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.
If a theists calls in a report of a forest fire that would be objective in your worldview?
If an atheist calls in to report the same forest fire that would not be objective in your world view?
Keith’s is reporting what the authors of the essay wrote. In that essay they mention that statistical methods exist to evaluate the data. If all, or one, of the developers of those statistical tests is a theist then the method cutoffs for subjective versus objective would be a valid assessment of the data objective or subjective nature but not so much so for the atheists?
Seems to me educating yourself on the statistical methods used to evaluate the data would be far more appropriate than any consideration of atheism versus theism.
PeterP, to fifth:
Nothing.
But fifth is desperate, and a drowning man will grasp at anything he thinks might float.
In my worldview objective truth is what God believes so whether a claim is objective depends only on if God believes it.
It does not depend in the slightest on who is making the claim all that matters is is it true?.
Again unlike keiths I am not concerned on who develops the method or agrees with the opinions,
For the Christian objectivity is not a popularity contest.
What I want to know is, How given that there is no objective authority in keiths worldview how can he possibly determine a given claim is objective rather than subjective.
The method is irrelevant if there is no authoritative standard as to what is objective.
All it can ever amount to is subjectively declaring that something like “7 is good while 6 is not”.
peace
dazz,
You forget revelation has no place in keiths world view.
All he can possibly have is subjective polls
He can say a conclusion is objective and claim if his critics were intelligent they would agree with his subjective opinion that it’s objective.
But that is nothing but bluster
peace
So, if I am following your logic, even though both the atheist and theist report the same forest fire that could not be considered an objective assessment of the situation at hand.
Really?
It could be that God revealed that knowledge to the developers of the statistical method in question. It doesn’t appear that you’ve considered that. Don’t you care about revealed knowledge even though it isn’t you that its been revealed to? You are basically claiming that God doesn’t agree with the method or the assessment of the data.
Seems like it is to me.
Keith’s hasn’t made the determination of objective or subjectiveness of the data used in the construction of the nested hierarchies. The authors of the essay (and/or those cited) have made that assessment. Why do you reject their assessment?
You have no idea if the methodology used to assess the data represents revealed knowledge or not. Yet you feel free to ridicule it. Why?
So in order to make the statement above God must have revealed to you that the statistical methodology is not revealed knowledge even though you, apparently, know nothing about the methodology? Seems like subjectivity on your part all the way down.
both you and Keith can see and report the same forest fire. Yours would be an objective assessment of that data point but Keith’s would not be since all he has is ‘subjective polls’ in his worldview. Is that a correct representation of your viewpoint?
If you both see the same forest fire that is objective.
nonsense
fifth:
Let’s unpack the errors here:
1) Fifth understands my position no better than he understands nested hierarchies, which as we’ve seen is extremely poorly;
2) revelation does have a place in my worldview. People reveal things to each other often, and fifth himself has stated that this constitutes revelation;
3) Fifth’s dichotomy is bogus: revelation and “subjective polls” do not exhaust the possibilities, though fifth may be unable to think of others;
4) Fifth’s own criterion undermines any claims he makes to objectivity. He writes
He reports that forest fire not knowing a) whether God believes the fire is there, or b) whether the fire really is there. By his own criterion, his report is not objective.
A typical fifthmonarchyman performance.
Wouldn’t perfect fidelity in asexual reproduction be required? Any real life examples?
Imply:to involve or indicate by inference, association, or necessary consequence rather than by direct statement
It seems someone might need to check with his objective source
Get it now?
peace
eta: fifth “Again imply is not remotely the same thing as entail”
That’s not what he said and not how it works.
He said real phylogenies, as in when we know there really is a genealogical process that generated the data, like observing living organisms have offspring over several generations. Or when human copy-writers copy documents by hand and spread them to other copy-writers, who in turn copy them and introduce small errors in them, which accumulate over time as they are copied and passed on to even more copy-writers.
