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.
But, wouldn’t chocolate make the steak taste funny? You evolutionists are clueless.
Like I have repeatedly said I don’t have a problem with common descent. I would just like understand the argument for concluding that is what happened.
I don’t think the nested hierarchy requires an explanation beyond the observation that in order to makes sense of things humans tend to group them from the general to the more specific.
I think you mean he deliberately faked common descent.
That conclusion would only make sense if a nested hierarchy in some way entailed common descent. Is that your position?
peace
ok lets try it.
categorize 10 species by color and by relative size.
Do you think you would get the same pattern?
peace
What’s that?
no, just like life it’s a nested hierarchy with anomalies at certain points on the tree.
I carefully read the relevant sections several times and I would disagree.
For example I did not catch where it explained how you can objectively choose which characteristics to categorize and determine their relative importance or how you can objectively choose how to measure them.
If you can do so I would be all ears.
peace
something like this
species 1 is larger than species 4 which is larger than species 7
peace
Instead of trying to explain what objective means why not offer a simple definition that does not exclude the sorts of personal bias that are impossible to escape given your worldview.
That should not be hard.
peace
Explanations for what? I just don’t think the observed pattern requires an explanation beyond “because it helps us to understand”
If you think it does make your case
peace
There’s your problem. The nested hierarchy of life isn’t just in the heads of those who group them. It’s something that really exists and can be discovered. If you aren’t sure this is true, I direct you to the thread What’s Wrong with this Paper? and the eponymous paper itself, Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003; 52:386-402. I chose that paper because the hierarchy is absurdly easy to see in the data.
Could you elaborate a little bit.
I must be misunderstanding you.
I think all processes are derivative evolutionary or not there is no such thing as magic. What am I missing
peace
It’s like trying to teach skepticism to Giorgio Tsoukalos.
Could it be…aliens?
Could it be…The Designer?
Glen Davidson
Coherence, I guess.
Glen Davidson
Of course I agree with this. I think it’s very providential (atheists would say lucky) that it just so happens that life can be categorized in a way so that we can easily make sense of it.
I don’t see any necessary reason why natural selection acting on random mutations needs to fall out in just that particular way.
It could just as easy be an amorphous blob radiating out from the center with no “nests”
peace
That could very well be.
I suppose I’m asking why you think a designed object is not derivative of the things in the designers experience.
peace
No, because the correlations are not subjective, or chosen for convenience, but entail empirical predictions. For instance, if you find an extant organism with mammary glands, it will have vertebrae, a cranium, a four-chambered heart, and bellows lungs, among many predictable traits.
You are still stating the converse of the correct inference. IF we have branching descent with variation (hypothesis or assumption), THEN we’ll observe a nested hierarchy of traits (entailment). This is a logical (mathematical) inference.
We do observe the nested hierarchy, so this supports (is consistent with), but does not prove the hypothesis. However, there is other evidence for the hypothesis, such as the fossil succession, and no alternative hypothesis that has withstood scrutiny.
Which is what I explained.
Look, I apparently can’t get across to you what you seem incapable of grasping.
Glen Davidson
OK,
have a good day then. 😉
peace
Of course it does. You can’t “objectively” group chemical elements into a nested hierarchy, they “objectively” group by electron configurations.
You’re stuck on your “goddidit,” isn’t it nice that they can be grouped more generally or more specifically? Providential. Or lucky to the atheists–according to you.
No, it’s not “lucky,” that would be the magic of “goddidit.” The science-minded look for the reason that life groups as it does, and even most creationists accept it until the conclusions are unbearable to them and/or their religion. Then it’s “common design” or some rubbish about providential groupings. It means nothing.
Glen Davidson
Walter Kloover,
I agree that it is hard to create an almost objective nested hierarchy with cars but computers are a different case as their key feature, user interface, is generated by binary code lets call it base 2.
As living organisms have parts of their key features created by base 4 code in both cases we would expect correlation between user interface, in the case of computers and morphology in the case of living organisms to correlate with the base 2 and base 4 codes that create these features.
As we look at a nested hierarchy of the Apple 2 and the Mac sharing the Apple 1 as a common ancestor we would expect the same correlation. You could get this based on the binary code of mechanical cad cam drawings of cars but it is less straight forward and probably will not correlate as well.
If both cases you would have multiple almost objective features or codes collaborating the nested structure. In either case it illustrates that design, based on base x codes, will create an almost objective nested hierarchy and explains the new innovations that common descent does not.
If you agree with my strenuous disagreement with what you had previously said, perhaps you should consider choosing your words more carefully so as to say what you actually mean rather than something radically different.
You are still the victim of several core misconceptions. First, natural selection acting on random mutations isn’t what causes the nested hierarchy; it’s what causes fixation of characters within lineages, which although they form the pieces of the hierarchy are not the hierarchy itself. Second, it doesn’t matter if selection or Jesus is what causes fixation of characters; in either case, nested hierarchy is still evidence of common descent.
