THERE IS a option for why like bodyplan equals like dna. FROM A COMMON BLUEPRINT FROM A CREATOR.
It would be that morpholgy would be biochemically alike. Why not? Its not proving common descent BUT ONCE AGAIN presuming its true and imagining one is proving it.
Is this a common objectiopn?? Who is making it besides creationists??
The objection stands!
No he should stay. Be peaceful. The case is not being well made why dna does not follow bodyplan unrelated to reproductive relationships of creatures. A common blueprint would also explain , better, why there is a branching in biology. If you have eyeballs you have the genes for them. Yet its not proof that there was a original eyeball creature/common descent. Thats just a line of rasoning, without other options, and lack of imagination, especially in light of historic creationism.
why not? if similar DNA means similar function then we should expect to find a correlation between similar morphology and similar genetics.
Now youâre just repeating yourself. This the same thing you said to begin with, and Theobald explained what is wrong with it in his âcriticismsâ response. Itâs not mere similarity in sequence you need to explain, itâs why the trees are similar.
Iâm sorry but it just doesnât seem like you understand the difference.
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so bascially you are asking why a mammal protein x should be closer to other mammal than to say a reptile? (since mammal should group with other mammals).
Two more problems with this idea:
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As has been pointed out to you, if similar genetics implies similar function, that doesnât translate to similar function implying similar genetics. Further, similar genetics doesnât necessarily imply similar function; small changes in DNA can result in big changes in function.
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If this argument applies to anything, it applies only to functional DNA, which makes up only a small percentage of the typical genome.
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sure. but in most cases there is such correlation.
im not sure about that. but lets focus a single topic each time.
Where would you get that idea?
Your problem, not mine.
How many cases have you analyzed?
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Phylogenetically closer, across different and independent data sets. We take a specific protein shared among all the species in question(an enzyme for example) that does something like degrade starch polymers into itâs monomers, from all these species and we determine itâs sequence from each.Call it Enzyme 1. So in species A it has some sequence, in B it has another similar one, in C and in D we get two more similar sequences.
The first thing we notice is that the sequence encoding enzyme 1 is not identical between them despite the fact that it does the same thing in all these species. The function is identical, it degrades starch polymers into monomers, but the sequence is not.
Okay, we then use an algorithm to make a phylogenetic tree based on the gene-sequences for this enzyme from all these species. We get a particular tree from this algorithm. We notice that species A is more closely related to species B than to C or D, and that C and D are more closely related than they are to A or B. So we end up with a relationship like ((AB)(CD)).
Okay, then we take some entirely different region of the genome. Maybe we pick a gene that codes for a protein that that is part of the complex that pumps protons while converting ATP into AMP, like the ATPase enzyme. Call it enzyme 2. So another enzyme, doing an entirely different and unrelated chemical reaction. We do the same thing, we sequence it in all these species and we notice that the sequence is not identical despite the fact that it has the same function. In all species it is part of the complex that pumps protons across the membrane while converting ATP into AMP. We proceed to make a phylogenetic tree again, and we obtain the same relationship ((AB)(CD)).
We do it with a third genetic sequence, take some entirely different region of the genome. Maybe we do what John Harshman suggested, we take a piece of nonfunctional DNA, like an intron, or an intergenic region thatâs a dead remnant of a transposon or another kind of pseudogene. We do all the same things as previously over again. We notice the sequence is not identical between our species, despite the fact that itâs nonfunctional. We give the four nonfunctional sequences to the algorithm again, and we get a tree again with the same relationship ((AB)(CD)).
Now the question is, why should they reproduce the same relationship? Why is A always grouped with B, and C grouped with D?
Clearly the gene-sequence of the starch enzyme in species A, is not functionally constrained to be phylogenetically grouped with the starch enzyme in species B. That would not make sense. Why should it be like that? Youâd have to posit some sort of completely mysterious cross-species correlation that, for reasons I simply canât imagine, constrain them to sort phylogenetically more closely to each other than to others. In other words, for some unimaginable reason, nucleotides in the gene in species A, are forced to have a sequence that a phylogenetic algorithm will end up putting as the closest relative of the sequence for the same gene in species B. Why? It doesnât make sense.
