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.
I would strongly disagree with this statement.
We know that common descent could produce a nested hierarchy but we have no idea what it “ought” to produce.
peace
What it’s like to (try to) teach this stuff to fifth, Mung, Erik, and colewd:
SImple. Your nested hierarchy is arbitrary, dependent on choosing a particular character to define each level of the hierarchy, and not only does it depend on which characters you choose, it also depends on the order in which they are chosen. Real nested hierarchies don’t depend on character choice or order, but on all the data you gather (without a priori intent to support a particular relationship) considered simultaneously. That is, the data themselves must have a hierarchical structure that the analysis merely recognizes.
Not in the slightest.
If I’m unclear why not ask clarifying questions?
It’s what I would do.
peace
You may have a slight semblance of a point. In addition to simple descent, it’s also required that there be branching of lineages and that character state changes occur at various times within lineages. But this is generally understood as entailed in the usual meaning of the term “common descent”. Would you agree that with those additions, a nested hierarchy would be expected?
so in order to formulate a true nested hierarchy you need to not intend to create a nested hierarchy??
Is that your position??
How can we know the intentions of those who drew up the tree?
peace
I don’t actually think that’s what you would do. I think your major goal is to appear wiser than anyone else, and whatever tricks you think will serve that end are what comes out. If you’re unclear why not try harder to say what you mean, if you do indeed mean anything?
So when you say “common descent” you really mean to imply much of Darwinism?
ie if you accept common descent you accept the whole kit an caboodle and not just descent from a common ancestor.
peace
No, that isn’t my position. You have the argumentation style of Ratbert. We don’t need intentions. DNA sequences are what they are. Each is a continuous series of characters, and nobody picks out just the parts they like; they analyze the entire sequence. Or, if you want intentions, you could ask me what my intent was in assembling the various sequences I have used in the papers we have from time to time discussed: the answer is that I intended to determine the phyogenies of the various groups sequenced. I didn’t pick the sequences because they gave me the results I wanted. I just took the results that came out of the analyses, including the tests for strong hierarchical structure.
I do try hard.
I think that much of the way things are arranged in the universe is simply because God intended the universe to be comprehensible to us.
God could do thing anyway he wants but he chooses to do things so that he can be understood by us.
I thought all of that was clear from the get go. If it’s still unclear just say so and I can try and elaborate further
peace
No. Your attempts to paraphrase me or determine the implications of what I say are consistently wrong, almost as if you have no real interest in understanding but just want to score some cheap point.
“Darwinism”, if I understand your meaning, is chiefly concerned with the mechanisms that cause variation and fixation within populations. Those mechanisms are not relevant to the nested hierarchy, so I mean to imply nothing of the sort you claim. Again, here’s all that’s necessary:
1. Descent from common ancestors.
2. Some amount of change, from whatever cause, within lineages.
3. Branching of lineages.
Note that there is nothing about the causes of change. Given those three conditions, there should be a nested hierarchy. Would you agree?
Why arrange life into a consistent nested hierarchy rather than some other comprehensible pattern? Because that particular pattern implies common descent, which if there is no common descent actually makes the universe less comprehensible.
Why analyze DNA sequences and not something else?
So you assumed common descent. OK
That is interesting but I’d like to know the intent of the fellows who discovered the purported objective nested hierarchy
because according to you in order for their conclusion to be objective they would have needed to not intend to find a nested hierarchy
peace
I’m not aware of a comprehensible pattern that moves from the general to the specific that is not a nested hierarchy.
And when we humans make sense of the world we tend to group things from the general to the specific
peace
I don’t believe this is true. So we should be able to pick any DNA sequence at all and arrive at the same nested hierarchy?
I must be simply glacial then. 🙂
I’m not sure what you mean by no common descent and since common descent is not the only valid reading of a nested hierarchy I’m not sure how it’s presence makes the world less comprehensible
Semantic field theory does not make language less comprehensible if every word is not descended from a common ancestor.
peace
The point is that you’ve spent years arguing about common descent and the nested hierarchy, but still don’t know what constitutes a nested hierarchy. Do you see why the diagram is not a nested hierarchy, arbitrary or otherwise?
A single element can’t constitute a hierarchy. However, crows share more physical character traits with sparrows than they do with humans, who are also omnivorous and bipedal. Like this:
{{crows, sparrows}, humans}
Think about it. Are you arguing that we can’t objectively classify crows closer to sparrows than humans based on an overview of all their physical character traits?
Exactly my point. We can’t just look at the nested hierarchy and assume common descent or conclude common descent or whatever. We have to resort to additional hypotheses.
Dumb. As. Rocks.