Third, no, it couldn’t “just as easy be an amorphous blob”. The theory of common descent has three components: 1) inheritance within lineages; 2) changes of character state within lineages; and 3) splitting of lineages. Given these three things, nested hierarchy is hard to avoid. You have not suggested an alternative explanation of nested hierarchy, unless you want to reclaim the explanation you have just repudiated, i.e. a rejection of its reality.
I don’t believe that at all. You can’t just make an assertion, label it a fact, and use it as support for another assertion.
there you go with the “objective” thing again.
Is it “objective” to categorize by electron configurations rather than colors in the electromagnetic emission spectrum?
Please explain your answer
thanks
The reason in this case is because it helps us understand. That is a pretty good reason in my book.
When you say “reason” I think you mean cause as in what caused the pattern we see.
now that is a good question
To me common descent seems like more of an effect than a cause.
peace
Why do we have discernible lineages at all then? If it does not come from random mutation or natural selection
How can random variation cause fixation?
How does selection cause fixation rather than selecting what is already fixed?
now these are interesting questions.
Why exactly? If you could give a succinct couple of sentence argument that would be great.
Again why are there discernible lineages at all rather than something like primordial soup. Inheritance of traits flowing back and forth between individual organisms like antibiotic resistance does.
peace
Honestly Bill, you’re just making shit up. It is obvious. You have no idea whether any of the things you write are even true, you just type them out.
How about you proceed to stop making claims, and proceed to SHOW the truth of the claims?
You remember when I claimed that independent genes would converge on the same tree, given common descent? That was a claim. Then I showed with an example that the claim was in fact true.
What do you do? You never SHOW that the things you say are true, you just say them and move on. John Harshman is right, you are just piling claims on top of each other. The number of things you have asserted without being demonstrated to be true just grows and grows.
You have nothing else than your ability to keep making more claims you don’t know how to support.
I do not understand the question.
By random variation in reproductive success of individuals, i.e. genetic drift. But I don’t see the relevance to what we’re talking about here.
I think, based on this nonsense question, that you may not know what “fixation” means. It’s not about repair. It refers to a change in frequency from less than 1 to 1. Of course, if the frequency is at 1, no selection happens.
Not to me; one is elementary and the other is nonsensical.
If changes happen on lineages, and if branching daughter lineages inherit the changes
that happened in the parent lineage, those inherited changes are markers of group membership. The changes that happen in ancestral lineages are markers for all descendant lineages. Look at all the changes, and you get groups within groups within groups.
It doesn’t matter why there are discernable lineages. I could explain why if you really want, but it’s irrelevant except that it’s a necessary prior condition for the sort of common descent that results in a nested hierarchy. You might as well ask, when I tell you that hydrogen fusion explains the heat of the sun, why hydrogen isn’t inherently cold.
Rumraket,
Software code similarity will correlate with user interface similarity. Dos operating system code will have a certain look and mac operating system code will have a certain look. Prior generation software will have a similar look if the user interface is the same but will contain less code. This is partially due to the software standards that exists in the computer industry and code that exists in the public domain.
The common design claim of computer software and hardware is a fact.
Here is an abstract of GUI (Graphical user interface development)
Your claim that the nested hierarchy needed to be crafted by God to fool us is bogus. Design to compatibility and standards will do this on its own.
Oh my God, I’m not interested in explaining the analogy, or in this case, the disanalogy.
Learn about Mendeleev and the periodic table. I explained as much as I should have to, and there is a large number of resources that covers it better than I could (as well as later developments, like the recognition of quantum effects in chemistry). A huge problem is that you really lack the basic knowledge to discuss science.
Utterly meaningless. It’s like saying that mineral properties exist because these help us to understand. Your means of “understanding” always consists of God making things so that they can be “understood,” only magically, not fundamentally. It’s like you really think God is against us learning via inference.
With a good answer that whooshes past you as you resort to your old “goddidit” trope.
To me it seems to be both, like most phenomena are. Quantum phenomena being a possible exception, as in their being more cause than effect (at least as we normally understand “effect” to be, that is, a result determined by earlier “exact causes,” not mere probabilities).
Of course your problem with common descent is that it’s an effect predicted by the mechanics of reproduction with variation, while you want to think it’s just magic.
Glen Davidson
John Harshman,
I realize computers are not your area of expertise. There are computer guys here that can engage. If I am wrong it will certainly surface in the discussion.
Yes, you are wrong.
The Apple I was not, in any reasonable sense, an ancestor of the Mac. Rather, the Mac was a completely new design, though from the same people who designed the Apple I and Apple II.
colewd, to John:
As if they were yours, Bill.
I’m still trying to figure out what you were thinking when you wrote this:
This is hopelessly confused. You are not a computer expert, Bill. Nor an expert of any kind, as far as I can tell.
You cannot escape your personal bias by commitment. Your open commitment to subjectivity, and to your absurd definitions, preclude you from understanding and judging anybody else’s worldview.
You neither know, nor understand, the absurdities-upon-absurdities of your own worldview, and you have no idea what my worldview is. You only know the “worldview” of the atheists of your fantasies.