And clearly there is no functional constraint operating on the starch enzyme that should force it to be reproduce the same branching relationship as the ATPase enzyme. That also would not make sense. Why should there be a constraint that forces similar trees from different shared genes?
And clearly the nonfunctional DNA piece is under no other functional constraint than to not be deleterious. Not being deleterious has nothing to do with what kind of phylogenetic tree an algorithm will produce, so clearly there can be no functional reason why a tree derived from a nonfunctional DNA sequence is constrained to yield a tree similar to a functional one.
None of it makes any sense from the perspective of what these genes do. Their functions are unrelated to each other. The gene-sequence of enzyme 1 doesnât affect the gene-sequence of enzyme 2 or vice-versa, and neither of them affect or are affected by the nonfunctional one. Even more obviously, the tree produced by an algorithm from the gene-sequences of enzyme 1 in our four species, do not in any way constrain the tree produced by the gene-sequences of enzyme 2, or the tree produced by the algorithm from the nonfunctional sequence. Thereâs no sensible reasons the trees would in any way constrain each other.
There is only one explanation that makes sense. A rather simple and straightforward one. They derive from a common ancestral species, and they reproduce the same relationship because they each resided in populations that went through the same genealogical history. So theyâre not constrained to yield the trees they do for any functional reasons, theyâre constrained to do so for historical reasons: They share a genealogical history.
That is the ONLY explanation that makes any logical sense.
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Thanks for this explanation. It was incredibly helpful!
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i think that its actually does make sense. for instance: a fish protein should group with other fishes since fishes have many things in common: they have similar morphology, similar habitat etc. so it make sense to think that they will share more similarity among a specific protein than with say a mammal or a reptile. and if its true for a single protein it should be true for other fish proteins. i dont see why it doesnt make sense for you.
Yes. In order to see that it would be necessary to read what he wrote, which you clearly did not do.
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@scd I think I understand what you are saying⌠You should read this post here, which includes a similar assertion and where Joshua follows up with this:
It is not that it doesnât make sense, or that it isnât intuitive, it is that it isnât accurate.
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But theyâre NOT grouped based on similarity. I donât know how many times I have to repeat that.
The TREES are similar, THAT is what you are being asked to explain. Not the fact that the proteins are similar. Since we know what the proteins do, it actually becomes mysterious that theyâre not completely identical, since they do the exact same thing in each species, as I was careful to explain. But you can even put that aside.
That the trees are similar, which were derived from different independent sequences, some of which are even nonfunctional. Why should a nonfunctional sequence be constrained to yield a tree similar to one derived from a functional gene? Or to yet another nonfunctional sequence? Why do different species even have similar nonfunctional sequences in them, and (again), why do they reproduce the same trees?
I believe I actually explained why that would not be the case by pointing out how no such constraint actually operates on these sequences. Why should the tree derived from one protein affect another proteinâs tree, and why should it affect the tree derived from a nonfunctional sequence?
Iâm running out of ways of explaining this and I donât know what to do short of you having to literally go take courses in molecular evolution. I suppose some times being tutored and having to work out problems and tests for yourself canât be substituted for by just reading stuff in your own spare time. I will say, though, that the kind of mindset you take with you to a certain question makes a big difference for comprehension. When youâre reading something technical looking for something to disagree with, or perhaps being unwilling to let go of your preconceptions and âtry onâ another pespective, then argument and debate is hopeless. Wanting to understand is essential.
I emplore you to at least TRY to understand why we would say the things we do. You donât have to agree with it, but if you can figure out why we say it(hint: itâs not fear of Godâs judgement), as in try to consider âwhat would have to be true, for their arguments to be valid?â.