There are of course certain complications: the sufficiency of data, erasure of information over time, horizontal transfer, lineage sorting. All these can be dealt with. Science doesn’t deal with absolutes. But most DNA sequences will produce very similar nested hierarchies, which is as good as we can expect. For example, around 20% of DNA sequences show gorillas as the closest relative to humans, closer than chimps. That’s lineage sorting. But almost all those sequences will agree on the rest of primate phylogeny. Are you intending a serious challenge to nested hierarchy, or just a cheap point?
I notice you have not presented your additional hypothesis. Why?
By “no common descent” I refer to separate creation of species (or such other entities as you may think are “kinds”). I don’t know of any other valid reading of a nested hierarchy; you certainly haven’t suggested any. Again: nested hierarchy is expected from common descent and we know of nothing else for which that pattern is expected. If god poofs a nested hierarchy into existence, he should expect that people will infer common descent from that, leading to a false understanding of the world. A word that leads to false understanding is not comprehensible.
So is it the number of traits that are shared or is it which traits are shared? I think crows and humans are more alike in their intelligence than crows and sparrows.
{{crows, humans}, sparrows}
Think about it. What is it that makes that classification objective, scientific consensus? And is it really about how similar they are in totality?
I’m not sure what you mean by “moves from the general to the specific”, and suspect that any comprehensible patter that doesn’t do that will not be considered a nested hierarchy. But you certainly have not provided any examples of nested hierarchies, nor is there any reason why god should create that particular comprehensible pattern as opposed to any other. We certainly have examples of patterns that are not nested hierarchies; the periodic table springs to mind, as does the classification of igneous rocks.
Aside from life, other nested hierarchies we know of are imposed rather than discovered. I think of the Eons, Eras, Periods, and Ages of the geological time scale, for example.
I had already presented it upthread. I really should start a new OP on it.
What did you have in mind? DNA sequences offer a massive amount of objectively gathered and scored data.
As a general guide, assume that every sentence you begin with “so” is factually incorrect. Your childish point-scoring annoys me.
Is it objective or isn’t it? Sometimes you seem to think it is, other times not. But I am one of the fellows who discovered it, so feel free to ask me.
I bring you not peace, but a sword.
Where did you do this? The claim to have already done something in some unspecified place could uncharitably be viewed as obfuscation.
I don’t believe this is true for the exact same reason I stated before. If, as you say, “most DNA sequences will produce very similar nested hierarchies” then we should be able to pick and choose at random and get pretty much the same tree most of the time. Are you saying that this is in fact the case, that randomly selected DNA sequences will more often than not produce the same tree?
I was working on a new OP and thought I’d put it in the OP. But for you:
Notably, you sidestepped the question rather than answering. Do you really think it is reasonable to argue that a close look at the character traits of crows, sparrows, and humans won’t objectively place crows and sparrows closer together?
ETA: skeleton, bones, pulmonary function, brain structure, feathers, red blood cells. Then there’s genetics, where we can actually quantify the similarities and differences.
With the various caveats I have already mentioned, yes. That’s what we see.
Thanks, but not one of those is a clear statement of an explanatory hypothesis, and taken together they contain a number of mutual contradictions. Perhaps I should wait for your new OP. Please try very hard to make your hypothesis clear. Harder than you have previously.
The phrase “Crown Group” is use a lot in evolutionary biology. The phrase is not listed in Joe Felsenstein’s book.
Anybody not on my ignore list is welcome to give their explanation of what a crown group is.
Mung:
Because what makes the hierarchy objective is the fact that many independent lines of evidence point to it.
If creationism were true, there would be no reason to expect such a convergence. That’s why creationism is laughed at by evolutionary biologists and other knowledgeable folks.
It’s flat-earth stupid, embraced only by crackpots.
A crown group is a clade that includes the most recent common ancestor of two or more living species and all its descendants.
keiths:
Erik:
No. The pattern is there and begs for an explanation. Evolutionists have one.
What’s yours? Coincidence? The Designer just happens to be an anal-retentive evolution mimic? He hates the eggheads and wants to fool them into accepting common descent?
Why cling to a position that makes no sense? Do you want to remain ignorant? Do you want to be laughed at by the people who understand this stuff?
Which nested hierarchy are you referring to? You speak of “the hierarchy” as if there is only one. Yet when Theobald speaks, he speaks as if they are legion.
Theobald:
Many phylogenies can be constructed, each one of which is more or less “a unique, well-supported, objective nested hierarchy.” Do you really think that only one such phylogeny can be constructed?
What?? I have no problem with common descent.
This is the first time I can recall arguing about nested hierarchy. I do recall you bringing up common descent almost every time I talk to to you.
That and my inability to ever get a strait answer out of you and your acting like you are a collective rather than an individual are things I remember most about our interactions.
It seems nothing much has changed
why?? and who made you the authority.