These are real genealogical processes, and they yield data. As in, we know the phylogenies are objective, because we were there to observe it happen. They’re real phylogenies from genealogical processes. We don’t just “think” they’re real phylogenies, there are cases where we know because we saw them form.
Such known-to-be-real phylogenies give high values in the statistical tests designed by mathematicians to test for hierarchical structure. And when we make up subjective phylogenies by a process that does not involve copying, branching, and introduction of small errors over generations, then we don’t get high statistical significance of hierarchical structure from them.
This then gives us confidence that when the tests for hierarchical structure, find that there is high levels of hierarchical structure in the data, it is because the data was generated by a true genealogical process.
Explanation for what? If we are we looking for an answer to the question Why does the data look like a tree? then “common descent” may be called an explanation for the tree-like structure of descent, as can “creation plan” (the term in Darwin’s times) or “common design” (ID-ist term). But as long as they are superficially the same and causally indistinguishable, then why prefer any of these terms to any other and does the claimed explanation really explain anything?
These three (common descent, creation plan, and common design) are different in terms of ontology, they entail different causes. We are not only seeking to explain the tree-like pattern. We are looking for origin of species, i.e. a causal mechanism how (and perhaps why) evolution occurs, yielding the tree-like pattern.
Common descent says that all current species descended from one or a few by themselves, whereas creation plan says that the species were made that way and no species can by themselves depart much from what it is. Just like manuscripts cannot replicate themselves with variations – they are replicated with variations: Superficially the same result, but different causal direction.
The analogy with manuscripts does not deny adaptation. Manuscripts are inanimate and cannot replicate themselves in the first place, but biological organisms can and nobody denies that there is variation when organisms propagate. However, the biological variation across generations does not exceed the distinctions of “kind”. Admittedly, “kind” remains an empirically disputed term, but the theoretical definition of it is clear enough. The situation is no different with the term “species” in biology.
Darwinian common descent implies a seamless track record of species morphing into each other and that experimental replication of it is a possibility. On the one hand, it has links to eugenics and transhumanism. On the other, it implies that species should always change across generations. There should be no “living fossils” or their occurrence should require special conditions, such as unchanging environment for millions of years.
On the “creation plan” view, adaptation cannot be too drastic – it cannot cross the borders of “kinds”. “Living fossils” across any age should be commonplace. Emergence of new species – certainly of new “kinds” – should be extraordinary and rare. Natural hybridization should be rare and its experimental extension not too drastically better. The big picture of the evolution of biosphere would be as it currently is, but to properly explain what drives it, more causes are required than acknowledged by Darwinians.
A functional reason why “designer” would do this is to maintain harmony in nature. And “forcing” is required because the species don’t do it by themselves.
Each and every thing in the universe consists of the same limited elements or specific combinations of those. Why should the same principle of harmony (so that beauty, diversity, and economy/minimalism are all satisfied at the same time) not apply in the biosphere? When the same principle applies everywhere, there is nothing deceptive in it.
Conversely, what is the functional reason for e.g. bacteria and insects to evolve (by themselves) into anything else? When only plants, fungi, bacteria and insects covered the earth, were there some further ecological niches to be filled that required more life forms? What inherent (genetic or other) capacity do bacteria and fungi have that compels or at least enables them to evolve into e.g. fish? Has that capacity been identified? Now that would be truly a prediction in the correct meaning: What species will come next after us?
What does that even mean? What “harmony” is maintained by forcing independent genetic loci to exhibit a statistically significant similarity in their branching orders if analyzed by a phylogenetic algorithm?
not at all,…………… That is not even a remotely close to a correct representation of my viewpoint…………… If fact it’s pretty much the opposite of my view point.
As I said before in my worldview an assessment’s objectivity is not determined by who is doing the reporting or the method that is used to validate it. It’s determined by whether the assessment is true (ie corresponds to objective reality.)
Keiths is claiming that his assessment is objectively true while mine is false. I’m asking him justify that claim given his worldview.
Keep in mind that I disagree with his assessment, To me his hierarchy does not look any more objective than the hierarchies I posted.
