Why do you think the separate creation of species would predict the absence of a nested hierarchy?
On the contrary I think that special creation or common design would predict a nested hierarchy based on what we know about the interdependency in many human designs like software. By interdependency I mean different software programs sharing the same modules.
I am not sure at the end of the day that reproduction and natural variation would predict a nested hierarchy unless we can find enough predictable variation to this process.
Because there is nothing that would connect the species in that way. You don’t even attempt it.
Ah, but they don’t share modules in a nested, hierarchical way. Further, a module does not change from program to program, yet the sequences of genes in the various species can be quite different, and the differences are arranged in a nested hierarchy. Your prediction, such as it is, fails. Though you don’t realize it, you have just tested “common design”, and it was not supported.
Word salad again. Now, if we can try to decipher it, you’re back in your central confusion of the pattern of differences vs. the causes of differences. Nested hierarchy is not caused by “reproduction and natural variation”. It’s caused by common descent with branching. True, there must be variation in order to make the hierarchy visible to us. But the causes of that variation are not relevant. Even if we look into the causes, we find that natural variation results in exactly the sorts of differences we do find: transitions more common than transversions, indels somewhat less common, big indels less common than small ones, etc. You are free to be unsure, but there is no rational basis for your feelings.
Based on what I know about the re-use of modules in software, I would predict that they would not form a nested hierarchy, because that hasn’t happened in any of the software development projects I’ve been involved in.
It’s not that separate creation would generate an absence of nested hierarchy. Rather, we know from real-world examples that separate creation has no need to adhere to a strictly nested hierarchy. That a ludicrously large selection of “designs” should fall into a nested hierarchy and never violate it is, therefore, unexpected under this assumption, at least without further explanation as to why a nested hierarchy should emerge in that picture. Common descent, on the other hand, predicts a hierarchical pattern without any further assumptions, because inheritance of traits but less than perfect reproduction is pretty much the essence of “descent”.
That is a poor example of hierarchical structures, though, because it is no example of any such thing at all. You said it yourself, programs share modules. They fetch from a common pool of libraries what ever features they need for their operation. Parts can be mixed and matched at will, with no need to keep dysfunctional old features, and no restriction against reintroducing long removed ones. Consequently programs generally defy cladistic classification. While you may find some hierarchies between programs that run on the same base engine (there is code common to all office programs from the same suite, say, or a family tree of web-browsers based on Mozilla’s core, or games built upon the id-tech engine), this does not generalize. Software designers are under no obligation to start out with and modify some elder completed work.
We can talk about Github after you have made an attempt at explaining what you meant by “The standard programs that are shared can be modified.” and whether or not you have an example of the thing you meant by “The standard programs that are shared can be modified.” occurring or having occurred.
That’s sufficiently vague. Most animals have a central nervous system. That’s not a nested hierarchy. Now, various features of nervous systems do follow a nested hierarchy, but of course that’s what we expect from common descent. There’s no such thing as re-used modules, which is what you have clalimed would result from separate creation.
Now you’ve transitioned from modules to programs. Sure, modules and programs can be modified, but modules generally are not, and when they’re modified they are not modified in such a way as to form a nested hierarchy. Fail.
No, we can observe them happening within populations. The fact that the spectrum of changes we observe in real time is the same as the spectrum of differences among species is evidence for common descent. Fail.
What you don’t think is not relevant. Think of it this way. You have agreed that there is a tree, a nested hierarchy. What is the proper interpretation of that tree? The most natural one is as history, with the earliest time at the bottom, the root, and the present day at the top, the twigs. It’s the historical process of descent with branching that produces that tree. Now of course reproduction, generation following generation, is the mechanism of descent. But I don’t think that’s what you’re talking about. You’re still trying to talk about individual changes or differences rather than their pattern. As I have said countless times already: common descent and branching cause the tree, i.e. the nested hierarchy of differences among taxa. After so many years, you still refuse to understand the most basic concepts.
Common system? You have a nervous system. A goat has a nervous system. Do you really think you are equipped with the nervous system of a goat? Because that is what modular means. Let me repeat that idea. Modules are exactly, precisely, the same, - that is the whole idea - and if they are not the same, they are not a module.
The gene Venn diagram is evidence of re-used modules.
