Let’s have a serious discussion about phylogenetic systematics.
What are the assumptions, the methods, and the inferences that can be drawn from phylogenetic analysis.
For example, is there anything to the creationist claim that phylogenetic systematics assumes common ancestry and does it even matter?
I’ll be using a number of different references such as Molecular Evolution: A Phylogenetic Approach and Molecular Evolution and Phylogenetics.
This thread will not be password protected, but it will be protected by angels.
No, that isn’t correct. I am concluding loss of flight because the tree requires either multiple losses of flight or a gain of flight after loss. And common descent isn’t a working hypothesis, it’s a conclusion from the data.
Inheritance doesn’t result in sequence variation. Mutation and fixation result in sequence variation.
I don’t understand why you think the sequence similarity looks like common descent in one study but not in others. What percent difference do you think would mark the upper limit of variation in common descent, and why?
I don’t think the great majority of people have data I do not or have studied this significant data you say exists. And a created universe is not relevant. We’re talking about events in the past hundred million years at most, so far./blockquote>
I’m following the biological data where it leads; you are not. I don’t know what other data you are thinking of, but I suspect you know as little about it as you do about biology.
But it isn’t a random walk. If a sequence hits a mine, it’s eliminated from the population. Natural selection ensures that only safe paths through the mine field are followed. You are working with a serious misunderstanding. Anyway, the bulk of the differences are silent. As for design being required for new function, you have no evidence of that, and it’s irrelevant anyway. Even if that were true, guided evolution and common descent are a better explanation of the data than separate creation. Again, how do you account for the nested hierarchy?
As others have pointed out, your example doesn’t work. There actually is no nested hierarchy even of Mac laptops. And note that the components, when re-used, are identical. Not the case with genes.
Common descent plus difference divergence times certainly does. I don’t understand your objection.
It might be interesting, but only if you have some criterion to use in identifying that line. Do you?
This also puzzles me. How are you getting “60x”?
Complete with useless wings? Like the stubs that kiwis have?
Design is less than useless to explain this, it’s simply contrary to any kind of design we’ve ever seen.
Glen Davidson
Lets think about this.
you say YES a TREE is assumed. Thats not the point in this stuff.
its the exclusivity of how a tree could exist or seeem to exist.
A assumption is that common DESIGN did not , could not, be a option.
Not from investigation or giving it ten minutes but a absolute assumption of NO!!
There you , on behalf of others, go again!
You say morphology shows a tree and later molecular scoring shows a tree.
COMMON DESCENT is tested and proved!
Yet if common design was true it also would show a ORIGINAL tree at creation and then show a design for adaptations that also would be alike in unrelated creatures. Indeed show spectrums/
EXAMPLE. Human colours. A creator could make Adam with one colour, and then adaption needs would create other colours .Not more creation but within the design system.
Your side is saying thats not even a option . Instead human colours show a tree from each branching from each other and so common descent from some colour.
Our side says YES a original colour but no branching by evolvimng system. Instead a innate design in the system.
Why would YOU then say ONLY common descent can explain likeness of characters in a spectrum??
Why??
No! Its a failure of intelligent scientific investigation.
They ruled out a creator and a creators design AND then say morph/genes likeness prove common descent.
Common design would be this way too. In morphology and genetics being hand in glove.
Common descent being said to be shown by likeness in traits/characters in morph/genes is plain not true until other options are shown not true.
cDesign easily explains likeness.
Yes a creator on creation week could give everyone euyeballs that look very alike in all ways.
Yet its not proof of common descent. Trees easily show the truth of a creator.
In fact we can thank evolutionists for bringing the issue up.
The special creation original biology would be unknown. further IF cDesign was true it would include in same design morphing ability. Then this would include a spectrum within biology.
Example is human colour.
Common design would use human colour to say there was first a single colour and then branching from it.
Yet cDesign would say there was a original colour and from created designs withing bodyplans colours appeared as needed. no evolving from a common colour descent!!
yet looking at colours both sides could convince themselves.
Once again its up to common descent folks to demonstrate why thery have the right to deny other options for similarity.
Is it they just didn’t think of cDesign! Lack of imagination. or a crusading rejection of God and origins?!
Creationists could embrace common descent reasonings to make a great creationist point before great audiences.
Square this with the following.