Keith does not have an objective authority to appeal to. All he has is his subjective opinion verses mine.
In his worldview the best he can ever do is appeal to more subjective opinions that agree with him and hope that majority rules.
Two subjective opinions in agreement do not equal objectivity
peace
Right, Just because I report a forest fire does not mean that there actually is a forest fire.
I could be mistaken, I might be biased to think that just because I see smoke over the ridge I’ve seen a forest fire when in fact it’s a neighbor’s raging campfire.
The only way my report is objective is if there is actually a forest fire.
peace
All that is required is identical individuals that share a common ancestor
maybe these
http://piecubed.co.uk/bananas-facts/
Even if non-branching common decent does not exist in the real world that does not mean that common descent is the same thing as branching descent.
your source will work just fine.
It says right there Imply might or might not involve necessary consequence but as stated before entail will always involve necessary consequence
see the difference?
peace
The common sense harmony that says that mammals will give birth to mammals instead of fish
peace
fifth:
That’s not what you’ve told us. According to you, the only way your report is objective is if God believes there is a forest fire:
When you report the fire, you don’t know whether God believes it is there. Any claim of objectivity you make is therefore unsupported.
You’ve shot yourself in the foot, as usual.
fifth:
“My hierarchy”? What are you talking about? I haven’t posted one.
Meanwhile, your examples show us that you don’t even understand the concept of a nested hierarchy, much less an objective nested hierarchy.
God being omniscient believes there is a forest fire if there actually is a forest fire
I never claim objectivity for my subjective assessments.
That is your game remember 😉
You claim that the nested hierarchy is objective. I’m asking you to justify that claim.
peace
Erik:
A “functional reason”? Come on, Erik.
Rumraket:
Or equivalently, as I put it to Sal in the other thread:
How is “creation plan” an explanation of the data looking like a tree? The data look like a tree because the creator happened to want them to? Surely even you can see that’s not an explanation at all. Why would the creator pick that particular plan, the only one that gives us the same data as common descent?
Are there three? How does “creation plan” differ from “common design”? in the previous paragraph you seem to be saying that they are synonyms.
Sure, we would like to explain how evolution and speciation works, but those are separate questions from the origin of the treelike pattern in the data. Neither is necessary to explain the other. Focus on the matter at hand.
I’ll stop you right there. No, that isn’t what common descent says. You are again conflating the origin of variation with the origin of the pattern of variation. Common descent is still common descent if god lovingly crafts each and every mutation.
Manuscripts are a much better analogy to common descent than separate creation, aren’t they? The scribe acts as a replication process. The process introduces errors, which are inherited. The resulting hierarchical structure is in fact antithetical to the “creation plan”, which was to create perfect copies of the manuscript.
I’m afraid it is. Ambiguity of the term “species” is another prediction of common descent, provided only that speciation is not generally by saltation. We should in that case see all possible gradations from one clear species to two clear species. Then again if species are separate, created “kinds”, they really ought to be unambiguous. Wouldn’t you think? Or if “kinds” are something other than species, they should still be unambiguous. And you have no evidence for your claim that variation is limited to within kinds.
There are no living fossils at the level of DNA sequences. Species do always change across generations. There are no species more than a few million years old, even if we assume that differences in skeletal morphology are the only distinctions.
True by the definition of “kind”. But how do you recognize “kinds” to test this assertion?
I’m not sure what this means. But you seem to be implying pre-Cambrian rabbits, and there are none. Living fossils, if you refer to species lasting for hundreds of millions of years, do not exist.
Define “rare”. Certainly the fossil record shows species emerging by the millions at different times. Anyway, how does creation predict rarity of new kinds? Why can’t god create new kinds all the time? You must have some additional model in mind. What is your model of the “creation plan”?
It seems to me that, given separate kinds, natural hybridization should be entirely absent between them, not just rare. I do love the weasel wording “not too drastically better”, though. Thus all experimental speciation is dismissed with a phrase.