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@scd Are you beginning to see the difference between what is intuitive and what is borne out from the data?
ok. maybe that image will help us to communicate better because a language barrier. here is the phylogeny of the cytochrome c protein:
(image from britannica site)
you can see that the cytochrome c tree also fit with the creatures similarity in general. so for instance human and a monkey share more similarity on that protein than say human and a tuna. now, this similarity/difference (even the headline called âPhylogeny base on nucleotide differenceâ) comparison indeed give us a tree. and this tree indeed base on level of similarity\disimilarity. now, if i got it wrong again please tell me where im wrong and we will continue from there. i can also discuss about the non-functional sequence argument but lets focus each point at time.
First of all, in many ways not really.
Second, superficial appearances can be deceiving. The morphological similarities arenât scored here in any rigorous way, so we are left trying to eyeball it from some silhouettes, which is completely meaningless and subjective. You need to show me a phylogeny based on morphology, scored by similarity.
Iâm looking at the Tuna, and Iâm trying to determine how âsimilarâ it looks to the moth. Itâs not obvious to me how similar they look at all(how do I score this? Where is the character matrix we should use?). They are separated by a score of 38.2 nucleotide differences in the cytochrome C gene. (I donât really understand the algorithm used here, some of the minimum number of substitutions are indicated to be negative, which makes little sense to me).
I compare the moth to humans, and I get
Human-Moth 33.4
Tuna-Moth 38.2
Is human more similar to moth? By what characters?
I try Pigeon to moth and get 30.6. Are Pigeons even more similar to moths than humans and tuna? Itâs not obvious to me that they are.
Rabbit (30.3) is more similar to moth than dog is (32) in nucleotide sequence from cytochrome C. But itâs not obvious to me that a rabbit looks more like a moth than a dog does. Hey, maybe they do to you, who knows? Without an objective method of scoring their characters, itâs impossible to tell.
Rattlesnake is apparently slightly more similar to humans than tuna by cytochrome C sequence. I donât know why, they have no limbs, at least tuna do.
Is the turtle obviously more different from pigs than chickens are? Pigs and turtles run around on all fours, chickens fly. Cytochrome c says yes.
It gets even less obvious with the fungi. How similar do bakerâs yeast look to pigs versus chickens to you? Is bakerâs yeas obviously more similar than Candida is? Cytochrome c says yes. Etc. etc.
Now the problem here isnât so much that you can find examples of morphological similarity also corresponding to genetic similarity, certainly you can. The claim was never that this canât be done or isnât ever the case.
The question you were posed is why we obtain this result(why are the trees similar, which has not been demonstrated in this case), when we have zero evidence for any functional constraints between the data sets. What is it about the morphology of humans that constrains the cytochrome c-sequence to be phylogenetically grouped closer to the cytochrome c-sequence of monkey, than the cytochrome c-sequence of rabbit? You seem to be saying that itâs because humans are morphologically more similar to monkeys than to rabbits. Even supposing that is actually the case, that still doesnât explain why the trees are similar.
Why should there be any degree of correspondence here? Cytochrome c is a protein in the electron transport chain. Itâs involved in core energy metabolism(involved in turning food into work), it has nothing to do with the order of appearance, shape, or size of anyoneâs limbs, bones, organs, numbers or position of eyes. Even supposing cytochrome c was involved in some developmental patterning somewhere, why would that constrain itâs nucleotide sequence to yield a phylogenetic tree that mirrors the morphological tree? Even if they were both based on similarity scores that would still not explain why oneâs tree mirrors the other when they are independent data sets. Thatâs the whole point here.
If what you want to accomplish is to show that consilience of independent phylogenies isnât evidence for common descent, what you need to be doing is demonstrating their non-independence in such a way that their putative non-independence would end up constraining the trees inferred from them to be similar for whatever functional reason.
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âso for instance human and a monkey share more similarity on that protein than say human and a tunaâ
Actually, you canât read that off the tree. Iâm sure that claim is true for most of the species shown, but the tree doesnât show it. What it shows are inferred numbers of changes along particular branches, and the sums of those changes will not match the pairwise distances between two taxa. Nor does âbased on nucleotide differencesâ mean what you think it does. I suspect that this tree was built by least squares fit of a simple matching distance matrix, but one canât be sure without a real reference.
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I know! Repeating it infinitely wonât be enough. 
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