So, which way is it? Conclusion or assumption? At first definitely an assumption, as admitted by biologists beginning with Darwin. And, also beginning with Darwin, it’s presented as if a definitive conclusion, even though the data does not justify the conclusion.
Now this,
Yes, but a formal validation of the *tree* is not a validation of *common descent*. These two are different things. The tree is what the data *looks like* but common descent is what species supposedly *do*. The claim that the species do that requires its own evidence.
To get back to the same old manuscripts analogy, ancient manuscripts are also arranged into trees. It’s what the data extracted from them *looks like* but NOBODY claims that manuscripts evolve into each other. There are scribes (ID-ists can now exclaim: Designer!) who make and replicate the manuscripts across generations, and the result gives a phylogenetic picture.
ETA. With regard to species and biological organisms, everybody has agreed all along that there is variation across populations. And that biosphere overall looks like nested hierarchies. This is uncontroversial. The contentious point is if this represents unbroken evolution of species by “natural selection” i.e. the diversification in the apparent order occured all by itself with no guiding force, or a creation plan i.e. that biosphere was compelled “from above” to assume the current shape (with variation within reasonably specifiable limits).
The problem with the latter theory is that forces “from above” leave no traces for science to study after the fact, only for philosophy. The problem with the former theory is that there is no proper analogy to biological evolution in any other field of inquiry, scientific or philosophical. Things just don’t get better and stronger and smarter by themselves; they tend to wear down and fall apart rather.
And as most would agree that manuscripts don’t change and that it is at the copying stage, when new manuscripts are copied from old, that the changes occur, so it is with biological evolution. Individuals don’t change genetically but when offspring are produced they are not perfect copies of their parents. This is the source of variation for selection to work on.
There is a guiding force. The niche!
You mean when you take your wifey and move away from your parents and go living in the jungle, then you evolve? You don’t just die? Let’s say you don’t die, and you actually become competent to climb the trees to catch a banana and you pass on this competence to your kids. Now, was it the niche that guided you or was it your own innate-and-trained ability to comprehend the niche and adapt to it? Your story is woefully inadequate.
I know Ernst Mayr basically says this that a little variation-adaptation is the same thing as evolution in the big scale, but the problem with it is that it’s just a say-so. Any five-year-old can come up with a say-so like this. As a minimum, we need a say-so that makes sense and has a reasonable analogy.
“Most would agree”??? Who the hell would disagree and why? Why give any room for idiots when we are talking science?
For simplicity, let’s not do probabilities and modalities. Let’s do only straightforward deduction of certainties. This is not a complicated issue in the first place, so let’s stop obfuscation.
Erik,
When people try to lampoon evolution, they almost invariably sound idiotic – and not for the reasons they think.
“Sound idiotic” or *are idiotic*? And why “almost invariably”? Which of these is the case now? Speak clearly or remain ignored.
Erik,
Sound idiotic. Hence the choice of those very words.
Because they don’t always get it so hopelessly wrong as you did above.
Some J-Mac-ish hilarious bullshit from Erik there, LMFAO
Care to substantiate for a change?
Choice of words is very problematic with evolutionists. They may be talking about an assumption that a little while later transmorphs into “conclusion from the data” where the data may be of a different category. I don’t blame you. You have your role models here and you simply follow them.
Erik,
Yeah, if you say so Erik.
Sausage!
It makes about as much sense as always just saying “niche.”
Allan Miller,
I didn’t ask for agreement. I asked for substantiation. You have not given any.
Erik,
You’re just deflecting anyway.
I was commenting on the inaccuracy of your ludicrous, phoodooesque lampoon. Of course I didn’t go into detail, because I have seen you consistently fail to grasp the notions you presume to critique on many prior occasions. For all your arrogance, you are one of the more obtuse posters here, and that’s saying something.
Anyway, this won’t get my mince pies made.
Well Erik, you appeared idiotic to me, for the following reason:
Immediately after Alan Fox has pointed out how you are mis-stating the manuscript analogy, viz:
You repeat the ‘individuals evolve’ error in your pathetic lampoon, thus:
Positively phodooesque.
Actually, Alan Fox mis-stated the way I applied the analogy.