Again, the causes of variation are not relevant to what you claimed to be doing at the start: explaining the treelike nature of the data. You have not explained that at all. Instead you attack evolution by strictly natural processes, an irrelevant target.
Whatever that possibly means. How does “harmony in nature” require or produce a treelike structure in data?
I’m talking about this purported objective nested hierarchy that entails (implies?) common descent you keep yammering on about.
Again with the appeal to secret esoteric knowledge.
If your going to use the purported objective nested hierarchy as support for common descent you’d think that you could explain in simple terms exactly why your examples count and mine don’t
peace
Because categorizing from the general to the more specific is what we humans do to makes sense of the world, and the world seems to make sense.
peace
It’s easiest to see with DNA sequence data, and easiest when the combination of evolutionary rates and branch lengths is optimal. I suggest the data in What’s Wrong with this Paper? as an exemplar. The sequence data are gathered by a replicable process: no matter who does the sequencing, they get the same sequence. Character coding and alignment are straightforward, again with no variation among workers. And phylogenetic analysis is simple too, algorithmic, with no subjective choices. Finally, the nested hierarchy is objective because there is no way to arrive at a different tree given those data, or any random sub-sample of the data, or a subsample by a priori partition. That particular tree is forced by the data, which were not gathered or arranged for that purpose.
keiths:
fifth:
First, you don’t know that God is omniscient. You’re simply assuming it. Second, it wouldn’t help you even if he were omniscient, because you don’t know what he believes.
keiths:
fifth:
You can’t claim objectivity period, by your criterion. You’ve shot yourself in the foot.
This stuff is above your pay grade, fifth.
first you say the above……then you say this below
So you must have been mistaken when you said this:
If you’ve both seen and report the same forest fire his assessment is every bit as objective as yours since there actually is a fire, you both see and report it. So you were mistaken with your previous claim that all Keiths has is ‘subjective polls’ and is equally. His report is as objective as yours in every sense of the concept.
fifthmonarchyman: The only way my report is objective is if there is actually a forest fire.
The two statements above from you seem to be at odds with each other.
So I assume now seeing your own statements that you would agree that both you and Keiths have made objective reports of the forest fire and that contrary to your previous claims Keiths does have objectivity in his worldview despite being an atheist according to your criteria:
fifthmonarchyman: The only way my report is objective is if there is actually a forest fire.
No, that doesn’t work. Why should there be such a thing as “general” and “specific”, with multiple levels of generality and specificity in a nested hierarchy? In the case of life, it isn’t a human invention; it’s there to be recognized. For other stuff, not so much.
John:
fifth, once again demonstrating that he doesn’t understand the difference between subjective and objective nested hierarchies:
The choice of the data and the choice to construct a tree instead of a venn diagram are subjective right?
If I was to pick other things to focus on I would have other trees or other shapes entirely right?
peace
Because if there were not I’m not sure how we could make sense of it.
peace
That’s right. In particular, Darwin used it to refer to branching descent through a process of species divergence and reproductive isolation.
Assuming a haploid organism such as a bacteria, they would still typically branch. One into two, two into four, four into eight, etc.. Over enough generations, mutations would result in a nested hierarchy.
You may be suggesting a strictly linear descent, a single organism giving rise to a single organism giving rise to a single organism etc. This wouldn’t give rise to a nested hierarchy as there would only be one leaf. However, that is clearly not what is meant by the term as used the Darwin or evolutionary biologists.
Merriam-Webster: imply, to involve or indicate by inference, association, or necessary consequence.
That you may use the term in the looser sense is fine, but it’s up to you to make your meaning clear. As we are discussing hypothetico-deduction, an implication refers to a logical or material consequence of the assumption: If Hypothesis then Consequence. If Branching Descent with Variation then Nested Hierarchy.
what other stuff exactly, be specific?
better yet why not answer my original question
What systematic would rule out common descent?
peace
now we are getting somewhere
So just to be clear—– the claim is that if we can categorize any groups into a nested hierarchy we can assume with certainty that they have a common ancestor
right?