Reaching someone like yourself, who lives immersed in an absurd self-defeating fantasy, combined wth your commitment to rhetorical bullshit, makes it futile. So I won’t bother.
again I don’t have a problem with common descent just with the way you support your conclusion.
So when you say that common descent is the best explanation for the nested hierarchy what you really mean is that the mechanics of reproduction with variation is the best explanation for the nested hierarchy.
Is that a fair representation of your position?
what in your opinion are the “mechanics of reproduction” and what is the explanation for them?
peace
How do you decide if a phenomena like common descent is acting as the cause and not just an mediating effect of the actual more fundamental cause?
I have no idea what you mean by understanding “magically” there is no such thing as magic.
If the universe was incoherent and unintelligible how could you ever hope to understand it?
I have no idea what you are getting at here.
I observe a nested hierarchy and I learn by inference that this part of the universe was meant to be understood.
You think you learn something else entirely by inference when you observe the pattern.
The question is which of our inferences is valid.
peace
I recommend this little book for those uninitiated in the discovery of the periodic table
It will knock your socks off
also speaking of the differences in the periodic table and what we see in life
check this out
http://www.amnat.org/an/newpapers/NovPianka.html
quote:
Five prominent ecologists present new insights into a concept first suggested by the late Robert H. MacArthur over half a century ago. MacArthur suggested a Periodic Table of ecological niches could be constructed similar to the chemist’s Periodic Table of Elements, which are ordered by a combination of their atomic number (protons), configuration of electrons, and certain chemical properties
end quote:
talk about way cool
peace
How the designer do what it do, does he use common descent or something else?
In your case, it seems to failed in its mission
Case for what?
peace
Sure it does we are looking for explanations of the pattern we see and we would not see the pattern if it weren’t for discernable lineages. Understanding why they exist gets us closer to an explanation
That is not what I would ask,
I might ask why does hydrogen fuses in the sun but not in the Goodyear blimp and why there is no much hydrogen available to fuse in the sun.
Those explanations would get us closer to what actually explains the heat of the sun than your first response.
peace
I would say baring another explanation that common descent is as good a guess as any but I would not want to be close minded about it.
ETA
I do not want to imply that God “did it” by common descent but only that it was a good guess that common descent was true.
As I said common descent looks to be to be more of an effect than a cause
case for what?
That understanding life on earth is not completely beyond our grasp?
If life was incomprehensible we would not be having this conversation we would be discussing why God was so mean to not situate life in a pattern we could understand
peace
The effect of a group of organisms sharing a most recent common ancestor?
fifth:
I guess fifth’s father never sat him down to have The Conversation.
colewd to Walter Kloover:
Rumraket:
There’s something very special — as in “short bus” special — about Bill, who can produce a steaming pile like that and then say to someone else:
You are tarring everybody with your lack of imagination.
If life appeared as if it was designed, we’d be able to determine that by analogy with our own designs, right? If animals appeared with no precursors, entact and entire we’d simply determine they were indeed so created and that something must have created them.
Whatever the pattern clever people would work it out and come to some conclusion.
To put it another way: I don’t hear you complaining about the incomprehensibility of quantum mechanics. You don’t understand it I’m quite sure, beyond the “pop science” level anyway.
So why is god not so mean there as to situate physics in a pattern you can understand? Why is anything beyond newtonian mechanics required, given how comprehensible that is and if god was going for comprehensibility?
The real point is your entire “argument” (such as it is) is built on cherry-picking. One thing is comprehensible because god is so great, but another is incomprehensible (you don’t understand it!) because……….?
And if you are going to use the “we could understand” as an escape hatch, pray tell how you actually *know* that other people understand it even if you don’t? Going to rely on those scientists who claim to understand it word are you? How ironic?
So you reject common descent on the basis that it is an incomplete explanation but you embrace common design that, by your own admission, is equally impotent at providing that explanation. How can the latter be a far superior explanation while not explaining the origin of derived characters? Remember that it is YOU that insists that this needs to be explained as well.
Is it now? Not to me. So tell me why plants “ingest” CO2 and animals “ingest” O2.
BTW, plants also require oxygen at night.
Crack a book.
https://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction
Out of interest, what is the first error on that page?
It all began with a watch…
If you are wrong? How about you find that out first before you just blather shit up?
Not on my watch!
I can’t get John Harshman’s opinion by reading wikipieda
peace
No what happened when the ancestor reproduced.
My siblings and I are here because Mom and dad made a family not because of our common descent.
We share the same color of skin (mostly) because mom and dad had skin of that color and passed it on to us not because of common descent
One effect of mom and dad choosing to have a family is that my siblings and I share a common ancestor
peace
peace
You are right I was thinking the Hindenburg. It was late I have a cold.
Is that really what you choose to focus on in that comment?
peace
Again I’m not making an argument. I’m hoping that some one will provide a succinct cogent argument for common descent. preferably one that can be summarised in a couple of sentences
no such luck as of yet.
peace