They could form a nested hierarchy if they are being modified by the same designer.
Again you confuse the mutations happening with them resulting in function and becoming fixed in the population.
The basic concepts are logically flawed.
The tree is an abstract human concept and simply a way to arrange data. Common descent and branching are not a cause. They are the effect of the reproductive process.
Reproduction and natural variation is the cause you are appealing to.
What you don’t expect from common descent is the modification of those systems from one animal to the next.
This is an assertion.
No this is you imposing common descent on the observation. What happens in species and what happens in populations is different.
The problem is with the branching process (variation associated with reproduction) accounting for what we observe. In order for branching to account for what we observe the branching needs to find new function and reach fixation. The pattern of the data is not adequate to determine if common descent can account for the observed changes.
Descent is not a mechanism it is an effect of the reproductive mechanism.
Common descent and branching do not cause anything they are the effect of reproduction.
How so? What are the modules? Are they identical between species?
You persist in spouting vague one-liners. Of course anything could form a nested hierarchy if the designer wanted one. But why would he? And what’s being modified? That implies modification of existing species. But modification of existing species is common descent, not separate creation. You need to get your story straight, express it clearly, and make it vulnerable to falsification by the data. So far, none of those.
That’s just mindless parroting of the structure though not the content of my statements, and it’s word salad. Note that the bulk of fixations are neutral and do not result in function. The sequence starts as junk and ends as junk.
How can you tell, when you don’t (and won’t) understand them?
Would you or would you not agree that if common descent happened it would result in a treelike structure of data?
No, no, no. Those are the source I would appeal to in explaining differences among species, not hierarchical structure.
True. You expect that from evolution. What you expect from common descent is that modifications, if they happen, will show a nested hierarchy among species, and different modifications in different systems will show the same hierarchy. But that wasn’t a response to what I said, which you avoid.
That’s my understanding of what “module” means. It appears to be the understanding of the other folks, some of whom have much more familiarity with the subject than I do. Are we talking about modules, or are we talking about programs?
If it’s different, why does it look the same?
That’s not what a branching process is. You don’t seem to have any real idea of what we’re talking about. Still think this is about the origin of variation rather than the pattern of variation. Nothing you say here is about branching, which is the reproductive separation of lineages or populations.
Common descent doesn’t account for the observed changes. Common descent accounts for the pattern, nested hierarchy, of observed changes (or differences, if you prefer a more neutral term). Once again your most basic confusion prevents you from understanding anything we’re talking about here.
Effects of a mechanism can in turn be mechanisms that result in other effects.
Descent is an effect of reproduction, but common descent and branching are something more. Of course you seem unaware of what we mean by branching, so that’s a big communication problem. More important, however, is your persistent initial confusion about pattern vs. causes of variation.
I can’t see a way in which any of this conversation can be useful. You learn nothing, you understand nothing, and you avoid everything. Perhaps we should stop.
A nested hierarchy would form from a design strategy of conserving sequences and morphological features. Modifying existing animals does not make any sense given the different gene and chromosome patterns.
I agree.
If common descent happened between all deer species I would not expect to see new genes and different chromosome patterns we are currently observing. We may see a tree pattern that is better than the null for snp’s that were fixed by drift.
Fair enough
Are you claiming that if we infer a nested hierarchy that points to a single point of origin for all life?
You are looking at a functional sequence. How can you tell if it is the original sequence of something that has been modified.
I got it thanks.
If common descent is claim of a life merging from a single point of origin is examining the pattern enough to support this claim?
I agree but branching descent is not a mechanism in itself.
I think the claim of common descent points to a claim of a single point of origin. Is the pattern enough to support this claim? Since this topic has probably reached its useful life maybe that discussion could be a new post.
If you are looking at a button on your shirt, how do you know it is the original button? Maybe a leprechaun replaced it while you were asleep last night.
You are misunderstanding what science is about. Science is not about absolute truth (if there even is such a thing). Science is about the best explanations that account for the evidence.
Believe what you want about shirt buttons and that leprechaun, but your weird belief won’t help with maintaining and using your shirt. Believe what you want about magic poofing of deer chromosomes, but that belief won’t help at all at understanding our natural environment.
If you want to personally believe in magic poofing, nobody will care. Why are you trying to persuade others to agree with you?