…says fifth, once again demonstrating that he doesn’t understand the difference between subjective and objective nested hierarchies.
Fercrissakes, fifth. Read that section of Theobald — for comprehension. If you’re baffled by it, quote the parts you don’t understand and we’ll paraphrase them for you.
You are still missing the point.
The problem is not that keiths report is not objective the problem is that he has no justification for claiming that his report is objective.
He can’t possibly have that justification given his worldview
Keiths lives in my world whether he wants to admit it or not.
Objectivity is indeed possible keiths just has no justification for believing it’s possible given his worldview.
He clearly believes objectivity is possible or else he would not make the claim that his report is objective.
Hence his walk does not match his talk and his communication contains a bare contradiction.
get it?
peace
Zach is not as of yet pitching his tent with you on the ever elusive and slippery notion of demonstrable objectivity.
When he does that I will answer him accordingly
peace
Your’s aren’t objective. 🙂
No. That’s the converse statement.
B = Branching descent (with variation from a common ancestor)
N = Nested hierarchy of traits
If B then N is a necessary (logical) implication. It follows directly from the mathematics of the pattern. N supports B, but doesn’t prove B.
There are a variety of ways to strengthen our confidence in B. We might look for other types of evidence, such as the fossil succession. We might also consider other hypotheses, and see whether they fit the data as well or better.
How is winning by definition working out for you?
As per your criteria: the fire exists, he (and you) see it, it is an objective fact (the fire exists) and according to your criteria he is as justified as you are in reporting the fire and that is not a subjective opinion but an objective fact. So unless you wish to resort to the ridiculous stance that your assessment of the fire is objective and his is subjective because of his worldview versus yours it stands that Keiths is capable of making objective claims and is completely justified in making that claim even as an atheist.
As per your criteria for the objective nature of the forest fire, it exists, you also agree that his report is objective and he is justified in making that claim
Get it now?
It isn’t his claim that contains a bare contradiction but it is yours via your very own statements.
I think it is the other way around yet you fail to admit this despite it fitting all of your own criteria for objectivity..if the fire exists the report of the fire is objective regardless if the person reporting it is an atheist or a theist.
That’s not what you said earlier John.
Here’s the original hypothesis again:
Yes. Copying and modifying is exactly the sort of thing designers do.
But now you are saying this would not be separate origins but that this too would be common descent?
Is this an “evolutionary process” as defined by Theobald? So the nested hierarchy produced by manuscript copying is an “objective” nested hierarchy?
ETA:
You’re speaking of manuscript copying here, correct? You consider that a genealogical process, and one that is objective because it was observed?
But designers also start over and create designs that have no antecedents. Did you forget about that? Why is it the “designer” of life never seems to do that?
It would be separate origins but we’d perceive it as common descent. This is why the “foot in the door” quote is relevant.
Nobody is denying that if your god existed it could create each individual creature that has ever existed directly, only making it seem like they were descended from each other when in reality they were not.
God revealed that to you. 🙂
fifth,
That’s yet another comment confirming that you don’t understand the difference between subjective and objective nested hierarchies.
You apparently think that “objective nested hierarchy” simply means “a nested hierarchy which happens to portray a true pattern of descent.” That’s not what the phrase means.
Read that section of Theobald. He explains his meaning.
Your flailing is not bringing glory to God. Exercise some discipline and read Theobald. If you’re baffled by it, quote the parts that confuse you so that we can paraphrase them for you.
Given you don’t accept there is such a thing in the first place Joe G, where are you going with this?
I think he means that only god can determine if it’s objective or not, and you are not god so….
But that’s not what we’re talking about when most people speak of common descent. No one was there to observe the origin of the first eukaryotic organism, or the first chordate organism.
The questions I’ve been asking Sal (for weeks!) apply to all of you creationist and creationist-sympathizing lunkheads:
Erik, colewd, fifth, Mung: how would you answer?
So? Nobody was there to see the first volcano appear either, yet we know it would have had something to do with molten rock. Or do you dispute that?