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.
That’s not an argument, it’s a basic fallacy in logic.
What determines when and where proteins get modified? Is protein phosphorylation inherited? Here, I’ll answer for you: DNA, and no. You can’t show me a single difference between species that isn’t at bottom due to difference in DNA sequence.
Once again you have equated “protein coding” with “functional” and attributing that fallacy to me. You need to stop that. Of course there are many regulatory sequences too. Still, they add up to only around 10% of the genome. Now, all you have here is your personal incredulity, which counts for nothing.
Can we agree that whatever it is that makes species different, it must be something that’s stably inherited over thousands of generations? What is it in a population that’s stably inherited over thousands of generations? I can think of only one thing. How about you? It certainly isn’t protein phosphorylation, or histone glycosilation, or DNA methylation.
So you’re saying that causes can’t be inferred from effects? Bye bye, science, if so. I would argue that both languages and manuscripts have a form of descent, and that’s why they show nested hierarchy. Of course the form differs greatly among the three. But we still can infer descent. The mechanism of descent can be determined in other ways, and we know that mechanism in all three cases: copying by scribes, transmission from individual to individual, and reproduction. We may not know everything that causes the various changes that accrue, but we don’t have to.
We are not, in this particular thread, talking about the causes at of evolution at all. We’re talking about the causes of nested hierarchy.
Ah, but living things do self-replicate, don’t they? That’s the form that descent takes in living things. Do you have reason to suspect anything else? If so, what?
keiths:
Erik:
No. The presentation should be appropriate to the intended audience.
Unless one is writing for an exceptionally dim and under-educated audience, there is no need to mention, for example, that organisms can reproduce on their own while manuscripts cannot.
In any case, the central question here is not whether this or that writer has deployed the manuscript analogy properly. It’s whether the evidence supports the notion of common descent. The answer is yes, overwhelmingly.
Evolutionists can explain the pattern in the data. What is your explanation?
We can agree that the scribe is the agent of replication, but so what? Where’s the “creation plan” that results in the nested hierarchy there? The scribe is making mistakes, which later scribes copy slavishly, adding their own mistakes. Do you want to advance this as a model for the nested hierarchy of life? Is god an incompetent scribe, then? Please specify exactly what your alternative to common descent as an explanation for nested hierarchy in life is.
Sure, you can cut and paste links. But can you read? Does anything in that article or any of the references in it disagree with what I wrote, and if so, which part? To refresh your memory: “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.” Of course, in order to respond you’d actually have to read.
Sure. Why do cladograms tend to show only two branches at each point?
Can you make an objective nested hierarchy of the worst thinkers at TSZ?
What flaw or flaws do you think I think I have found? I’d really like to know.
Where does Theobald say that?
So when you speak of THE objective nested hierarchy you are simply being imprecise. Got it. Thanks.
So people create drawings that display a nested hierarchy and each one of these may or may not be an objective nested hierarchy. Good so far?
And Theobald. He appears to think that languages evolve by descent with modification and are genealogical and thus one or more “objective nested hierarchies” can be produced from the data without resorting to only analyzing specific characters.
“Common descent” alone doesn’t explain the pattern.
He guessed the same answer twice.
Classic keiths. Make up a straw man and rip it to shreds. You have to be the only one on the site reading this thread who thinks that Erik is actually arguing what you claim here that he is arguing.
Where has he ever stated that his conclusion is that organisms don’t self-replicate? Evidence please.
Because a hierarchy entails at least two elements — by definition.
We apologize if we misrepresented your views, however, a review of your comments shows you do have a problem with common descent. As the primary evidence for common descent IS the nested hierarchy, it would behoove you to understand the pattern. But there seem to be more serious problems with your position.
You mean “Yes”. You are arguing that we can’t objectively classify crows closer to sparrows than humans based on an overview of all their physical character traits. Just want to be clear on this point.
Try just looking at the skin of the three organisms, or just the lungs, or just the brains. You will keep coming back to the very same relationships: {{crows, sparrows}, humans}.
That’s not what keiths says. keiths says it is the consilience that makes a nested hierarchy objective. Which is sort of absurd, now that I think about it, because in order to have consilience you have to have more than one nested hierarchy.
More pictures please.
The glycome and interactome.
http://www.sciencedirect.com/science/article/pii/S0303264717301983
and
http://dev.biologists.org/content/142/20/3456
It’s noteworthy that unlike proteins, DNA does not directly provide a template for sugars. Sugars are template by well — everything in the cell. Hypothetically DNA that is no longer around might have contributed to the present day sugar architecture, so here we have a heritable structure that isn’t directly template by existing DNA.
I’ve shown the heparan sulfate molecule several times at TSZ. No-one seemed to care at the time, but here it is again:
Additionally:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033155/
I’m not sure what common design is supposed to be but I don’t think you have demonstrated why any particular pattern is expected or not given a particular explanation.
