
Finally, the measure of phylogenetic signal in a group of organisms is an objective measure through the use of computer algorithms.
I struggle to find anything that is accurate on that page.
That’s rather easy. Just with third base wobble you can change a DNA sequence by about 25% without changing the peptide sequence. About 90% of the human genome is not under selective pressure so it doesn’t affect morphology, and that 90% follows the same pattern as anatomy. For example, the phylogeny of LTR’s from shared ERV’s matches quite well to the consensus phylogeny for apes:
The theory of evolution predicted that tetrapods evolved from lobe finned fish, and finding fossils with a mixture of fish and tetrapod features confirms that prediction.
Other than trying to bring traffic to your own site I don’t see why you’d want to drag the conversation over there.
Since the thread is here I’ll respond here:
I said:
Phylogenetic trees are with protein-coding genes. Only a tiny number of molecular characters (used in phylogenetic trees) are responsible for the kind of morphological characters used.
Cytochrome b gene is independent of the kind of gross morphological characters used in phylogenetic analyses. This is trivially true - there’s no known mechanism by which the sequence of cytochrome b could influence the anatomy.
You replied:
Irrelevant.
Same as 1.
It’s not irrelevant at all - if molecular characters aren’t functionally correlated with morphological characters then there’s no reason to expect them to produce similar tree topologies independently (other than the unfalsifiable and lazy “God did it that way because he wanted to”).
I said:
This is analogous to you claiming that the number of blades of grass in your garden specifically affects the tides around the world.
You replied:
Not at all. You try to mentally separate genes from the genome. They are not separately inherited (acquired)
I’m not trying to “mentally separate genes from the genome” (whatever that’s supposed to mean). My point is that you’re claiming that all characters used in phylogenetic analyses are not actually independent. That means that the thymine in site X of mouse cytochrome b and the adenine in the same site in chicken cytochrome b are not independent characters from feathers in chicken, and lack of feathers in mouse. I’m pointing out that this is ridiculous, using an analogy.
I said:
If I understand what you’re saying, I’d agree that they’re correlated (not 100%, mind), but the reason for this correlation is genetic drift and common descent, not some kind of functional necessity. You seem to be arguing that molecular sequences and anatomical characters can’t possibly be independent, because they produce congruent phylogenetic trees, which is obviously fallacious.
You replied:
Yes, 100%. If it’s a human gene, it can only be found in humans with human genes and human morphology.
Maybe I gave you way too much credit in my interpretation of your previous comment. I thought you were making a much more nuanced point, but it turns out it was just the same tautology that I noticed later in the same post. Yes, human genes are only found in humans, otherwise they wouldn’t be described as “human genes”. That’s if by “human gene”, you mean a gene with a nucleotide sequence unique to humans. If however you mean a gene with an amino acid sequence unique to humans, then you’d be wrong, because there are dozens of genes with which the human gene has an identical amino acid sequence to the homologous chimpanzee gene.
I said:
You’re saying that “human sequences are only found in humans” which is trivially true. The question is, do the human-specific differences in those sequences contribute specifically to the human morphology relative to other mammals? The answer is usually “no”.
You replied:
Irrelevant. What matters is that genes, genome, and morphology are one package and never found independent of each other.
It’s not irrelevant at all. This is the crux of the argument. You’re claiming that these characters aren’t independent because they correlate together. I’ll repeat what I said before (and you failed to respond to): “You seem to be arguing that molecular sequences and anatomical characters can’t possibly be independent, because they produce congruent phylogenetic trees, which is obviously fallacious.”
To expand on that a little, think for a moment what would actually be expected under common descent. Would you fail to find human-specific sequences in the human genome? Would human-specific mutations fail to correlate with human-specific morphology? The answer is no on both counts. You’re basically argueing “phylogenetics is fallacious because we see exactly what we’d expect under common descent”.