Alan Fox says, “…most would agree that manuscripts don’t change…”
What I said, “…manuscripts evolve into each other…”
Notice the difference? Of course you don’t. But the difference is that, instead of saying that manuscripts change (full stop), the statement is that manuscripts evolve (over generations of course) yielding other manuscripts. And when I talked of Alan moving into the jungle, I explicitly mentioned his kids, the next generation.
So Alan Fox was not fixing anything. He was talking past the issue. As are you. Keep laughing.
I happen to critique notions such as assumption and conclusion in the quoted statements by Harshman and Felsenstein. There is really no detail here to go into. All you need to do is to stay on topic. But okay, talk about whatever else you like.
It begins as an assumption for the sake of argument. If there’s common descent, we expect to see this. Do we see this? Yes, we do. Would we expect to see this absent common descent? No, we would not. Ergo, common descent.
Unless you can come up with some other process that results in that sort of nested hierarchy, we can’t avoid the conclusion of common descent.
If you want to say that the designer creates species from scratch by copying existing species but making little errors in the copying process, go ahead. That is indeed an alternative explanation that would produce exactly the same results as common descent. Do you want to advance that as a hypothesis?
No, common descent neither supposes nor denies a guiding force behind evolution. The origin of variation is not relevant to the pattern. But I have to say that the pattern sure doesn’t look much like a master plan. No rational being who wanted to end up with the current state would begin billions of years ago with a world that looked nothing like today’s world and wander through such a twisty path for so long. The mammalian jaw and middle ear alone makes top-down planning absurd.
So you think natural selection doesn’t happen, then?
Oh good, you reached consensus.
So who is the creator according to the majority of the world population?
Watches don’t breed.
Everyone understands that. It’s just that alternatives are even more inadequate. We don’t know much. But what we do know seems to be internally consistent.
And God said, “Let there be light,” and there was light.
.
If you are so convinced you are correct and that evolution is bunk then why are you persisting here when you could be putting your efforts into writing a paper that would have a much wider audience?
I can testify to that!
Yes, yes you did.
You wrote:
That is an idiotic lampoon of evolution.
For a linguist, you sure find comprehension a challenge.
I disagree with this and I’ve been trying to point it out for some time now, apparently rather poorly.
If there is common descent we expect to see a tree. We see a tree, therefore common descent. We don’t see the tree because of common descent we see the tree because that’s what our tools and methods have us create. And as Erik has pointed out, repeatedly, we have trees without common descent, so trees don’t justify a conclusion of common descent.
Would we see a tree absent common descent? Maybe, maybe not. How would we know? Assume separate ancestry. Unique origins. You’d still get the same tree from the data. Why is assuming a random topography the best assumption to make when modeling unique origins? What justifies that assumption?
So “what we would expect absent common descent” is a red herring. It should have no part in this, because it’s hardly even a scientific concept.
I’ll advance that hypothesis. In fact, it looks remarkably similar to Erik’s analogy to manuscript copying.
If the designer creates species from scratch by copying existing species but making little errors in the copying process then we would expect to see a tree [You already granted that this is true.]. We do see a tree, thus we are justified in concluding that the designer creates species from scratch by copying existing species but making little errors in the copying process.
How is this any different from the argument you made in coming to a conclusion of common descent?
But Erik’s alternative is a counterfeit of common descent. I will agree that a creator who creates using an existing model with slight variation will give the exact appearance of common descent and so is not distinguishable from it. But is that the hypothesis you want to entertain? And it isn’t just seeing a tree that’s the evidence of descent. It’s seeing a tree that’s a significantly better fit to the data than any other tree or no tree.
Why would you get the same tree from the data, given separate ancestry? What would be your assumption, and why?
I don’t understand how you get to this conclusion. You will need to explain your reasoning more completely.
That’s because it is Erik’s analogy to manuscript copying.
Agreed. This scenario would leave the same observable result and produce the same trees we see. But is that really a plausible alternative? Can’t we just use Occam’s Razor to reject this hypothesis? This is certainly not the creator that anyone believes in, an incompetent copier with no particular goal in mind. Isn’t common descent a very much simpler explanation?
I’ve always been willing to agree that a designer who mimics common descent can’t be distinguished from common descent. But I’ve always supposed that nobody would accept such a designer as explanation. Are you the first? Are you sincere?
Out of sheer dumb luck, of course
It must be a Christmas miracle!