If you did that you might go a long way toward proving your argument
peace
By element I thought you were referring to characteristics and not items being evaluated. It’s just another example of you and I talking past one another
I find that more often than not you and I are talking about different things. That is true even when it comes to something as basic as what counts as personal identity
It’s this sort of thing that makes communication with you frustrating and ultimately not worthwhile.
no my comments show I have a problem with the way common descent is supported.
If that is the case it’s you who need to explain why my examples are fundamentally different than yours. Repeatedly protesting that I don’t understand does not an argument make.
No,
I mean that “we” (I’m not sure if this means you or you and I) subjectively choose which traits to look at and something like creating an “overview of all their physical character traits” requires subjective choices as well
For example we must choose the relative importance that will be placed on each trait.
If our choices are objective then our pattern will be objective as well.
You are proving my point
If we subjectively choose a trait to look at we will come up with a particular pattern that corresponds to the trait we choose.
If we look at just skin we get one pattern if we look at just intelligence we get another.
The pattern we get depends on the subjective choices we make
peace
Sets are made up of elements. A hierarchical classification is an ordered set. (We’re not trying to be difficult.)
The most important evidence of common descent is the nested hierarchy of character traits, so you have to understand why that is so. It’s a mathematical result (a logical implication) that branching descent with variation leads to a nested hierarchy of traits.
In a nested hierarchy, each element or subset is contained within a single superset. Each egg belongs in only one nest! Hence, the square in your hierarchy is not properly nested. The square is in two supersets at once. A traditional military organization forms a nested hierarchy. There are several companies in a battalion, and each company belongs to only one battalion; several battalions make up a regiment, and each battalion belongs to only one regiment; and so on.
The leaves on a biological tree when grouped by branch and stem also form a nested hierarchy. Branching descent forms a topological tree.
No. It means that if we look at all the character traits a pattern emerges. Think about it. Your position means asserting that an anatomist can’t objectively recognize a bird when she examines one. The fact that you must hold to such an absurd position should lead you to reconsider.
Which trait would make sparrows closer to humans than crows?
Which other traits would make crows closer to humans than sparrows?
If one evaluates 100 traits and the same pattern ( tree) emerges in 99 out of the hundred what would account for that convergence on a single tree?
A God that does not create confusion?
Thanks.
peace
The distinction between common descent and its consequent observed nested hierarchy versus the theory of biological evolution has already been made. The analogy between analysis of of manuscripts and phylogenetic anaylsis is a good one. It breaks down if you try and force fit it to the explanations for adaptation, speciation and extinction.
Erik might be interested to have a look at chapter four of Richard Dawkins’ The Ancestor’s Tale (Try this link, it should take you to the Google books version) where Dawkins writes;
He has a look at literary analysis applied to Chaucer’s Canterbury Tales and goes on to discuss phylogenetic analysis with regard to gibbons.
A familiar name pops up when Dawkins refers to long branch attraction and “…the dangerous sounding ‘Felsenstein zone’, named after the distinguished American biologist, Joe Felsenstein”.
Which character traits? Merely saying “character traits” doesn’t tell us anything. It’s so vague that it’s meaningless.
Does this book present the best case for universal common ancestry?
Excellent example of a question that’s easy to ask and impossible to answer! 🙂
I do recommend it as a novel approach in looking at the overarching pattern in reverse. Try my link for a start.
Zachriel:
Here are three skeletons:
Here are pictures of 3 skeletons here:
Lungfish (a Sarcopyterygiian fish)
http://theskepticalzone.com/wp/wp-content/uploads/2017/10/04_African-lungfish_Skeleton1.jpg
Tuna (an Actinogypteriian fish):
http://theskepticalzone.com/wp/wp-content/uploads/2017/10/caljsiol_sio1ca175_060_118a1.gif
Pigeon (a bird, a tetrapod):
http://theskepticalzone.com/wp/wp-content/uploads/2017/10/bird_skeleton1.jpg
How would you group them together in your nested hierarchical scheme when putting the pairs of skeletons in a group to the exclusion of the 3rd member.
Would you put:
1. lungfish and tuna in a group to the exclusion of the pigeon
2. lungfish and pigeon in a group to the exclusion of the tuna
3. tuna and pigeon in a group to the exclusion of the lungfish
Explain your justification for the grouping in your definition of nested hierarchy.
Out of interest, is it possible for you to do the same but for ‘kinds’?
Dawkins mentions this and admits counting character traits is problematic. It’s in the same chapter that you should be able to access via my link above. Page 157.
ETA prior to routine gene sequencing and molecular phylogenetics.