Depends on what character traits you decide to focus on.
humans and crows share the following traits that sparrows don’t have AFAIK
omnivore diet
tool use
the ability to mimic human speech
the ability to recognize individual humans
understanding analogies
If we were to focus on traits like those then crows would be closer to humans than they are to sparrows
No I’m arguing that any choice of traits is subjective by it’s very nature, choose something else get another tree.
For instance you just subjectively chose physical character traits rather than social traits or habitat.
I’m also arguing that the concept of “objective” is nonsensical given the atheist worldview.
peace
because God is not the author of confusion perhaps
Peace
Mung,
Why so helpless?
A tiny bit of thought would enable you (or a brighter person, anyway) to figure this out.
Look at Zachriel’s example of an objective nested hierarchy: {{crows, sparrows}, humans}. Evolutionary biologists would accept that hierarchy as accurately representing the evolutionary relationships of those three species. Does it follow that this is the only possible ONH, and that zebras, for instance, cannot be properly placed into it?
Think, Mung.
GlenDavidson,
How are the sources unrelated, Glen? They are all made of atoms. They are 100% related. Atoms can take different forms as in computers and living organisms.
Maybe your claim is really that life seems to use more consistent architectures then human designs.
Yes, the transcription translation mechanism has been around for a long time and appears consistent across life. Living designs start with a firm understand of atoms and molecules something that humans are learning about.
This is evidence that strongly supports design.
Good designs have architectures that last a long time. As humans get better at design we see architectures that last longer and longer. The C-Mos gate is an example. The D-Ram is another example.
fifth:
It’s exactly the opposite. God would create confusion by matching the trees, since that is the pattern expected under common descent, but not under common design.
Why would God choose to create this false and confusing appearance?
colewd:
LOL.
Shorter Bill:
Thanks John.
Do you have some examples. Are tetrapods a crown group?
It’s time that you learn what words mean. I know that this prattle makes avoidance of the actual issue an ongoing project, but you’re just babbling away now. Related doesn’t mean “they’re all made of atoms.” Pathetic.
No, that’s not true at all. Human designs are often much more consistent throughout their usage, as in essentially identical (with tweaks, perhaps). With organisms you’re not going to get identical information except under rare occasions (recent HGT, etc.) across disaparate groups. But of course life is more derivative, hence you end up with weird mosaics like Archaeopteryx that aren’t exactly the peak of flying perfection.
Add “understand” to your list of words that you don’t.
What you wrote isn’t even correct, let alone explained as “evidence that strongly supports design.”
Does that explain the descent of the testes? Hardly, it’s just what happens when testes evolve to be in a good safe place, and later function ends up needing to move substantially to a scrotum in order to keep cool enough. In the first place, why are mammals stuck with testes that must move to the scrotum, when birds are not? In the second place, if they’re going to end up in the scrotum (at least when all goes well), why not develop there?
You’re just claiming that the architecture is good and lasts a long time, when the fact is that context is what determines good architecture, or what-not. The descent of the testes is an unthinking “fix” of an architecture that doesn’t work well for mammals. As always, deny and deny. You really seem incapable of anything else.
And life is stuck with modifying often unpromising (from a design standpoint) material into something that works. At least it can happen, but it takes time and a lot of none-too-good transitionals, and even when it gets to a point of pretty good optimization, like rigid bird wings, the latter still end up being fused together out of several smaller bones that once became articulated in terrestrial dinosaurs. It works, but it’s overly complex development from a design standpoint. But evolution knows no better–or worse, the Designer knows no better.
Glen Davidson
Here, Theobald is referring to the results of the analysis of some particular data set, which covers only some portion of the tree of all life. Different portions, different phylogenies in that sense. But generally compatible ones.
Many groups have multiple definitions in use. Tetrapoda is one such. There is a general tendency to prefer crown group definitions for commonly used names. So Tetrapoda, these days, is most commonly defined as a crown group, e.g. the most recent common ancestor of Xenopus laevis and Homo sapiens and all its descendants. Under this definition, Ichthystega and various other early “amphibians” are not members of Tetrapoda.
GlenDavidson,
How much experience do you have designing living organisms?
You seem to understand the tradeoffs so well 🙂 Glen with all due respect you are spewing nonsense.
Glen, it does not appear that you have any experience in system design or you would never make this argument. Design takes account holistic tradeoffs. To point to a single weakness and say it is bad design is utter amateur land.
Glen you are telling just so stories to justify your position. Birds fly…they fly with phenomenal precision….this is only due to outstanding engineering. The story that this is the result of repeated random trial and error is ridiculous.
keiths,
Why are you spewing nonsense? Have you read John’s 2003 paper? The trees don’t always match, kieths. Genes are not moving as expected from one generation to another. It does not look like any intentional pattern was created only one that results from consistent design rules.