Nested Hierarchies (Tree of life)

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“Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms, but UCD “mechanism” has neither been observed or proved elsewhere nor is it a valid axiom (“self-evidently true”). Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. Cladistic analysis is not really hypothesis testing since statistics are not essential to the methodology, but if it were it would need to compare against the alternative hypothesis to UCD which is “common design”. And of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. Instead of hypothesis testing, “cladistic analysis” is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry subsets Anatomy is not independent of biochemistry since genome and morphology match 100% for any distinct organisms in a taxonomic hierarchy. Furthermore, parts of the genome are not separately inherited (acquired) and can never be found separate from the genome (decay and research aside). Cladistics based on different genes is as illogical as cladistics based on parts of an organism like limbs, digestive, or reproductive system since there are no functional organ systems independent of the organism with its morphology, genome and common genealogy. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. Furthermore, UCD is a redundant assumption given that shared characteristics and not descent are the basis of taxonomy – a field of study fundamentally unchanged since well before the common descent hypothesis. And of course, common descent cannot be the basis of taxonomy since no common descent has ever been observed. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”

Summary:

“Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution.
No assumption can be tested by the model that uses them.
Hypothesis testing requires an alternative (null) hypothesis and a procedure.
The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative
The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false.
The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry subsets fails.
A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure.

Pro-Con Notes

Con: Phylogenetic trees are with protein-coding genes. Only a tiny number of molecular characters (used in phylogenetic trees) are responsible for the kind of morphological characters used. Cytochrome b gene is independent of the kind of gross morphological characters used in phylogenetic analyses. This is trivially true – there’s no known mechanism by which the sequence of cytochrome b could influence the anatomy. The reason for this correlation [molecular sequences and anatomical characters] is genetic drift and common descent, not some kind of functional necessity. The question is, do the human-specific differences in those sequences contribute specifically to the human morphology relative to other mammals? The answer is usually “no”.

Pro: It is irrelevant if any gene affects morphology. Genes are not separately inherited (acquired). A human gene can only be found in humans with human genes and human morphology. What matters is that genes, genome, and morphology are one package and never found independent of each other. Parts of the genome are NOT separately inherited (acquired) and can NEVER be found separate from the genome. Cladistics based on different genes is SAME AS cladistics based on parts of the organism’s morphology like limbs, digestive, reproductive system, etc and is illogical as anyone knows there are no functional limbs, etc. independent of the organism with its morphology, genome and COMMON genealogy.

Con: Phylogeny is real from concordance of phylogenies from different sets of characters and different parts of the genome. Can you prove DNA segments are not independent?

Pro: The burden of proof is on those proposing the theory. However, it is trivial to show that all significant DNA segments are 100% correlated in an organism including with morphology. IOW, any two significant human DNA segments will only be found in humans that also display human morphology. If the method is right or wrong, classifications based on one DNA segment are to be expected to match classifications based on any another DNA segment.

Con: The common descent that is being inferred is the common descent of groups within the study, and there the consilience of phylogenies from morphology and from different parts of the genome is precisely relevant.

Pro: We know for a fact that morphology depends on the genome, so why is anyone surprised that indeed morphology matches the genome? Furthermore, one needs to demonstrate independence (an impossibility) and the relation can certainly be wrong even if the same trees based on different criteria (think shoe sizes, cloud shapes and automobiles in identical phylogeny by two or more different methods).

Con: Every model contains assumptions, and the fit of the model to data can be used to test whether the assumptions are valid for the data. A chi square test is a simple example. And an inference made in one study can then be used as an assumption in another

Pro: False. They’re called ‘assumptions’ and not ‘conclusions’ because they have to be tested independently through an entirely separated method or be accepted as axioms. as·sump·tion [əˈsəm(p)SH(ə)n] NOUN, a thing that is accepted as true or as certain to happen, without proof. More importantly, an example of a model that proves its own assumptions cannot be found anywhere in the hard sciences.

Con: In the vitamin-C pseudogene being broken in the very same way in different primate species, like humans, chimps, gorillas. The probability of breaking a gene in the very same way in three independent lineages is so small, that the best explanation is that the gene broke once, in a common ancestor, and we all inherited that version of the broken gene from that ancestor.

Pro: Was there no UCD assumption whatsoever before this “proof”? Darwin didn’t knew about this “proof”, yet him and generations after him were already taking UCD for granted without knowing of this “proof”. And who said that UCD is “the best explanation” for this? What other explanations have been considered, and how is this “best” compared to the others? Furthermore, the point of this OP is not that UCD is true or not, but that cladistics cannot prove UCD when UCD is in fact an assumption of the cladistic analysis.

Con: The genealogy of life could be a perfect tree (it isn’t a perfect one) without there being labels on life forms telling you where they fit into the tree.

Pro: One can’t build a genealogy without the labels: vital records, family records, interviews, etc. Yes, every person has a genealogy, but would you ever be able to build the family tree without the labels? And yes, the tree is an artificial human construct – lines and circles/squares of ink on paper or digital.

Con: Fossils can be linked to one another and extant life forms without presupposing UCD. It’s enough if we can infer common ancestry among the organisms in question.

Pro: Fossils can only be linked if one presupposes descent. Even between living, one has to presuppose descent or else it’s doppelgänger or whatever coincidence.

Con: Formulate a hypothesis and look to see whether your hypothesis is supported by the evidence and fits it better than the alternatives.

Pro: Yes, assume true only to make predictions that can be verified by the hypothesis BUT NOT BY the alternative hypothesis. This is NOT happening with UCD as it makes no predictions whatsoever and alternative hypothesis is eliminated before analysis. Even if it were the case (IT IS NOT), this would only say “hypothesis 1 fits better than hypothesis 2”, but NOT “hypothesis 1 is thus proven true”. Furthermore, “Tree of life” is curve fitting and not hypothesis testing as shown.

Con: What does “common design” mean and what would distinguish it from common descent?

Pro: That would be “designed by the same designer or designing entity”. It recognizes that Toyota vehicles are not designed by Ford and that organisms resemble each other – another black eye for Darwinistas that cannot explain why LUCA would have happened once and only once.

Links:

https://www.stattrek.com/hypothesis-test/hypothesis-testing.aspx

https://evolutionnews.org/2018/07/bio-complexity-presents-a-better-model-than-common-ancestry-for-explaining-the-pattern-of-nature/

http://www.ucmp.berkeley.edu/clad/clad1.html assumptions

http://www.ucmp.berkeley.edu/clad/clad2.html method

http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy

http://www.sci-news.com/genetics/article01036.html

https://www.theatlantic.com/science/archive/2017/10/how-a-quarter-of-the-cow-genome-came-from-reptiles/542868/

http://phenomena.nationalgeographic.com/2013/01/01/how-a-quarter-of-the-cow-genome-came-from-snakes/

https://academic.oup.com/nar/article/27/17/3389/2376259

https://evolutionnews.org/2015/02/problem_6_molec/

https://www.the-scientist.com/research/uprooting-the-tree-of-life-52798