🙂
No dazz. John clearly explained that luck had nothing to do with it.
At the very least we can try to think about how something other than common descent would “create” new species, and see what follows.
Bill Cole has been trying to make some rationalizations in the common descent vs common design thread about how a putative designer could be operating. He thought that if the designer is merely using “common designs”, which he took to be things that are merely similar, then we’d still get consilience of independent phylogenies.
He was wrong. In order for consilience of independent phylogenies to result from a design process, then designer has to be deliberately creating new species by mimicking the process of common descent, as in creating a species, then copying it (splitting) into two new species, then making small alterations in these new species, then deleting the ancestor, then copying the two new species into four new species, then making small alterations in the four new species, then deleting the two ancestral ones etc. etc.
Or, if all the species were created simultaneously, then the designer would have to be deliberately going into the genomes and tweaking the genes of these species such that all the genes overwhelmingly converge on the same phylogeny. There’d be no functional reason to do this, it would ONLY have to because for reasons that can’t be believed by a thinking person, the designer WANTS to deceive us.
But the designer would not be mimicking common descent.
My hypothesis is serious, as is Erik’s. It helps clarify the mistake in reasoning that accompanies the confusion between assuming and concluding. But no, I do not really think that God specially created each species. I do however believe he used a process of descent with modification where the modifications were not “mistakes” or “errors” in copying..
Your caricature is, if anything, Lamarkian rather than Darwinian.
The guidance is that organisms in a population compete for living space – the niche – and breeding opportunities. Success in leaving offspring varies and the niche sifts out the less successful. That non-random element is, I believe, enough to bring about the evolutionary pattern of change that we observe, as in the nested hierarchy.
DNA_Jock,
Ninja’d!
I’m sure that most would agree but I can’t be certain everyone does.
Phylogenetics relies on Bayesian inference, I think.
Nothing is certain but death and taxes! 🙂
Which issue? Phylogenetic analysis? I find it hard going. When John Harshman explains, it’s fascinating but “not complicated’? Beg to differ!
Rumraket,
John Harshman,
The tree is how the data is arranged. The data does not require a conclusion of loss of flight because there is so much sequence variation.
What is driving the mutation?
John Harshman,
I previously did not either and was blind to new evidence that was around me which only started to exist when I opened my eyes.
I am proposing an alternative explanation you are not despite the problem with the data.
You need to provide evidence of a safe path with a workable probability of getting to the other side without extinction.
The components are not necessarily identical. Just like genes they can have slight variation to enable a modified function. The example does work very well.
I think 1% or less difference in both sequence variation, phosphorylation patterns and alternative splicing patterns would support common descent. Anything greater would create the mine field dilemma especially with complex nuclear proteins. Based on this my tentative conclusion is that crocks share a common ancestor but flightless birds do not.
This reasoning is fallacious. There would be no process of common descent to mimic. You’re proposing that the designer is mimicking a process that does not actually exist, which appears absurd on its face.
I have already shown you, it does not yield similar trees. Why does it not yield similar trees? Because the number of possible changes, and therefore the number of possible trees, is so vast, it would be unbelievably unlikely that simply introducing changes for whatever functional reasons, would also just so happen to yield similar trees.
In order to get similar trees from different genes, *something* has to be constraining the changes towards the same branching topology.
Two things are known that can do this:
1. Common descent.
2. A designer that is deliberately forcing the genes to exhibit a similar genealogical branching pattern.
But why would the designer be deliberately forcing the genes to exhibit a similar genealogical branching pattern? There’s no functional reason to do this. That would be extremely deceptive, because it makes it look like the organisms really did go through a branching genealogical process.
Why? Explain why.
There is nothing absurd about what I wrote.
The scenario is described is analogous to what happens with common descent of species.
Rumraket,
Why do you believe there are so many possible changes if the design is efficient? Every different animal contains nucleotides and amino acids and the genetic code. There are many ways to make a nand gate but designers use standards to make designs more efficient. Efficient design restricts choices as evidenced by Mac designs and forms a hierarchy of similarity and differences.
I did explain why. Let me try again. You cannot mimic something that cannot be mimicked. Would you at least agree with that?
And what sorts of things cannot be mimicked? Things that do not exist. Would you also agree with that?
If “common descent” does not exist it cannot be mimicked.
Q.E.D.