If Dawkins sets forth the case for universal common ancestry in the book I’ll probably buy it, given that I’ve been asking for months now if anyone knows of a book that sets for the case for universal common ancestry.
Mung,
Well, have a look for free and follow my link.
More bad omics. Are these in fact stably inherited over thousands of generations? I don’t think they are.
Mung,
We’ve been referring you to Theobald’s 29+ Evidences for Macroevolution for months, if not years. Whence your resistance to reading anything more than snippets from it?
Given the subtitle — The Scientific Case for Common Descent — it ought to pique the interest of anyone who genuinely wants to understand, you know, the scientific case for common descent.
Why won’t you read it?
John Harshman,
Can you support this claim? How do you think DNA effects a small molecule like vitamin d which is a mission critical transcription factor?
And you cannot show me that all differences are due to DNA. Thats why this is open for debate.
A trait is an observable attribute of an organism.
At this point, we’re trying to determine whether we can objectively classify crows and sparrows as closer than humans. Do you agree with fifthmonarchyman’s suggestion that such an objective classification is not possible?
—
ETA: The skeleton of the tuna does not seem complete.
Mung,
So you will accept that weasel can show how cumulative selection can create a spliceosome 🙂
So? I didn’t ask what a trait is. I asked which traits you select in order to create your nested hierarchy. Cladists think some traits are more important than others.
fifth,
Separate creation of organisms that nevertheless share common design features.
Just think about it. Use pencil and paper, if necessary. Start with an ancestral organism and assign a stylized genetic sequence to it. Simulate a process of common descent in which ancestral sequences are passed from parent to offspring with occasional copying errors. As new variants arise, place them in a tree in a way that represents the genealogical relationships. Label each node with the modified genetic sequence it possesses.
Note the distinctive pattern that emerges, in which a variation, once it arises, is passed down from the ancestor in which it appears to that ancestor’s own descendants, rather than getting scattered arbitrarily all over the tree.
Note that this distinctive pattern is reinforced as more and more variations arise and are passed down from ancestors to their own descendants. The new variations fit into the same pattern.
Now envision a process of common design, in which new design variations can be shared freely without any regard for ancestor-descendant relationships. Without that limitation, the distinctive pattern associated with common descent no longer arises.
Keep playing around with this, on paper, until the signficance and distinctiveness of the common descent pattern becomes obvious to you.
I didn’t ask for a book on macroevolution.
You don’t see any difference between common descent and macroevolution? Because others keep telling us that there is no evolution in common descent.
Both the metabolic process that produces the molecule and its rate of production are metabolic processes. Changes in those processes depend on changes in regulatory DNA and/or proteins involved in metabolism.
Anything that accounts for differences among species must be inherited across many generations. DNA is the only thing that’s inherited across many generations. Therefore DNA accounts for differences among species. OK, now show that one of my premises is incorrect, which would make it up for debate. Otherwise, not.
Nobody keeps telling you that. Common descent is a part of evolution, but only a part. Theobald has evidence for various parts of evolution, including common descent. Read only those parts if you like.
John:
colewd:
Bill, did you really graduate from college?
If so, were your parents major donors, by any chance?
We choose only heritable traits. Generally, for convenience, we choose traits that can be coded into discrete states. It helps if those states don’t vary much within species but do vary among species. That’s about it. The point is that the choice of traits is not supposed to be biased toward any particular result. It’s easy with DNA sequences. You just take the entire sequence, without regard for which positions support what tree. Unbiased.
Mung:
I repeat:
Mung,
Scrunch your eyes closed, cover your ears, and concentrate on this question: If the subtitle of 29+ Evidences is The Scientific Case for Common Descent, do you think there’s a chance it might present the scientific case for common descent?
Why your pitiful evasions?
It’s what I do.
I ask for a book. You refer me to something that is not a book. It’s what you do. Hi Mung, I understand this isn’t what you asked for, but please do check out this online article.
As if the format, rather than the content, were what mattered.
Dude, try to get a grip.
John Harshman,
The rate of productions of the molecule does not depend on the rate of production of metabolic processes. The rate of production depends on absorption of sunlight or ingestion of the molecule.
John, you have claimed that common descent does not account for all differences among species.
In humans, it depends somewhat on that. Some species can just make their own. Not relevant, though.
That’s right. It accounts for the pattern of differences among species. It accounts for none of the differences. However, characteristics possessed by a species that make individuals similar within but different between species must be heritable, right? Do try to focus on relevant points.
I’ve been trying to get a grip on a book. You haven’t helped. 🙂
And I had reasons for asking for a book. Your average reader is more likely to have read a book like The Ancestor’s Tale than to have read Theobald’s article. I want to know what is being presented to the general public, not to internet nerds.
Theobald’s article is more like this book:
Macroevolution: Explanation, Interpretation and Evidence